Publications HAL du labo/EPI 104665;1002240

2019

Journal articles

titre
Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes
auteur
Sylvain Legrand, Thibault Caron, Florian Maumus, Sol Schvartzman, Leandro Quadrana, Sophie Gallina, Maxime Pauwels, Clément Mazoyer, Lucie Huyghe, Vincent Colot, Marc Hanikenne, Vincent Castric
article
Mobile DNA, 2019, 10 (1), pp.1-17. ⟨10.1186/s13100-019-0171-6⟩
resume
Background: Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results: Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion: Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion.
DOI
DOI : 10.1186/s13100-019-0171-6
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https://hal.science/hal-02265374/file/Legrand%20et%20al.%20-%202019%20-%20Mobile%20DNA.pdf BibTex
titre
A reference genome for pea provides insight into legume genome evolution
auteur
Jonathan J. Kreplak, Mohammed-Amin Madoui, Petr Cápal, Petr Novak, Karine Labadie, Gregoire Aubert, Philipp Bayer, Krishna Gali, Robert Syme, Dorrie Main, Anthony Klein, Aurélie Berard, Iva Vrbová, Cyril Fournier, Leo D’agata, Caroline Belser, Wahiba Berrabah, Helena Toegelová, Zbyněk Milec, Jan Vrána, Hueytyng Lee, Ayité Kougbeadjo, Morgane Terezol, Cécile C. Huneau, Chala Turo, Nacer Mohellibi, Pavel Neumann, Matthieu Falque, Karine Gallardo, Rebecca Mcgee, Bunyamin Tar’an, Abdelhafid Bendahmane, Jean-Marc Aury, Jacqueline Batley, Marie-Christine Le Paslier, Noel Ellis, Thomas Warkentin, Clarice Coyne, Jérôme Salse, David Edwards, Judith Lichtenzveig, Jiří Macas, Jaroslav Doležel, Patrick Wincker, Judith Burstin
article
Nature Genetics, 2019, 51 (9), pp.1411-1422. ⟨10.1038/s41588-019-0480-1⟩
resume
We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.
DOI
DOI : 10.1038/s41588-019-0480-1
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titre
Progress in single-access information systems for wheat and rice crop improvement
auteur
Armin Scheben, Chon-Kit Kenneth Chan, Locedie Mansueto, Ramil Mauleon, Pierre Larmande, Nickolai Alexandrov, Rod Wing, Kenneth Mcnally, Hadi Quesneville, David Edwards
article
Briefings in Bioinformatics, 2019, 20 (2), pp.565-571. ⟨10.1093/bib/bby016⟩
DOI
DOI : 10.1093/bib/bby016
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titre
Dealing with multi-source and multi-scale information in plant phenomics: the ontology-driven Phenotyping Hybrid Information System
auteur
Pascal Neveu, Anne Tireau, Nadine Hilgert, Vincent Negre, Jonathan Mineau-Cesari, Nicolas Brichet, Romain Chapuis, Isabelle Sanchez, Cyril Pommier, Brigitte Charnomordic, Francois Tardieu, Llorenç Cabrera Bosquet
article
New Phytologist, 2019, 221 (1), pp.588-601. ⟨10.1111/nph.15385⟩
resume
Summary : . Phenomic datasets need to be accessible to the scientific community. Their reanalysis requires tracing relevant information on thousands of plants, sensors and events. . The open-source Phenotyping Hybrid Information System (PHIS) is proposed for plant phenotyping experiments in various categories of installations (field, glasshouse). It unambiguously identifies all objects and traits in an experiment and establishes their relations via ontologies and semantics that apply to both field and controlled conditions. For instance, the genotype is declared for a plant or plot and is associated with all objects related to it. Events such as successive plant positions, anomalies and annotations are associated with objects so they can be easily retrieved. . Its ontology-driven architecture is a powerful tool for integrating and managing data from multiple experiments and platforms, for creating relationships between objects and enriching datasets with knowledge and metadata. It interoperates with external resources via web services, thereby allowing data integration into other systems; for example, modelling platforms or external databases. . It has the potential for rapid diffusion because of its ability to integrate, manage and visualize multi-source and multi-scale data, but also because it is based on 10 yr of trial and error in our groups.
DOI
DOI : 10.1111/nph.15385
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https://hal.inrae.fr/hal-02627721/file/publis18-mistea-029_neveu_daling_1.pdf BibTex
titre
Tracing the ancestry of modern bread wheats
auteur
Caroline Pont, Thibault Leroy, Michael Seidel, Alessandro Tondelli, Wandrille Duchemin, David Armisen, Daniel Lang, Daniela Bustos-Korts, Nadia Goué, François Balfourier, Márta Molnár-Láng, Jacob Lage, Benjamin Kilian, Darren Waite, Sarah Dyer, Thomas Letellier, Michael Alaux, Joanne Russell, Beat Keller, Fred van Eeuwijk, Manuel Spannagl, Klaus F. X. Mayer, Robbie Waugh, Nils Stein, Luigi Cattivelli, Georg Haberer, Gilles Charmet, Jerome Salse
article
Nature Genetics, 2019, 51 (5), pp.905-911. ⟨10.1038/s41588-019-0393-z⟩
resume
Tracing the ancestry of modern bread wheats
DOI
DOI : 10.1038/s41588-019-0393-z
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https://hal.science/hal-02154676/file/2019_Pont_Whealbi_MS_revision_FINAL.pdf BibTex
titre
The walnut genetic resources of INRA: chronological phenotypic data and ontology
auteur
Anthony Bernard, Teresa Barreneche, Marine Delmas, Sophie Durand, Cyril Pommier, Fabrice Lheureux, Eloïse Tranchand, Marianne Naudin, Elisabeth Dirlewanger
article
BMC Research Notes, 2019, 12 (1), pp.662. ⟨10.1186/s13104-019-4678-1⟩
DOI
DOI : 10.1186/s13104-019-4678-1
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https://hal.inrae.fr/hal-02626113/file/2019-Bernard-BMC_Research_Notes_1.pdf BibTex
titre
Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturiapirina, Venturia aucupariae and Venturia asperata
auteur
Bruno Le Cam, Dan Sargent, Jerome Gouzy, Joëlle Amselem, Marie-Noëlle Bellanger, Olivier Bouchez, Spencer Brown, Valérie Caffier, Marie de Gracia Coquerel, Robert Debuchy, Ludovic Duvaux, Thibaut Payen, Mélanie Sannier, Jason Shiller, Jérôme Collemare, Christophe Lemaire
article
G3, 2019, 9 (8), pp.2405-2414. ⟨10.1534/g3.119.400047⟩
resume
The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.
DOI
DOI : 10.1534/g3.119.400047
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titre
Assessment of genetically modified soybean MON 87708 × MON 89788 × A5547‐127, for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2016‐135)
auteur
Konstantinos Paraskevopoulos, Matthew Ramon, Tamas Dalmay, Patrick Du Jardin, Josep Casacuberta, Philippe Guerche, Huw Jones, Fabien Nogué, Christophe Robaglia, Nils Rostoks
article
EFSA Journal, 2019, 17 (7), ⟨10.2903/j.efsa.2019.5733⟩
resume
Soybean MON 877089MON 897889A5547-127 (three-event stack soybean) was produced byconventional crossing to combine three single events: MON 87708, MON 89788 and A5547-127. TheGMO Panel previously assessed the three single events and did not identify safety concerns. No newdata on the single events, leading to modification of the original conclusions on their safety have beenidentified. The molecular characterisation, comparative analysis (agronomic, phenotypic andcompositional characteristics) and the outcome of the toxicological, allergenicity and nutritionalassessment indicate that the combination of the single soybean events and of the newly expressedproteins in the three-event stack soybean does not give rise to food and feed safety and nutritionalconcerns. The GMO Panel concludes that the three-event stack soybean, as described in thisapplication, is as safe as and nutritionally equivalent to its conventional counterpart and the non-GMreference varieties tested. The nutritional impact of food/feed derived from the three-event stacksoybean is expected to be the same as that of food/feed derived from the conventional counterpartand non-GM reference varieties. In the case of accidental release of viable seeds of the three-eventstack soybean into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of thethree-event stack soybean. Post-market monitoring of food/feed is not considered necessary. The GMOPanel concludes that the three-event stack soybean is as safe as its conventional counterpart and thetested non-GM reference varieties with respect to potential effects on human and animal health andthe environment.
DOI
DOI : 10.2903/j.efsa.2019.5733
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https://hal.inrae.fr/hal-02915335/file/sp.efsa.2018.EN-1466.pdf BibTex
titre
BrAPI - an Application Programming Interface for Plant Breeding Applications.
auteur
Rafael Abbeloos, Jan Erik Backlund, Martin Basterrechea Salido, Guillaume Bauchet, Omar Benites-Alfaro, Clay Birkett, Viana C Calaminos, Pierre Carceller, Guillaume Cornut, Bruno Vasques Costa, Jeremy D Edwards, Richard Finkers, Star Yanxin Gao, Mehmood Ghaffar, Philip Glaser, Valentin Guignon, Puthick Hok, Andrzej Kilian, Patrick König, Jack Elendil B Lagare, Matthias Lange, Marie-Angélique Laporte, Pierre Larmande, David Lebauer, David Lyon, David Marshall, Dave Matthews, Iain Milne, Naymesh Mistry, Nicolas Morales, Lukas Mueller, Pascal Neveu, Evangelia Papoutsoglou, Brian Pearce, Ivan Perez-Masias, Cyril Pommier, Ricardo H Ramirez-Gonzalez, Abhishek Rathore, Angel M Raque, Sebastian Raubach, Trevor Rife, Kelly Robbins, Mathieu Rouard, Chaitanya Sarma, Uwe Scholz, Peter Selby, Guilhem Sempere, Paul Shaw, Reinhard Simon, Nahuel Soldevilla, Gordon Stephen, Qi Sun, Clarysabel Tovar, Grzegorz Uszynski, Maikel Verouden
article
Bioinformatics, 2019, 35 (20), pp.4147-4155. ⟨10.1093/bioinformatics/btz190⟩
resume
Motivation Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data is often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service Application Programming Interface (API) specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. Â The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. Availability and Implementation More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.
DOI
DOI : 10.1093/bioinformatics/btz190
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https://hal.inrae.fr/hal-02626802/file/Publis19-mistea-005_Abbeloos_BrAPI_1.pdf BibTex
titre
Paleogenomic insights into the origins of French grapevine diversity
auteur
Jasmin Ramos-Madrigal, Anne Kathrine Wiborg Runge, Laurent Bouby, Thierry Lacombe, José Alfredo Samaniego Castruita, Anne-Françoise Adam-Blondon, Isabel Figueiral, Charlotte Hallavant, José Miguel Martinez-Zapater, Caroline Schaal, Reinhard Topfer, Bent Petersen, Thomas Sicheritz-Ponten, Patrice This, Roberto Bacilieri, Thomas P. Gilbert, Nathan Wales
article
Nature Plants, 2019, 5, pp.595-603. ⟨10.1038/s41477-019-0437-5⟩
DOI
DOI : 10.1038/s41477-019-0437-5
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https://hal.science/hal-02187462/file/2019_Ramos_Nature-Plants_postprint.pdf BibTex
titre
Applying FAIR principles to plant phenotypic data management in GnpIS
auteur
Cyril Pommier, Célia Michotey, Guillaume Cornut, Pierre Roumet, Eric Duchêne, Raphaël Flores, Aristide Lebreton, Michael Alaux, Sophie Durand, Erik Kimmel, Thomas Letellier, Guillaume Merceron, Mathilde Lainé, Claire Guerche, Mikaël Loaec, Delphine Steinbach, Marie-Angélique Laporte, Elisabeth Arnaud, Hadi Quesneville, Anne-Francoise Adam-Blondon
article
Plant Phenomics, 2019, 2019, pp.1-15. ⟨10.34133/2019/1671403⟩
resume
GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems.
DOI
DOI : 10.34133/2019/1671403
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https://hal.inrae.fr/hal-02624031/file/2019_Pommier_Plant%20Phenomics_1.pdf BibTex
titre
RepetDB: a unified resource for transposable element references
auteur
Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michael Alaux, Françoise Alfama Depauw, Véronique Jamilloux, Florian Maumus, Thomas Letellier, Isabelle Luyten, Cyril Pommier, Anne-Francoise Adam-Blondon, Hadi Quesneville
article
Mobile DNA, 2019, 10, pp.1-8. ⟨10.1186/s13100-019-0150-y⟩
resume
Background: Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data. However, all automated procedures are error-prone, and an automated procedure for TE identification and classification would be no exception. It is therefore crucial to provide not only the TE reference sequences, but also evidence justifying their classification, at the scale of the whole genome. A few TE databases already exist, but none provides evidence to justify TE classification. Moreover, biological information about the sequences remains globally poor. Results: We present here the RepetDB database developed in the framework of GnpIS, a genetic and genomic information system. RepetDB is designed to store and retrieve detected, classified and annotated TEs in a standardized manner. RepetDB is an implementation with extensions of InterMine, an open-source data warehouse framework used here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence. InterMine can display diverse information for each sequence and allows simple to very complex queries. Finally, TE data are displayed via a worldwide data discovery portal. RepetDB is accessible at urgi.versailles.inra.fr/repetdb. Conclusions: RepetDB is designed to be a TE knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates the exploration of specific TE families, superfamilies or orders across a large range of species. It also makes possible cross-species searches and comparisons of TE family content between genomes.
DOI
DOI : 10.1186/s13100-019-0150-y
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https://hal.inrae.fr/hal-02625212/file/2019_Amselem_Mobile%20DNA_1.pdf BibTex

2018

Journal articles

titre
Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms
auteur
Achal Rastogi, Uma Maheswari, Richard Dorrell, Fabio Rocha Jimenez Vieira, Florian Maumus, Adam Kustka, James Mccarthy, Andy Allen, Paul Kersey, Chris Bowler, Leïla Tirichine
article
Scientific Reports, 2018, 8 (1), pp.1-14. ⟨10.1038/s41598-018-23106-x⟩
resume
Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes. The new annotation additionally permitted the discovery of extensive alternative splicing in diatoms, including intron retention and exon skipping, which increase the diversity of transcripts generated in changing environments. In addition, we have used up-to-date reference sequence libraries to dissect the taxonomic origins of diatom genes. We show that the P. tricornutum genome is enriched in lineage-specific genes, with up to 47% of the gene models present only possessing orthologues in other stramenopile groups. Finally, we have performed a comprehensive de novo annotation of repetitive elements showing novel classes of transposable elements such as SINE, MITE and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene function, evolution and ecology.
DOI
DOI : 10.1038/s41598-018-23106-x
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https://hal.science/hal-02366536/file/2018_Rastogi_Scientific%20Reports_1.pdf BibTex
titre
Gene flow contributes to diversification of the major fungal pathogen $Candida\ albicans$
auteur
Jeanne Ropars, Corinne Maufrais, Dorothée Diogo, Marina Marcet-Houben, Aurélie Perin, Natacha Sertour, Kevin Mosca, Emmanuelle Permal, Guillaume Laval, Christiane Bouchier, Laurence Ma, Katja Schwartz, Kerstin Voelz, Robin C May, Julie Poulain, Christophe Battail, Patrick Wincker, Andrew M Borman, Anuradha Chowdhary, Shangrong Fan, Soo Hyun Kim, Patrice Le Pape, Orazio Romeo, Jong Hee Shin, Toni Gabaldon, Gavin Sherlock, Marie-Elisabeth Bougnoux, Christophe D'Enfert
article
Nature Communications, 2018, 9 (1), pp.2253. ⟨10.1038/s41467-018-04787-4⟩
resume
Elucidating population structure and levels of genetic diversity and recombination is necessary to understand the evolution and adaptation of species. $Candida\ albicans$ is the second most frequent agent of human fungal infections worldwide, causing high-mortality rates. Here we present the genomic sequences of 182 C. $albicans$ isolates collected worldwide, including commensal isolates, as well as ones responsible for superficial and invasive infections, constituting the largest dataset to date for this major fungal pathogen. Although, C. $albicans$ shows a predominantly clonal population structure, we find evidence of gene flow between previously known and newly identified genetic clusters, supporting the occurrence of (para)sexuality in nature. A highly clonal lineage, which experimentally shows reduced fitness, has undergone pseudogenization in genes required for virulence and morphogenesis, which may explain its niche restriction. $Candida\ albicans$ thus takes advantage of both clonality and gene flow to diversify.
DOI
DOI : 10.1038/s41467-018-04787-4
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https://pasteur.hal.science/pasteur-01815656/file/s41467-018-04787-4.pdf BibTex
titre
Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data
auteur
Michael Alaux, Jane Rogers, Thomas Letellier, Raphaël Flores, Françoise Alfama, Cyril Pommier, Nacer Mohellibi, Sophie Durand, Erik Kimmel, Célia Michotey, Claire Guerche, Mikaël Loaec, Mathilde Lainé, Delphine Steinbach, Frédéric Choulet, Hélène Rimbert, Philippe Leroy, Nicolas Guilhot, Jérôme Salse, Catherine Feuillet, . International Wheat Genome Sequencing Consortium (iwgsc), Etienne Paux, Kellye Eversole, Anne-Francoise Adam-Blondon, Hadi Quesneville
article
Genome Biology, 2018, 19 (1), pp.905-911. ⟨10.1186/s13059-018-1491-4⟩
resume
The Wheat@URGI portal has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in-depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.
DOI
DOI : 10.1186/s13059-018-1491-4
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https://hal.science/hal-02278879/file/2018_Alaux_Genome%20Biology_1.pdf BibTex
titre
Shifting the limits in wheat research and breeding using a fully annotated reference genome
auteur
. International Wheat Genome Sequencing Consortium (iwgsc), Arnaud Bellec, Helene Berges, Sonia Vautrin, Michael Alaux, Françoise Alfama, Anne-Francoise Adam-Blondon, Raphaël Flores, Claire Guerche, Thomas Letellier, Mikaël Loaec, Hadi Quesneville, Rudi Appels, Philippe Rigault, Frédéric Choulet, Ambre-Aurore Josselin, François Balfourier, Etienne Paux, Hélène Rimbert, Nicolas Guilhot, Philippe Leroy, Dominique Arnaud, Smahane Chalabi, Pierre Sourdille, Benoît Darrier
article
Science, 2018, 361 (6403), pp.7191. ⟨10.1126/science.aar7191⟩
resume
An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
DOI
DOI : 10.1126/science.aar7191
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titre
A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
auteur
L. Hibrand Saint-Oyant, T. Ruttink, L. Hamama, I. Kirov, D. Lakhwani, N. N Zhou, P M Bourke, N. Daccord, L. Leus, D. Schulz, H. van de Geest, T. Hesselink, K. van Laere, K. Debray, S. Balzergue, T. Thouroude, A. Chastellier, J. Jeauffre, L. Voisine, S. Gaillard, T J A Borm, P. Arens, R E Voorrips, C. Maliepaard, E. Neu, M. Linde, Marie-Christine Le Paslier, A. Bérard, R. Bounon, J. Clotault, Nathalie Choisne, H. Quesneville, K. Kawamura, S. Aubourg, Soulaiman Sakr, M J M Smulders, E. Schijlen, E. Bucher, T. Debener, J. de Riek, F. Foucher
article
Nature Plants, 2018, 4 (7), pp.473 - 484. ⟨10.1038/s41477-018-0166-1⟩
resume
Rose is the queen of flowers, holding great symbolic and cultural value. Roses appeared as decoration on 5,000-year-old Asian pottery 1 , and Romans cultivated roses for their flowers and essential oil 2. Today, no ornamental plants have greater economic importance than roses. They are cultivated worldwide and are sold as garden plants, in pots or as cut flowers, the latter accounting for approximately 30% of the market. Roses are also used for scent production and for culinary purposes 3. Despite their genetic complexity and lack of biotechnological resources, rose represents a model for ornamental plant species, allowing the investigation of traits such as bloom seasonality or flower morphology. Furthermore, rose displays a range of unique features as a result of its complex evolutionary and breeding history , including interspecific hybridization events and polyploidi-zation 4-6. Roses belong to the genus Rosa (Rosoideae, Rosaceae), which contains more than 150 species 7 of varying ploidy levels, ranging from 2n = 2× to 10× 8,9. Many modern roses are tetra-ploid and can be genetically classified as 'segmental' allopolyploids (a mixture between allopolyploidy and autopolyploidy) 10 , whereas dog-roses display unequal meiosis to maintain pentaploidy 11,12. Rose breeding has a long and generally unresolved history in Europe and Asia, most likely involving several interspecific hybridization events. Importantly, many very-old varieties are still maintained in private and public rose gardens and are a living historical archive of rose breeding and selection 13. Large and well-documented her-barium collections, combined with genomic advances, offer excellent opportunities to reconstruct phylogenetic relationships within the species. Roses have been subject to selection for several traits that are not usually encountered in other crops. In particular, aesthetic criteria have been a principal focus of rose breeding over the past 250 years, next to plant vigour and resistances to biotic and abiotic stresses. Among the aesthetic traits, flower colour and architecture (from 5-petalled 'simple' flowers to 100-petalled 'double' flowers), floral scent and prickle formation on the stem and leaves have been the main targets of the breeders' eyes (and noses). Although these traits can be interpreted as signs of the domestication process, they originally evolved through adaptation to natural conditions. Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequenc-ing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae. NATuRE PLANTS | www.nature.com/natureplants
DOI
DOI : 10.1038/s41477-018-0166-1
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titre
The Rosa genome provides new insights into the domestication of modern roses
auteur
Olivier Raymond, Jerome Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud, Arnaud Lemainque, Philippe Vergne, Sandrine Moja, Nathalie Choisne, Caroline C. Pont, Sébastien Carrere, Jean Claude Caissard, Arnaud Couloux, Ludovic Cottret, Jean-Marc Aury, Judit Szécsi, David D. Latrasse, Mohammed Madoui, Léa Francois, Xiaopeng Fu, Shu-Hua Yang, Annick Dubois, Florence Piola, Antoine Larrieu, Magali Perez, Karine Labadie, Lauriane Perrier, Benjamin Govetto, Yoan Labrousse, Priscilla Villand, Claudia Bardoux, Véronique Boltz, Celine Lopez-Roques, Pascal Heitzler, Teva Vernoux, Michiel Vandenbussche, Hadi Quesneville, Adnane Boualem, Abdelhafid Bendahmane, Chang Liu, Manuel Le Bris, Jérôme Salse, Sylvie Baudino, Moussa Benhamed, Patrick Wincker, Mohammed Bendahmane
article
Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩
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Roses have high cultural and economic importance as ornamental plants and in the perfume industry. We report the rose whole-genome sequencing and assembly and resequencing of major genotypes that contributed to rose domestication. We generated a homozygous genotype from a heterozygous diploid modern rose progenitor, Rosa chinensis ‘Old Blush’. Using single-molecule real-time sequencing and a meta-assembly approach, we obtained one of the most comprehensive plant genomes to date. Diversity analyses highlighted the mosaic origin of ‘La France’, one of the first hybrids combining the growth vigor of European species and the recurrent blooming of Chinese species. Genomic segments of Chinese ancestry identified new candidate genes for recurrent blooming. Reconstructing regulatory and secondary metabolism pathways allowed us to propose a model of interconnected regulation of scent and flower color. This genome provides a foundation for understanding the mechanisms governing rose traits and should accelerate improvement in roses, Rosaceae and ornamentals.
DOI
DOI : 10.1038/s41588-018-0110-3
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The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
auteur
Daniel Lang, Kristian Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, Fabian Haas, Carl Li, Guillaume Blanc, Heidrun H. Gundlach, Michiel van Bel, Rabea Meyberg, Cristina Vives, Jordi Morata, Aikaterini Symeonidi, Manuel Hiss, Wellington Muchero, Lee Kamisugi, Omar A. Saleh, Eva Decker, Nico van Gessel, Jane Grimwood, Richard Hayes, Sean Graham, Lee Gunter, Daniel Mcdaniel, Sebastian N.W. Hoernstein, Anders Larsson, Fay-Wei Li, Pierre-François Perroud, Jeremy Phillips, Priya Ranjan, Daniel Rokshar, Carl Rothfels, Lucas Schneider, Shengqiang Shu, Dennis Stevenson, Fritz Thümmler, Michael Tillich, Juan Villarreal Aguilar, Thomas Widiez, Gane Ka-Shu Wong, Ann Wymore, Yong Zhang, Andreas Zimmer, Ralph Quatrano, Klaus F.X. Mayer, David Goodstein, Josep Casacuberta, Klaas Vandepoele, Ralf Reski, Andrew Cuming, Gerald Tuskan, Florian Maumus, Jérôme Salse, Jeremy Schmutz, Stefan Rensing
article
Plant Journal, 2018, 93 (3), pp.515 - 533. ⟨10.1111/tpj.13801⟩
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The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
DOI
DOI : 10.1111/tpj.13801
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Corrigendum: Towards recommendations for metadata and data handling in plant phenotyping
auteur
Pawel Krajewski, Dijun Chen, Hanna Cwiek, Aalt D. J. van Dijk, Fabio Fiorani, Paul Kersey, Christian Klukas, Matthias Lange, Augustyn Markiewicz, Jan Peter Nap, Jan van Oeveren, Cyril Pommier, Uwe Scholz, Marco van Schriek, Björn Usadel, Stephan Weise
article
Journal of Experimental Botany, 2018, 69 (7), pp.1819-1819. ⟨10.1093/jxb/ery006⟩
DOI
DOI : 10.1093/jxb/ery006
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Assessment of genetically modified maize 4114 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2014‐123)
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Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messéan, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Fernando Alvarez, Michele Ardizzone, Konstantinos Paraskevopoulos, Hermann Broll, Yann Devos, Antonio Fernandez Dumont, Anna Lanzoni, Franco Maria Neri, Irina Olaru, Nikoletta Papadopoulou
article
EFSA Journal, 2018, 16 (5), ⟨10.2903/j.efsa.2018.5280⟩
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aize 4114 was developed through Agrobacterium tumefaciens-mediated transformation to provide protection against certain lepidopteran and coleopteran pests by expression of the Cry1F, Cry34Ab1 and Cry35Abl proteins derived from Bacillus thuringiensis, and tolerance to the herbicidal active ingredient glufosinate-ammonium by expression of the PAT protein derived from Streptomyces viridochromogenes. The molecular characterisation data did not identify issues requiring assessment for food/feed safety. None of the compositional, agronomic and phenotypic differences identified between maize 4114 and the non-genetically modified (GM) comparator(s) required further assessment. There were no concerns regarding the potential toxicity and allergenicity of the newly expressed proteins CrylF, Cry34Abl, Cry35Abl and PAT, and no evidence that the genetic modification might significantly change the overall allergenicity of maize 4114. The nutritional value of food/feed derived from maize 4114 is not expected to differ from that derived from non-GM maize varieties and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize 4114 grains into the environment, maize 4114 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize 4114. The genetically modified organism (GMO) Panel concludes that maize 4114 is as safe as the non-GM comparator(s) and non-GM reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.
DOI
DOI : 10.2903/j.efsa.2018.5280
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Oak genome reveals facets of long lifespan
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Christophe Plomion, Jean-Marc Aury, Joelle Amselem, Thibault Leroy, Florent Murat, Sébastien Duplessis, Sébastien Faye, Nicolas Francillonne, Karine Labadie, Grégoire Le Provost, Isabelle Lesur Kupin, Jérôme Bartholome, Patricia Faivre-Rampant, Annegret Kohler, Jean-Charles Leplé, Nathalie Chantret, Jun Chen, Anne Dievart, Tina Alaeitabar, Valérie Barbe, Caroline Belser, Helene Berges, Catherine Bodenes, Marie-Béatrice Bogeat-Triboulot, Marie-Lara Bouffaud, Benjamin Brachi, Emilie Chancerel, David Cohen, Arnaud Couloux, Corinne da Silva, Carole Dossat, François Ehrenmann, Christine Gaspin, Jacqueline Grima Pettenati, Erwan Guichoux, Arnaud Hecker, Sylvie Herrmann, Philippe Hugueney, Irène Hummel, Christophe C. Klopp, Céline Lalanne, Martin Lascoux, Eric Lasserre, Arnaud Lemainque, Marie Laure Desprez-Loustau, Isabelle Luyten, Mohammed-Amin Madoui, Sophie Mangenot, Clémence Marchal, Florian Maumus, Jonathan Mercier, Célia Michotey, Olivier Panaud, Nathalie Picault, Nicolas Rouhier, Olivier Rué, Camille Rustenholz, Franck Salin, Marçal Soler, Mika Tarkka, Amandine Velt, Amy E. Zanne, Francis Martin, Patrick Wincker, Hadi Quesneville, Antoine Kremer, Jerome Salse
article
Nature Plants, 2018, 4 (7), pp.440-452. ⟨10.1038/s41477-018-0172-3⟩
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Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associatedwith such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6 and provides direct fitness benefits in the arms race with short-lived pests andpathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
DOI
DOI : 10.1038/s41477-018-0172-3
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Tracheophyte genomes keep track of the deep evolution of the Caulimoviridae
auteur
Seydina Issa Diop, Andrew D. W. Geering, Françoise Alfama-Depauw, Mikaël Loaec, Pierre-Yves Teycheney, Florian Maumus
article
Scientific Reports, 2018, 8, pp.1-9. ⟨10.1038/s41598-017-16399-x⟩
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Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one and as many as five different caulimovirid genera were frequently detected, and florendoviruses were the most widely distributed, followed by petuviruses. From the analysis of the distribution of different caulimovirid genera within different plant species, we propose a working evolutionary scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million years ago) followed by vertical transmission and by several cross-division host swaps.
DOI
DOI : 10.1038/s41598-017-16399-x
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A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea
auteur
Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint-Jean, Gregory Carrier
article
BMC Genomics, 2018, 19 (1), pp.378. ⟨10.1186/s12864-018-4763-1⟩
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Background: Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. Results: To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi.org/10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements. Conclusion: This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.
DOI
DOI : 10.1186/s12864-018-4763-1
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Assessment of genetically modified maize Bt11 x MIR162 x 1507 x GA21 and three subcombinations independently of their origin, for food and feed uses under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐DE‐2010‐86)
auteur
Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messean, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Michele Ardizzone, Silvia Federici, Antonio Fernandez Dumont, Gennaro Carotenuto, Anna Lanzoni, Franco Maria Neri, Nikoletta Papadopoulou, Konstantinos Paraskevopoulos
article
EFSA Journal, 2018, 16 (7), ⟨10.2903/j.efsa.2018.5309⟩
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In this opinion, the GMO Panel assessed the four-event stack maize Btll x MIR162 x 1507 x GA21 and three of its subcombinations, independently of their origin. The GMO Panel previously assessed the four single events and seven of their combinations and did not identify safety concerns. No new data on the single events or the seven subcombinations leading to modification of the original conclusions were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single events in the four-event stack maize did not give rise to food/feed safety issues. Based on the nutritional assessment of the compositional characteristics of maize Btll x MIR162 x 1507 x GA21, foods and feeds derived from the genetically modified (GM) maize are expected to have the same nutritional impact as those derived from non-GM maize varieties. In the case of accidental release of viable grains of maize Btll x MIR162 x 1507 x GA21 into the environment, this would not raise environmental safety concerns. The GMO Panel concludes that maize Btll x MIR162 x 1507 x GA21 is nutritionally equivalent to and as safe as its non-GM comparator in the context of the scope of this application. For the three subcombinations included in the scope, for which no experimental data were provided, the GMO Panel assessed the likelihood of interactions among the single events and concluded that their combinations would not raise safety concerns. These maize subcombinations are therefore expected to be as safe as the single events, the previously assessed subcombinations and the four-event stack maize. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize Btll x MIR162 x 1507 x GA21 and its subcombinations. A minority opinion expressed by a GMO Panel member is appended to this opinion. (C) 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.
DOI
DOI : 10.2903/j.efsa.2018.5309
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Ten steps to get started in Genome Assembly and Annotation
auteur
Victoria Dominguez del Angel, Erik Hjerde, Lieven Sterck, Salvadors Capella-Gutierrez, Cedric Notredame, Olga Vinnere Pettersson, Joelle Amselem, Laurent Bouri, Stephanie Bocs, Christophe C. Klopp, Jean-Francois Gibrat, Anna Vlasova, Brane L. Leskosek, Lucile Soler, Mahesh Binzer-Panchal, Henrik Lantz
article
F1000Research, 2018, 7, pp.148-19. ⟨10.12688/f1000research.13598.1⟩
resume
As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, intended to be stable over time, and cover all aspects from start to finish of a general assembly and annotation project. Intrinsic properties of genomes are discussed, as is the importance of using high quality DNA. Different sequencing technologies and generally applicable workflows for genome assembly are also detailed. We cover structural and functional annotation and encourage readers to also annotate transposable elements, something that is often omitted from annotation workflows. The importance of data management is stressed, and we give advice on where to submit data and how to make your results Findable, Accessible, Interoperable, and Reusable (FAIR).
DOI
DOI : 10.12688/f1000research.13598.1
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Redistribution of CHH Methylation and Small Interfering RNAs across the Genome of Tomato ddm1 Mutants
auteur
Shira Corem, Adi Doron Faigenboim, Ophélie Jouffroy, Florian Maumus, Tzahi Arazi, Nicolas Bouche
article
The Plant cell, 2018, 30 (7), pp.1628-1644. ⟨10.1105/tpc.18.00167⟩
resume
In plants, cytosine methylation, an epigenetic mark critical for transposon silencing, is maintained over generations by key enzymes that directly methylate DNA and is facilitated by chromatin remodelers, like DECREASE IN DNA METHYLATION1 (DDM1). Short-interfering RNAs (siRNAs) also mediate transposon DNA methylation through a process called RNA-directed DNA methylation (RdDM). In tomato (Solanum lycopersicum), siRNAs are primarily mapped to gene-rich chromosome arms, and not to pericentromeric regions as in Arabidopsis thaliana. Tomato encodes two DDM1 genes. To better understand their functions and interaction with the RdDM pathway, we targeted the corresponding genes via the CRISPR/Cas9 technology, resulting in the isolation of Slddm1a and Slddm1b knockout mutants. Unlike the single mutants, Slddm1a Slddm1b double mutant plants display pleiotropic vegetative and reproductive phenotypes, associated with severe hypomethylation of the heterochromatic transposons in both the CG and CHG methylation contexts. The methylation in the CHH context increased for some heterochromatic transposons and conversely decreased for others localized in euchromatin. We found that the number of heterochromatin-associated siRNAs, including RdDM-specific small RNAs, increased significantly, likely limiting the transcriptional reactivation of transposons in Slddm1a Slddm1b. Taken together, we propose that the global production of siRNAs and the CHH methylation mediated by the RdDM pathway are restricted to chromosome arms in tomato. Our data suggest that both pathways are greatly enhanced in heterochromatin when DDM1 functions are lost, at the expense of silencing mechanisms normally occurring in euchromatin.
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DOI : 10.1105/tpc.18.00167
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Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants
auteur
Josep Casacubera, Fabien Nogué, Hanspeter Naegeli, Andrew Nicholas Birch, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Barbara Manachini, Antoine Messéan, Elsa Ebbesen Nielsen, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Simon Moxon, Korbinian Schneeberger, Silvia Federici, Matthew Ramon, Nikoletta Papadopoulou, Huw Jones
article
EFSA Journal, 2018, 16 (7), ⟨10.2903/j.efsa.2018.5345⟩
resume
As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel, 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. The European Commission has mandated EFSA to develop a technical note to the applicants on, and checking of, the quality of the methodology, analysis and reporting covering complete sequencing of the insert and flanking regions, insertion site analysis of the GM event, and generational stability and integrity. This Technical Note puts together requirements and recommendations for when DNA sequencing is part of the molecular characterisation of GM plants, in particular for the characterisation of the inserted genetic material at each insertion site and flanking regions, the determination of the copy number of all detectable inserts, and the analysis of the genetic stability of the inserts, when addressed by Sanger sequencing or NGS. This document reflects the current knowledge in scientific‐technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. From 1 October 2018, this Technical Note will replace the JRC guideline of 2016 (updated April 2017) related to the verification and quality assessment of the sequencing of the insert(s) and flanking regions. It does not take into consideration the verification and validation of the detection method which remains under the remit of the JRC.
DOI
DOI : 10.2903/j.efsa.2018.5345
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The Chara genome
auteur
Tomoaki Nishiyama, Hidetoshi Sakayama, Jan de Vries, Henrik Buschmann, Denis Saint-Marcoux, Kristian K. Ullrich, Fabian B. Haas, Lisa Vanderstraeten, Dirk Becker, Daniel Lang, Stanislav Vosolsobě, Stephane Rombauts, Per K. I. Wilhelmsson, Philipp Janitza, Ramona Kern, Alexander Heyl, Florian Rümpler, Luz Irina A. Calderón Villalobos, John M. Clay, Roman Skokan, Atsushi Toyoda, Yutaka Suzuki, Hiroshi Kagoshima, Elio Schijlen, Navindra Tajeshwar, Bruno Catarino, Alexander J. Hetherington, Assia Saltykova, Clémence Bonnot, Holger Breuninger, Aikaterini Symeonidi, Guru V. Radhakrishnan, Filip van Nieuwerburgh, Dieter Deforce, Caren Chang, Kenneth G. Karol, Rainer Hedrich, Peter Ulvskov, Gernot Glöckner, Charles F. Delwiche, Jan Petrasek, Yves van de Peer, Jìrí Friml, Mary Beilby, Liam Dolan, Yuji Kohara, Sumio Sugano, Asao Fujiyama, Pierre-Marc Delaux, Marcel Quint, Günter Theissen, Martin Hagemann, Jesper Harholt, Christophe Dunand, Sabine Zachgo, Jane Langdale, Florian Maumus, Dominique van Der Straeten, Sven B. Gould, Stefan A. Rensing
article
Cell, 2018, 174 (2), pp.448-464.e24. ⟨10.1016/j.cell.2018.06.033⟩
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Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.
DOI
DOI : 10.1016/j.cell.2018.06.033
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AgroDataRing: Une infrastructure partagée et mutualisée pour le stockage longue durée
auteur
Pierre Adenot, Stéphane Bansard, David Benaben, Veronique Brunaud, Christophe Caron, Alexandre Dehne Garcia, Christophe Duperier, Adrien Falce, Olivier Filangi, Franck Giacomoni, Fabienne Granier, Philippe Grevet, Nicolas Guilhot, Annie Hofstetter, Johann Joets, Thierry Hotelier, Olivier Langella, Ludovic Legrand, Mikaël Loaec, Virginie Lollier, Patrick Moreau, Emmanuelle Morin, Hadi Quesneville, Tovo Rabemanantsoa, Gerald Salin, Dominique Tessier
article
Cahier des Techniques de l'INRA, 2018, pp.1-7
resume
Les communautés scientifiques se trouvent aujourd’hui confrontées à un changement de paradigme autour de la gestion des données, nécessitant une meilleure gestion du cycle de vie des données avec notamment leur traitement et intégration, et leur partage. À la suite du chantier « Data Partage » lancé dès 2012 à l’Inra, le groupe de travail « e-infra Storage » a initié en 2016 une réflexion collective autour des besoins de l’Institut en matière de dispositif de stockage des données patrimoniales scientifiques qui a abouti à la co-construction d’une infrastructure partagée et mutualisée : AgroDataRing.
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https://hal.science/hal-02097192/file/AgroDataRing.pdf BibTex
titre
Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs
auteur
Valerie Laucou, Amandine Launay, Roberto Bacilieri, Thierry Lacombe, Anne-Francoise Adam-Blondon, Aurélie Berard, Aurélie Chauveau, Maria Teresa de Andrés, Ludger Hausmann, Javier Ibanez, Marie-Christine Le Paslier, David Maghradze, José Miguel Martinez-Zapater, Erika Maul, Maharajah Ponnaiah, Reinhard Topfer, Jean-Pierre Peros, Jean-Michel Boursiquot
article
PLoS ONE, 2018, 13 (2), 27 p. ⟨10.1371/journal.pone.0192540⟩
DOI
DOI : 10.1371/journal.pone.0192540
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https://hal.inrae.fr/hal-02628848/file/2018_Laucou_Plos%20One_1.pdf BibTex
titre
Assessment of genetically modified cotton GHB614 × LLCotton25 × MON 15985 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2011‐94)
auteur
Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messéan, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Hermann Broll, Andrea Gennaro, Franco Maria Neri, Konstantinos Paraskevopoulos
article
EFSA Journal, 2018, 16 (4), ⟨10.2903/j.efsa.2018.5213⟩
resume
The three-event stack cotton GHB614 x LLCotton25 x MON 15985 was produced by conventional crossing to combine three single cotton events, GHB614, LLCotton25 and MON 15985. The EFSA GMO Panel previously assessed the three single events and did not identify safety concerns. No new data on the single events that could lead to modification of the original conclusions on their safety were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single events and of the newly expressed proteins in the three-event stack cotton did not give rise to food and feed safety or nutritional issues. Food and feed derived from cotton GHB614 x LLCotton25 x MON 15985 are expected to have the same nutritional impact as those derived from the non-GM comparator. In the case of accidental release of viable GHB614 x LLCotton25 x MON 15985 cottonseeds into the environment, this three-event stack cotton would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton GHB614 x LLCotton25 x MON 15985. In conclusion, the GMO Panel considers that cotton GHB614 x LLCotton25 x MON 15985, as described in this application, is as safe as the non-GM comparator with respect to potential effects on human and animal health and the environment. (C) 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.
DOI
DOI : 10.2903/j.efsa.2018.5213
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titre
Statement complementing the EFSA Scientific Opinion on application (EFSA‐GMO‐DE‐2011‐95) for the placing on the market of genetically modified maize 5307 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Syngenta Crop Protection AG taking into consideration an additional toxicological study
auteur
Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messéan, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Konstantinos Paraskevopoulos, Anna Lanzoni
article
EFSA Journal, 2018, 16 (4), ⟨10.2903/j.efsa.2018.5233⟩
resume
The GMO Panel was previously not in the position to complete the food/feed safety assessment ofmaize 5307 due to an inadequate 28-day toxicity study necessary for an appropriate assessment ofeCry3.1Ab protein. Following a mandate from the European Commission, the GMO Panel assessed asupplementary 28-day toxicity study in mice on the eCry3.1Ab protein (1,000 mg/kg body weight (bw)per day) to complement its scientific opinion on application EFSA-GMO-DE-2011-95 for the placing onthe market of the maize 5307 for food and feed uses, import and processing. The supplementary28-day toxicity study did not show adverse effects. Taking into account the previous assessment andthe new information, the GMO Panel concludes that maize 5307, as assessed in the scientific opinionon application EFSA-GMO-DE-2011-95 (EFSA GMO Panel, 2015) and in the supplementary toxicitystudy, is as safe and nutritious as its conventional counterpart in the scope of this application.
DOI
DOI : 10.2903/j.efsa.2018.5233
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titre
Assessment of genetically modified cotton GHB614 × T304‐40 × GHB119 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2014‐122)
auteur
Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messean, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Michele Ardizzone, Antonio Fernández‐dumont, Andrea Gennaro, Anna Lanzoni, Franco Maria Neri, Nikoletta Papadopoulou, Konstantinos Paraskevopoulos
article
EFSA Journal, 2018, 16 (7), ⟨10.2903/j.efsa.2018.5349⟩
resume
The three-event stack cotton GHB614 x T304-40 x GHB119 was produced by conventional crossing to combine three single events, GHB614, T304-40 and GHB119. The genetically modified organisms (GMO) Panel previously assessed the three single cotton events and did not identify safety concerns. No new data on the single cotton events that could lead to modification of the original conclusions on their safety were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single cotton events and of the newly expressed proteins in the three-event stack cotton did not give rise to food and feed safety concern. The GMO Panel considers that the three-event stack cotton GHB614 x T304-40 x GHB119 has the same nutritional impact as its comparator and the non-GM reference varieties tested. The GMO Panel concludes that the three-event stack cotton GHB614 x T304-40 x GHB119, as described in this application, is nutritionally equivalent to and as safe as its comparator and the non-GM reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable GHB614 x T304-40 x GHB119 cottonseeds into the environment, this three-event stack would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton GHB614 x T304-40 x GHB119 seeds. The GMO Panel concludes that cotton GHB614 x T304-40 x GHB119, as described in this application, is as safe as its comparator and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment. (c) 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.
DOI
DOI : 10.2903/j.efsa.2018.5349
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titre
Assessment of genetically modified maize 1507 × NK603 for renewal of authorisation under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐RX‐008)
auteur
Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messean, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Fernando Alvarez, Michele Ardizzone, Giacomo de Sanctis, Antonio Fernández Dumont, Anna Lanzoni, Nikoletta Papadopoulou, Konstantinos Paraskevopoulos
article
EFSA Journal, 2018, 16 (7), ⟨10.2903/j.efsa.2018.5347⟩
resume
Following the submission of application EFSA-GMO-RX-008 under Regulation (EC) No 1829/2003 from Pioneer Hi-Bred International, Inc. and Dow AgroSciences LLC, the Panel on Genetically Modified Organisms of the European Food Safety Authority was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect-resistant, herbicide-tolerant genetically modified maize 1507 x NK603, for food and feed uses, import and processing, excluding cultivation within the EU. The data received in the context of this renewal application contained a systematic search and evaluation of literature, updated bioinformatic analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. In conclusion, under the assumption that the DNA sequence of the events in maize 1507 x NK603 considered for renewal are identical to the newly reported 1507 sequence and the NK603 sequence of the originally assessed two-event stack maize, the GMO Panel concludes that there is no evidence in the renewal application EFSA-GMO-RX-008 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize 1507 x NK603 (EFSA, 2006). (C) 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.
DOI
DOI : 10.2903/j.efsa.2018.5347
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titre
Assessment of genetically modified maize MON 87411 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐NL‐2015‐124)
auteur
Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messéan, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Michele Ardizzone, Giacomo de Sanctis, Antonio Fernandez Dumont, Andrea Gennaro, José Angel Gómez Ruiz, Anna Lanzoni, Franco Maria Neri, Nikoletta Papadopoulou, Konstantinos Paraskevopoulos, Matthew Ramon
article
EFSA Journal, 2018, 16 (6), ⟨10.2903/j.efsa.2018.5310⟩
resume
Maize MON 87411 was developed to confer resistance to corn rootworms (Diabrotica spp.) by the expression of a modified version of the Bacillus thuringiensis cry3Bb1 gene and a DvSnf7 dsRNA expression cassette, and tolerance to glyphosate-containing herbicides by the expression of a CP4 5-enolpyruvylshikimate-3-phosphate synthase (cp4 epsps) gene. The molecular characterisation data and bioinformatics analyses did not identify issues requiring assessment for food and feed safety. No statistically significant differences in the agronomic and phenotypic characteristics tested between maize MON 87411 and its conventional counterpart were identified. The compositional analysis of maize MON 87411 did not identify differences that required further assessment except for palmitic acid levels in grains from not treated maize MON 87411. The GMO Panel did not identify safety concerns regarding the toxicity and allergenicity of the Cry3Bb1 and CP4 EPSPS proteins, as expressed in maize MON 87411 and found no evidence that the genetic modification might significantly change the overall allergenicity of maize MON 87411. The nutritional impact of maize MON 87411-derived food and feed is expected to be the same as those derived from the conventional counterpart and non-GM commercial reference varieties. The GMO Panel concludes that maize MON 87411, as described in this application, is nutritionally equivalent to and as safe as the conventional counterpart and the non-GM maize reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MON 87411 grains into the environment, maize MON 87411 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 87411. The GMO Panel concludes that maize MON 87411, as described in this application, is as safe as its conventional counterpart and the tested non-GM maize reference varieties with respect to potential effects on human and animal health and the environment. (C) 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.
DOI
DOI : 10.2903/j.efsa.2018.5310
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titre
A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits
auteur
Laurence Hibrand-Saint Oyant, Tom Ruttink, Latifa Hamama, Ilya Kirov, Deepika Lakhwani, Ning-Ning Zhou, Peter Bourke, Nicolas Daccord, Leen Leus, Dietmar Schulz, Henri van de Geest, Thamara Hesselink, Katrijn van Laere, Sandrine Balzergue, Tatiana Thouroude, Annie Chastellier, Julien Jeauffre, Linda Voisine, Sylvain Gaillard, Theo Borm, Paul Arens, Roeland Voorrips, Chris Maliepaard, Enzo Neu, Marcus Linde, Marie-Christine Le Paslier, Aurelie Berard, Remi Bounon, Jeremy Clotault, Nathalie Choisne, Hadi Quesneville, Koji Kawamura, Sébastien Aubourg, Soulaiman Sakr, Rene Smulder, Elio Schijlen, Etienne Bucher, Thomas Debener, Jan de Riek, Fabrice Foucher
article
Nature Plants, 2018, 4, pp.473-484. ⟨10.1101/254102⟩
resume
Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits. We produced a haploid rose line from R. chinensis "Old Blush" and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
DOI
DOI : 10.1101/254102
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titre
Assessment of genetically modified maize MON 87403 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐BE‐2015‐125)
auteur
Hanspeter Naegeli, Andrew Nicholas Birch, Josep Casacuberta, Adinda de Schrijver, Mikołaj Antoni Gralak, Philippe Guerche, Huw Jones, Barbara Manachini, Antoine Messean, Elsa Ebbesen Nielsen, Fabien Nogué, Christophe Robaglia, Nils Rostoks, Jeremy Sweet, Cristoph Tebbe, Francesco Visioli, Jean-Michel Wal, Yann Devos, Hermann Broll, Matthew Ramon
article
EFSA Journal, 2018, 16 (3), ⟨10.2903/j.efsa.2018.5225⟩
resume
aize MON 87403 was developed to increase ear biomass at early reproductive phase through the expression of a modified AtHB17 gene from Arabidopsis thaliana, encoding a plant transcription factor of the HD-Zip II family. The molecular characterisation data and bioinformatic analyses did not identify issues requiring assessment for food and feed safety. No statistically significant differences in the agronomic and phenotypic characteristics tested between maize MON 87403 and its conventional counterpart were identified. The compositional analysis of maize MON 87403 did not identify differences that require further assessment. The GMO Panel did not identify safety concerns regarding the toxicity and allergenicity of the AtHB17113 protein, as expressed in maize MON 87403. The nutritional value of food and feed derived from maize MON 87403 is not expected to differ from that of food and feed derived from non-genetically modified (GM) maize varieties. Based on the outcome of the studies considered in the comparative analysis and molecular characterisation, the GMO Panel concludes that maize MON 87403 is as safe and nutritious as the conventional counterpart and the non-GM maize reference varieties tested. In the case of accidental release of viable maize MON 87403 grains into the environment, maize MON 87403 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 87403. In conclusion, the GMO Panel considers that maize MON 87403, as described in this application, is as safe as its conventional counterpart and the tested non-GM maize reference varieties with respect to potential effects on human and animal health and the environment. (C) 2018 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority.
DOI
DOI : 10.2903/j.efsa.2018.5225
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Habilitation à diriger des recherches

titre
Evolution and Impact of Transposable Elements and Viruses
auteur
Florian Maumus
article
Life Sciences [q-bio]. Université paris saclay, 2018
resume
Since my early career, I have been fascinated by the evolution of Selfish Genetic Elements (SGEs - including viruses and transposable elements) and their impact on the evolution of the genomes and epigenomes of their host organisms. By integrating host genomes repeatedly in a stochastic manner, SGEs can profoundly influence the biology of their hosts. They represent a predominant part of most eukaryotic genomes and constitute a major source of genetic and epigenetic changes. Friends or foes? The integration of SGEs in genomes causes deleterious mutations most of the time, but it occasionally mediates key evolutionary adaptations. My goal in research is to help elucidate the modes and consequences of these evolutionary tradeoffs, especially in plants and algae.
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https://hal.science/tel-04443412/file/Memoire_HDR_F_MAUMUS_ORSAY_print.pdf BibTex

Theses

titre
In silico approaches to the impact of transposable elements on the regulation of gene expression.
auteur
Ophélie Jouffroy
article
Biologie moléculaire. Université Paris Saclay (COmUE), 2018. Français. ⟨NNT : 2018SACLA044⟩
resume
Plant genomes are populated by different types of repetitive elements including transposable elements (TEs) and simple sequence repeats (SSRs) that can have a strong impact on genome size and dynamic as well as on the regulation of gene transcription. At least two-thirds of the tomato genome is composed of repeats. While their bulk impact on genome organization has been largely revealed by whole genome assembly, their influence on tomato biology and phenotype remains largely unaddressed. More specifically, the effects and roles of DNA repeats on the maturation of fleshy fruit, which is a complex process of key agro-economic interest, still needs to be investigated comprehensively and tomato is arguably an excellent model for such study. We have performed a comprehensive annotation of the tomato repeatome to explore its potential impact on tomato genome composition and gene transcription. Our results show that the tomato genome can be fractioned into three compartments with different gene and repeat density, each compartment presenting contrasting repeat and gene composition, repeat-gene associations and different gene transcriptional levels. In the context of fruit ripening, we found that repeats are present in the majority of differentially methylated regions (DMRs) and thousands of repeat associated DMRs are found in the proximity of genes, including hundreds that are differentially regulated during this process. Furthermore, we found that repeats are also present in the proximity of DNA binding sites of the key ripening protein RIN. We also observed that some repeat families are present at unexpected high frequency in the proximity of genes that are differentially expressed during tomato ripening. Given the link between these different entities, we wondered whether it was possible that some transposable elements of the tomato genome were selected during evolution for their impact on the genome. To address this question, we have developed a series of analyzes to try to detect in silico such elements. A total of 36 transposable elements families were found to present empirical properties of selection, and some are associated with particular gene functions. More refined analyzes of the sequences could then potentially make it possible to discover motifs of interest, in particular for the transcriptional regulation of genes.
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https://pastel.hal.science/tel-02516180/file/69644_JOUFFROY_2018_archivage.pdf BibTex

2017

Journal articles

titre
Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
auteur
Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldon, Anna Jordan, Irene Julca, Graeme J. Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara Lopez-Gomollon, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel R. G. Price, Akiko Sugio, Manuella van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C. C. Wilson, Cock van Oosterhout, David Swarbreck, Saskia A. Hogenhout
article
Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩
resume
BACKGROUND: The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. RESULTS: To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. CONCLUSIONS: Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution.
DOI
DOI : 10.1186/s13059-016-1145-3
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https://univ-rennes.hal.science/hal-01500475/file/Rapid%20transcriptional%20plasticity%20of%20duplicated-%20version%20of%20record.pdf BibTex
titre
A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
auteur
Aurelie Canaguier, Jérome Grimplet, Gabriele Di Gaspero, Simone Scalabrin, Eric Duchêne, Nathalie Choisne, Nacer Mohellibi, Cécile Guichard, Stéphane Rombauts, Isabelle Le Clainche, Aurélie Berard, Aurelie Chauveau, Rémi Bounon, Camille Rustenholz, Michele Morgante, Marie-Christine Le Paslier, Dominique Brunel, Anne-Françoise Adam-Blondon
article
Genomics Data, 2017, 14, pp.56-62. ⟨10.1016/j.gdata.2017.09.002⟩
resume
A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
DOI
DOI : 10.1016/j.gdata.2017.09.002
Accès au texte intégral et bibtex
https://hal.science/hal-01619926/file/2017_Canaguier_Genomics%20Data_%7BB0A62A30-EE2D-431B-8868-1A6C16A1A8C5%7D.pdf BibTex
titre
Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges
auteur
Anaïs Gouin, Anthony Bretaudeau, Kiwoong Nam, Sylvie Gimenez, Jean-Marc Aury, Bernard Duvic, Frederique Hilliou, Nicolas Durand, Nicolas Montagné, Isabelle Darboux, Suyog Kuwar, Thomas Chertemps, David Siaussat, Anne Bretschneider, Yves Moné, Seung-Joon Ahn, Sabine Hänniger, Anne-Sophie Gosselin Grenet, David Neunemann, Florian Maumus, Isabelle Luyten, Karine Labadie, Wei Xu, Fotini A. Koutroumpa, Jean-Michel Escoubas, Angel Llopis, Martine Maïbèche-Coisne, Fanny Salasc, Archana Tomar, Alisha R Anderson, Sher Afzal Khan, Pascaline Dumas, Marion Orsucci, Julie Guy, Caroline Belser, Adriana A. Alberti, Benjamin Noel, Arnaud Couloux, Jonathan Mercier, Sabine Nidelet, Emeric Dubois, Nai-Yong Liu, Isabelle Boulogne, Olivier Mirabeau, Gaelle Le Goff, Karl Gordon, John Oakeshott, Fernando L Consoli, Anne-Nathalie Volkoff, Howard W Fescemyer, James H Marden, Dawn S Luthe, Salvador Herrero, David G Heckel, Patrick Wincker, Gael J Kergoat, Joelle Amselem, Hadi Quesneville, Astrid T Groot, Emmanuelle Jacquin-Joly, Nicolas Nègre, Claire Lemaitre, Fabrice Legeai, Emmanuelle D’alençon, Philippe Fournier
article
Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩
resume
Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety of host-plants. Despite of its biological and practical importance - since insects eat 20% of crops - no exhaustive analysis of gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one of the world’s worst agricultural pests. This insect is polyphagous while the majority of other lepidopteran herbivores are specialist. It consists of two morphologically indistinguishable strains (“C” and “R”) that have different host plant ranges. To describe the evolutionary mechanisms that both enable the emergence of polyphagous herbivory and lead to the shift in the host preference, we analyzed whole genome sequences from laboratory and natural populations of both strains. We observed huge expansions of genes associated with chemosensation and detoxification compared with specialist Lepidoptera. These expansions are largely due to tandem duplication, a possible adaptation mechanism enabling polyphagy. Individuals from natural C and R populations show significant genomic differentiation. We found signatures of positive selection in genes involved in chemoreception, detoxification and digestion, and copy number variation in the two latter gene families, suggesting an adaptive role for structural variation.
DOI
DOI : 10.1038/s41598-017-10461-4
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https://inria.hal.science/hal-01633879/file/Gouin2017.pdf BibTex
titre
Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species
auteur
Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, Patrice Baa-Puyoulet, Anthony Bretaudeau, Bernardo Clavijo, Stefano Colella, Olivier Collin, Tamas Dalmay, Thomas Derrien, Honglin Feng, Toni Gabaldon, Anna Jordan, Irene Julca, Graeme J. Kettles, Krissana Kowitwanich, Dominique Lavenier, Paolo Lenzi, Sara Lopez-Gomollon, Damian Loska, Daniel Mapleson, Florian Maumus, Simon Moxon, Daniel R. G. Price, Akiko Sugio, Manuella Van Munster, Marilyne Uzest, Darren Waite, Georg Jander, Denis Tagu, Alex C. C. Wilson, Cock Van Oosterhout, David Swarbreck, Saskia A. Hogenhout
article
Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩
resume
no abstract
DOI
DOI : 10.1186/s13059-017-1202-6
Accès au texte intégral et bibtex
https://univ-rennes.hal.science/hal-01588181/file/erratum_1.pdf BibTex
titre
The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain
auteur
Cyril Charbonnel, Adnan Niazi, Emilie Elvira-Matelot, Elżbieta Nowak, Matthias Zytnicki, Anne De bures, Edouard Jobet, Alisson Opsomer, Nahid Shamandi, Marcin Nowotny, Christine Carapito, Jean-Philippe Reichheld, Herve H. Vaucheret, Julio Sáez-Vasquez
article
Nucleic Acids Research, 2017, 45 (20), pp.11891-11907. ⟨10.1093/nar/gkx820⟩
resume
RNase III enzymes cleave double stranded (ds)RNA. This is an essential step for regulating the processing of mRNA, rRNA, snoRNA and other small RNAs, including siRNA and miRNA. Arabidopsis thaliana encodes nine RNase III: four DICER-LIKE (DCL) and five RNASE THREE LIKE (RTL). To better understand the molecular functions of RNase III in plants we developed a biochemical assay using RTL1 as a model. We show that RTL1 does not degrade dsRNA randomly, but recognizes specific duplex sequences to direct accurate cleavage. Furthermore, we demonstrate that RNase III and dsRNA binding domains (dsRBD) are both required for dsRNA cleavage. Interestingly, the four DCL and the three RTL that carry dsRBD share a conserved cysteine (C230 in Arabidopsis RTL1) in their dsRBD. C230 is essential for RTL1 and DCL1 activities and is subjected to posttranscriptional modification. Indeed, under oxidizing conditions, glutathionylation of C230 inhibits RTL1 cleavage activity in a reversible manner involving glutaredoxins. We conclude that the redox state of the dsRBD ensures a fine-tune regulation of dsRNA processing by plant RNase III.
DOI
DOI : 10.1093/nar/gkx820
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https://hal.science/hal-02116017/file/The%20siRNA%20suppressor%20RTL1%20is%20redox-regulated%20through%20glutathionylation%20of%20conserved%20cysteine%20in%20the%20double-stranded-RNA-binding%20domain_1.pdf BibTex
titre
Combined Genomic and Genetic Data Integration of Major Agronomical Traits in Bread Wheat (Triticum aestivum L.)
auteur
Umar Quraishi, Caroline Pont, Qurat-Ul Ain, Raphaël Flores, Laura Burlot, Michaël Alaux, Hadi Quesneville, Jérôme Salse
article
Frontiers in Plant Science, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01843⟩
resume
The high resolution integration of bread wheat genetic and genomic resources accumulated during the last decades offers the opportunity to unveil candidate genes driving major agronomical traits to an unprecedented scale. We combined 27 public quantitative genetic studies and four genetic maps to deliver an exhaustive consensus map consisting of 140,315 molecular markers hosting 221, 73, and 82 Quantitative Trait Loci (QTL) for respectively yield, baking quality, and grain protein content (GPC) related traits. Projection of the consensus genetic map and associated QTLs onto the wheat syntenome made of 99,386 genes ordered on the 21 chromosomes delivered a complete and non-redundant repertoire of 18, 8, 6 metaQTLs for respectively yield, baking quality and GPC, altogether associated to 15,772 genes (delivering 28,630 SNP-based makers) including 37 major candidates. Overall, this study illustrates a translational research approach in transferring information gained from grass relatives to dissect the genomic regions hosting major loci governing key agronomical traits in bread wheat, their flanking markers and associated candidate genes to be now considered as a key resource for breeding programs.
DOI
DOI : 10.3389/fpls.2017.01843
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https://hal.science/hal-02285542/file/2017_Quraishi_Frontiers%20in%20Plant%20Science_1.pdf BibTex
titre
Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.
auteur
Thomas Mock, Robert P Otillar, Jan Strauss, Mark Mcmullan, Pirita Paajanen, Jeremy Schmutz, Asaf Salamov, Remo Sanges, Andrew Toseland, Ben J Ward, Andrew E Allen, Chris Dupont, Stephan Frickenhaus, Florian Maumus, Alaguraj Veluchamy, Taoyang Wu, Kerrie W Barry, Angela Falciatore, Maria I Ferrante, Antonio E Fortunato, Gernot Glöckner, Ansgar Gruber, Rachel Hipkin, Michael G Janech, Peter G Kroth, Florian Leese, Erika A Lindquist, Barbara R Lyon, Joel Martin, Chris Mayer, Micaela Parker, Hadi Quesneville, James A Raymond, Chris Uhlig, Ruben E Valas, Klaus U Valentin, Alexandra Z Worden, E Virginia Armbrust, Matthew D Clark, Chris Bowler, Beverley R Green, Vincent Moulton, Cock van Oosterhout, Igor V Grigoriev
article
Nature, 2017, 541, pp.536-540. ⟨10.1038/nature20803⟩
resume
The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus, based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
DOI
DOI : 10.1038/nature20803
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titre
A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene
auteur
Ziming Zhong, Thierry Marcel, Fanny E. Hartmann, Xin Ma, Clémence Plissonneau, Marcello Zala, Aurélie Ducasse, Johann Confais, Romain Compain, Nicolas Lapalu, Joëlle Amselem, Bruce A. Mcdonald, Daniel Croll, Javier Palma-Guerrero
article
New Phytologist, 2017, 214 (2), pp.619 - 631. ⟨10.1111/nph.14434⟩
resume
Zymoseptoria tritici is the causal agent of Septoria tritici blotch, a major pathogen of wheat globally and the most damaging pathogen of wheat in Europe. A gene-for-gene (GFG) interaction between Z. tritici and wheat cultivars carrying the Stb6 resistance gene has been postulated for many years, but the genes have not been identified. We identified AvrStb6 by combining quantitative trait locus mapping in a cross between two Swiss strains with a genome-wide association study using a natural population of c. 100 strains from France. We functionally validated AvrStb6 using ectopic transformations. AvrStb6 encodes a small, cysteine-rich, secreted protein that produces an avirulence phenotype on wheat cultivars carrying the Stb6 resistance gene. We found 16 nonsynonymous single nucleotide polymorphisms among the tested strains, indicating that AvrStb6 is evolving very rapidly. AvrStb6 is located in a highly polymorphic subtelomeric region and is surrounded by transposable elements, which may facilitate its rapid evolution to overcome Stb6 resistance. AvrStb6 is the first avirulence gene to be functionally validated in Z. tritici, contributing to our understanding of avirulence in apoplastic pathogens and the mechanisms underlying GFG interactions between Z. tritici and wheat.
DOI
DOI : 10.1111/nph.14434
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titre
De novo annotation of transposable elements : tackling the fat genome issue
auteur
Véronique Jamilloux, Josquin Daron, Frédéric Choulet, Hadi Quesneville
article
Proceedings of the IEEE, 2017, 105 (3), pp.474-481. ⟨10.1109/JPROC.2016.2590833⟩
resume
Transposable elements (TEs) constitute the most dynamic and the largest component of large plant genomes: for example, 80% to 90% of the maize genome and the wheat genome may be TEs. De novo TE annotation is therefore a computational challenge, and we investigated, using current tools in the REPET package, new strategies to overcome the difficulties. We tested our methodological developments on the sequence of the chromosome 3B of the hexaploid wheat; this chromosome is ∼1 Gb, one of the “fattest” genomes ever sequenced. We successfully established various strategies for annotating TEs in such a complex dataset. Our analyses show that all of our strategies can overcome the current limitations for de novo TE discovery in large plant genomes. Relative to annotation based on a library of known TEs, our de novo approaches improved genome coverage (from 84% to 90%), and the number of full length annotated copies from 14 830 to 15 905. We also developed two new metrics for qualifying TE annotation: NTE50 involves measuring the number, and LTE50 the smallest sizes of annotations that cover 50% of the genome. NTE50 decreased the number of annotations from 124 868 to 93 633 and LTE50 increased it from 1839 to 2659. This work shows how to obtain comprehensive and high-quality automatic TE annotation for a number of economically and agronomically important species.
DOI
DOI : 10.1109/JPROC.2016.2590833
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https://hal.inrae.fr/hal-02622009/file/De%20Novo%20Annotation%20of%20Transposable%20Elements%3A%20Tackling%20the%20Fat%20Genome%20Issue_1 BibTex
titre
De novo assembly of a new Solanum pennellii accession using nanopore sequencing
auteur
Maximilian H.-W. Schmidt, Alexander Vogel, Alisandra K. Denton, Benjamin Istace, Alexandra Wormit, Henri van de Geest, Marie E. Bolger, Saleh Alseekh, Janina Mass, Christian Pfaff, Ulrich Schurr, Roger Chetelat, Florian Maumus, Jean-Marc Aury, Sergey Koren, Alisdair R. Fernie, Daniel Zamir, Anthony M. Bolger, Bjoern Usadel
article
The Plant cell, 2017, 29, pp.2336-2348. ⟨10.1105/tpc.17.00521⟩
resume
Updates in nanopore technology have made it possible to obtain gigabases of sequence data. Prior to this, nanopore sequencing technology was mainly used to analyze microbial samples. Here, we describe the generation of a comprehensive nanopore sequencing data set with a median read length of 11,979 bp for a self-compatible accession of the wild tomato species Solanum pennellii. We describe the assembly of its genome to a contig N50 of 2.5 MB. The assembly pipeline comprised initial read correction with Canu and assembly with SMARTdenovo. The resulting raw nanopore-based de novo genome is structurally highly similar to that of the reference S. pennellii LA716 accession but has a high error rate and was rich in homopolymer deletions. After polishing the assembly with Illumina reads, we obtained an error rate of <0.02% when assessed versus the same Illumina data. We obtained a gene completeness of 96.53%, slightly surpassing that of the reference S. pennellii. Taken together, our data indicate that such long read sequencing data can be used to affordably sequence and assemble gigabase-sized plant genomes.
DOI
DOI : 10.1105/tpc.17.00521
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https://hal.inrae.fr/hal-02625700/file/2017_Schmidt_Plant%20Cell_1.pdf BibTex
titre
High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development
auteur
Nicolas Daccord, Jean-Marc Celton, G. Linsmith, C. Becker, Nathalie Choisne, E. Schijlen, H. van de Geest, L. Bianco, D. Micheletti, R. Velasco, E. A. Di Pierro, Jerome Gouzy, D. Jasper G. Rees, Philippe Guérif, Helene Muranty, Charles Eric Durel, Francois Laurens, Yves Lespinasse, Sylvain Gaillard, Sebastien Aubourg, Hadi Quesneville, D. Weigel, E. van de Weg, M. Troggio, Etienne Bucher
article
Nature Genetics, 2017, 49 (7), pp.1099-1108. ⟨10.1038/ng.3886⟩
resume
Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.
DOI
DOI : 10.1038/ng.3886
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https://hal.science/hal-01602554/file/publi17-lipm-021_daccord_high_1.pdf BibTex
titre
Developing data interoperability using standards: A wheat community use case
auteur
Esther Dzale Yeumo, Michaël Alaux, Elizabeth Arnaud, Sophie Aubin, Ute Baumann, Patrice Buche, Laurel Cooper, Robert P Davey, Richard Allan Fulss, Clement Jonquet, Marie-Angélique Laporte, Pierre Larmande, Cyril Pommier, Vassilis Protonotarios, Carmen Reverte, Rosemary Shrestha, Imma Subirats, Aravind Venkatesan, Alex Whan, Hadi Quesneville
article
F1000Research, 2017, 6 (1843), pp.1843. ⟨10.12688/f1000research.12234.1⟩
resume
In this article, we present a joint effort of the wheat research community, along with data and ontology experts, to develop wheat data interoperability guidelines. Interoperability is the ability of two or more systems and devices to cooperate and exchange data, and interpret that shared information. Interoperability is a growing concern to the wheat scientific community, and agriculture in general, as the need to interpret the deluge of data obtained through high-throughput technologies grows. Agreeing on common data formats, metadata, and vocabulary standards is an important step to obtain the required data interoperability level in order to add value by encouraging data sharing, and subsequently facilitate the extraction of new information from existing and new datasets. During a period of more than 18 months, the RDA Wheat Data Interoperability Working Group (WDI-WG) surveyed the wheat research community about the use of data standards, then discussed and selected a set of recommendations based on consensual criteria. The recommendations promote standards for data types identified by the wheat research community as the most important for the coming years: nucleotide sequence variants, genome annotations, phenotypes, germplasm data, gene expression experiments, and physical maps. For each of these data types, the guidelines recommend best practices in terms of use of data formats, metadata standards and ontologies. In addition to the best practices, the guidelines provide examples of tools and implementations that are likely to facilitate the adoption of the recommendations. To maximize the adoption of the recommendations, the WDI-WG used a community-driven approach that involved the wheat research community from the start, took into account their needs and practices, and provided them with a framework to keep the recommendations up to date. We also report this approach’s potential to be generalizable to other (agricultural) domains.
DOI
DOI : 10.12688/f1000research.12234.1
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-01652022/file/3fac9ce9-c58d-4642-b269-8c82d34ac3f8_12234_-_Hadi_Quesneville.pdf BibTex
titre
Towards a sustainable European viticulture sector
auteur
Anne-Francoise Adam-Blondon
article
Impact, 2017, pp.28-30
resume
Towards a sustainable European viticulture sector. The building blocks of Europe’s wine industry
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https://hal.science/hal-01543438/file/2017_Adam-Blondon_Impact_%7B611F7FA3-7259-47BE-BAB3-008EE2918892%7D.pdf BibTex
titre
Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters
auteur
Jean-Felix Dallery, Nicolas Lapalu, Antonios Zampounis, Sandrine Pigné, Isabelle Luyten, Joelle Amselem, Alexander H. J. Wittenberg, Shiguo Zhou, Marisa V. de Queiroz, Guillaume Robin, Annie Auger, Matthieu Hainaut, Bernard Henrissat, Ki-Tae Kim, Yong-Hwan Lee, Olivier Lespinet, David C. Schwartz, Michael R. Thon, Richard O'Connell
article
BMC Genomics, 2017, 18, ⟨10.1186/s12864-017-4083-x⟩
resume
Background: The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Results: Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat-and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. Conclusion: The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen.
DOI
DOI : 10.1186/s12864-017-4083-x
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https://hal.science/hal-01608503/file/BMC%20Dallery%202017_1.pdf BibTex
titre
Physical Map of the Short Arm of Bread Wheat Chromosome 3D
auteur
Kateřina Holušová, Jan Vrána, Barbora Balcárková, Zeev Frenkel, Benoît Darrier, Etienne Paux, Federica Cattonaro, Helene Berges, Thomas Letellier, Michael Alaux, Jaroslav Doležel, Jan Bartoš
article
PLANT GENOME, 2017, 10 (2), ⟨10.3835/plantgenome2017.03.0021⟩
resume
Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide. Although a reference genome sequence would represent a valuable resource for wheat improvement through genomics-assisted breeding and gene cloning, its generation has long been hampered by its allohexaploidy, high repeat content, and large size. As a part of a project coordinated by the International Wheat Genome Sequencing Consortium (IWGSC), a physical map of the short arm of wheat chromosome 3D (3DS) was prepared to facilitate reference genome assembly and positional gene cloning. It comprises 869 contigs with a cumulative length of 274.5 Mbp and represents 85.5% of the estimated chromosome arm size. Eighty-six Mbp of survey sequences from chromosome arm 3DS were assigned in silico to physical map contigs via next-generation sequencing of bacterial artificial chromosome pools, thus providing a high-density framework for physical map ordering along the chromosome arm. About 60% of the physical map was anchored in this single experiment. Finally, 1393 high-confidence genes were anchored to the physical map. Comparisons of gene space of the chromosome arm 3DS with genomes of closely related species [Brachypodium distachyon (L.) P. Beauv., rice (Oryza sativa L.), and sorghum [Sorghum bicolor (L.) Moench] and homeologous wheat chromosomes provided information about gene movement on the chromosome arm.
DOI
DOI : 10.3835/plantgenome2017.03.0021
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titre
Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales
auteur
Raúl Castanera, Gúmer Pérez, Leticia López-Varas, Joëlle Amselem, Kurt Labutti, Vasanth Singan, Anna Lipzen, Sajeet Haridas, Kerrie Barry, Igor V. Grigoriev, Antonio G. Pisabarro, Lucía Ramírez
article
BMC Genomics, 2017, 18 (1), pp.1-14. ⟨10.1186/s12864-017-4243-z⟩
resume
Background: Coniophora olivacea is a basidiomycete fungus belonging to the order Boletales that produces brown-rot decay on dead wood of conifers. The Boletales order comprises a diverse group of species including saprotrophs and ectomycorrhizal fungi that show important differences in genome size. Results: In this study we report the 39.07-megabase (Mb) draft genome assembly and annotation of C. olivacea. A total of 14,928 genes were annotated, including 470 putatively secreted proteins enriched in functions involved in lignocellulose degradation. Using similarity clustering and protein structure prediction we identified a new family of 10 putative lytic polysaccharide monooxygenase genes. This family is conserved in basidiomycota and lacks of previous functional annotation. Further analyses showed that C. olivacea has a low repetitive genome, with 2.91% of repeats and a restrained content of transposable elements (TEs). The annotation of TEs in four related Boletales yielded important differences in repeat content, ranging from 3.94 to 41.17% of the genome size. The distribution of insertion ages of LTR-retrotransposons showed that differential expansions of these repetitive elements have shaped the genome architecture of Boletales over the last 60 million years. Conclusions: Coniophora olivacea has a small, compact genome that shows macrosynteny with Coniophora puteana. The functional annotation revealed the enzymatic signature of a canonical brown-rot. The annotation and comparative genomics of transposable elements uncovered their particular contraction in the Coniophora genera, highlighting their role in the differential genome expansions found in Boletales species.
DOI
DOI : 10.1186/s12864-017-4243-z
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https://hal.inrae.fr/hal-02628469/file/2017_Castanera_BMC%20Genomics_1.pdf BibTex
titre
Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom
auteur
Swaraj Basu, Shrikant Patil, Daniel Mapleson, Monia Teresa Russo, Laura Vitale, Cristina Fevola, Florian Maumus, Raffaella Casotti, Thomas Mock, Mario Caccamo, Marina Montresor, Remo Sanges, Maria Immacolata Ferrante
article
New Phytologist, 2017, 215 (1), pp.140-156. ⟨10.1111/nph.14557⟩
resume
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes. We also identified a small number of conserved noncoding elements. Sexual reproduction impacted on cell cycle progression and induced an asymmetric response of the opposite mating types. G protein-coupled receptors and cyclic guanosine monophosphate (cGMP) are implicated in the response to sexual cues, which overall entails a modulation of cell cycle, meiosis-related and nutrient transporter genes, suggesting a fine control of nutrient uptake even under nutrient-replete conditions. The controllable life cycle and the genome sequence of P. multistriata allow the reconstruction of changes occurring in diatoms in a key phase of their life cycle, providing hints on the evolution and putative function of their genes and empowering studies on sexual reproduction.
DOI
DOI : 10.1111/nph.14557
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https://hal.science/hal-01607004/file/2017_Basu_New%20Phytologist_1.pdf BibTex
titre
De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue
auteur
Véronique Jamilloux, Josquin Daron, Frédéric Choulet, Hadi Quesneville
article
Proceedings of the IEEE, 2017, 105 (5), pp.978-978. ⟨10.1109/JPROC.2017.2680218⟩
resume
In [1], Fig. 1 is inconsistent with the text manuscript. First, the black curve corresponding to case 1 did not correspond to the result from the experiment described in the paper, but to another which was removed from the final manuscript. The second error was a typo with an inversion between the green and blue text indicating NTE50 and LTE50 for cases 4 and 5, respectively. We corrected this figure for the case 1 curve with the right experimental result, and fixed the typo so that it corresponds now perfectly with the manuscript text. Note that this does not affect the text in the manuscript, which remains correct.
DOI
DOI : 10.1109/JPROC.2017.2680218
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2016

Journal articles

titre
International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany
auteur
Pascale Lesage, Mireille Bétermier, Antoine Bridier-Nahmias, Michael Chandler, Séverine Chambeyron, Gael Cristofari, Nicolas Gilbert, Hadi Quesneville, Chantal Vaury, Jean-Nicolas Volff
article
Mobile DNA, 2016, 7 (1), pp.19. ⟨10.1186/s13100-016-0075-7⟩
resume
The third international conference on Transposable Elements (ICTE) was held 16-19 April 2016 in Saint Malo, France. Organized by the French Transposition Community (Research group of the CNRS: "Mobile genetic elements: from mechanism to populations, an integrative approach") and the French Society of Genetics, the conference's goal was to bring together researchers who study transposition in diverse organisms, using multiple experimental approaches. The meeting gathered 180 participants from all around the world. Most of them contributed through poster presentations, invited talks and short talks selected from poster abstracts. The talks were organized into six scientific sessions: "Taming mobile DNA: self and non-self recognition"; "Trans-generational inheritance"; "Mobile DNA genome structure and organization, from molecular mechanisms to applications"; "Remembrance of (retro) transposon past: mobile DNA in genome evolution"; and finally "The yin and the yang of mobile DNA in human health".
DOI
DOI : 10.1186/s13100-016-0075-7
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https://inserm.hal.science/inserm-01384467/file/13100_2016_Article_75.pdf BibTex
titre
The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II)(2)Cys(6) transcription factor BcBot6
auteur
Antoine Porquier, Guillaume Morgant, Javier Moraga, Berengere Dalmais, Isabelle Luyten, Adeline Simon, Jean-Marc Pradier, Joëlle Amselem, Isidro Gonzalez Collado, Muriel Viaud
article
Fungal Genetics and Biology, 2016, 96 (Nov 2016), pp.33-46. ⟨10.1016/j.fgb.2016.10.003⟩
resume
Botrydial (BOT) is a non-host specific phytotoxin produced by the polyphagous phytopathogenic fungus Botrytis cinerea. The genomic region of the BOT biosynthetic gene cluster was investigated and revealed two additional genes named Bcbot6 and Bcbot7. Analysis revealed that the G + C/A + T-equilibrated regions that contain the Bcbot genes alternate with A + T-rich regions made of relics of transposable elements that have undergone repeat-induced point mutations (RIP). Furthermore, BcBot6, a Zn(II)(2)Cys(6) putative transcription factor was identified as a nuclear protein and the major positive regulator of BOT biosynthesis. In addition, the phenotype of the Delta Bcbot6 mutant indicated that BcBot6 and therefore BOT are dispensable for the development, pathogenicity and response to abiotic stresses in the B. cinerea strain B05.10. Finally, our data revealed that B. pseudocinerea, that is also polyphagous and lives in sympatry with B. cinerea, lacks the ability to produce BOT. Identification of BcBot6 as the major regulator of BOT synthesis is the first step towards a comprehensive understanding of the complete regulation network of BUT synthesis and of its ecological role in the B. cinerea life cycle.
DOI
DOI : 10.1016/j.fgb.2016.10.003
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https://hal.science/hal-01532622/file/2016-The%2520botrydial%2520biosynthetic%2520gene%2520cluster%2520of%2520Botrytis%2520cinerea%2520displays%2520a%2520bipartite%2520genomic%2520structure%2520and%2520is%2520positively%2520regulated%2520by%2520the%2520putative%2520Zn%2528II%25292Cys6transcription%2520f.pdf BibTex
titre
Arabidopsis RNASE THREE LIKE2 Modulates the Expression of Protein-Coding Genes via 24-Nucleotide Small Interfering RNA-Directed DNA Methylation
auteur
Emilie Elvira-Matelot, Mélanie Hachet, Nahid Shamandi, Pascale Comella, Julio Sáez-Vasquez, Matthias Zytnicki, Herve H. Vaucheret
article
The Plant cell, 2016, 28 (2), pp.406-425. ⟨10.1105/tpc.15.00540⟩
resume
RNaseIII enzymes catalyze the cleavage of double-stranded RNA (dsRNA) and have diverse functions in RNA maturation. Arabidopsis thaliana RNASE THREE LIKE2 (RTL2), which carries one RNaseIII and two dsRNA binding (DRB) domains, is a unique Arabidopsis RNaseIII enzyme resembling the budding yeast small interfering RNA (siRNA)-producing Dcr1 enzyme. Here, we show that RTL2 modulates the production of a subset of small RNAs and that this activity depends on both its RNaseIII and DRB domains. However, the mode of action of RTL2 differs from that of Dcr1. Whereas Dcr1 directly cleaves dsRNAs into 23-nucleotide siRNAs, RTL2 likely cleaves dsRNAs into longer molecules, which are subsequently processed into small RNAs by the DICER-LIKE enzymes. Depending on the dsRNA considered, RTL2-mediated maturation either improves (RTL2-dependent loci) or reduces (RTL2-sensitive loci) the production of small RNAs. Because the vast majority of RTL2-regulated loci correspond to transposons and intergenic regions producing 24-nucleotide siRNAs that guide DNA methylation, RTL2 depletion modifies DNA methylation in these regions. Nevertheless, 13% of RTL2-regulated loci correspond to protein-coding genes. We show that changes in 24-nucleotide siRNA levels also affect DNA methylation levels at such loci and inversely correlate with mRNA steady state levels, thus implicating RTL2 in the regulation of protein-coding gene expression.
DOI
DOI : 10.1105/tpc.15.00540
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https://hal.science/hal-02116029/file/PC_TPC201500540RAR2.pdf BibTex
titre
TransPLANT resources for triticeae genomic data
auteur
Manuel Spannagl, Michael M. Alaux, Matthias Lange, Dan M. Bolser, Kai Christian Bader, Thomas Letellier, Erik Kimmel, Raphaël-Gauthier R.-G. Flores, Cyril Pommier, Arnaud Kerhornou, Brandon Walts, Thomas Nussbaumer, Christophe Grabmuller, Jinbo Chen, Christian Colmsee, Sebastian Beier, Martin Mascher, Thomas Schmutzer, Daniel Arend, Anil Thanki, Ricardo Ramirez-Gonzalez, Martin Ayling, Sarah Ayling, Mario Caccamo, Klaus F. X. Mayer, Uwe Scholz, Delphine Steinbach, Hadi Quesneville, Paul Kersey
article
PLANT GENOME, 2016, 9 (1), 13 p. ⟨10.3835/plantgenome2015.06.0038⟩
resume
The genome sequences of many important Triticeae species, including bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), remained uncharacterized for a long time because their high repeat content, large sizes, and polyploidy. As a result of improvements in sequencing technologies and novel analyses strategies, several of these have recently been deciphered. These efforts have generated new insights into Triticeae biology and genome organization and have important implications for downstream usage by breeders, experimental biologists, and comparative genomicists. transPLANT (http://www.transplantdb.eu) is an EU-funded project aimed at constructing hardware, software, and data infrastructure for genome-scale research in the life sciences. Since the Triticeae data are intrinsically complex, heterogenous, and distributed, the transPLANT consortium has undertaken efforts to develop common data formats and tools that enable the exchange and integration of data from distributed resources. Here we present an overview of the individual Triticeae genome resources hosted by transPLANT partners, introduce the objectives of transPLANT, and outline common developments and interfaces supporting integrated data access.
DOI
DOI : 10.3835/plantgenome2015.06.0038
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https://hal.inrae.fr/hal-02635899/file/tpg-9-1-plantgenome2015.06.0038_1.pdf BibTex
titre
The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea
auteur
Jeanine L. Olsen, Pierre Rouzé, Bram Verhelst, Yao-Cheng Y.-C. Lin, Till Bayer, Jonas Collen, Emanuela Dattolo, Emanuele de Paoli, Simon Dittami, Florian Maumus, Gurvan Michel, Anna Kersting, Chiara Lauritano, Rolf Lohaus, Mats Töpel, Thierry Tonon, Kevin Vanneste, Mojgan Amirebrahimi, Janina Brakel, Christoffer Boström, Mansi Chovatia, Jane Grimwood, Jerry W. Jenkins, Alexander Jueterbock, Amy Mraz, Wytze T. Stam, Hope Tice, Erich Bornberg-Bauer, Pamela J Green, Gareth A. Pearson, Gabriele Procaccini, Carlos M. Duarte, Jeremy J. Schmutz, Thorsten B.H. Reusch, Yves van de Peer
article
Nature, 2016, 530 (7590), pp.331-335. ⟨10.1038/nature16548⟩
resume
Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.
DOI
DOI : 10.1038/nature16548
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https://hal.sorbonne-universite.fr/hal-01289099/file/nature16548.pdf BibTex
titre
Towards an open grapevine information system
auteur
Anne-Françoise Adam-Blondon, Michael Alaux, Cyril Pommier, D Cantu, Z-M Cheng, Gr Cramer, C Davies, Serge Delrot, L Deluc, G Di Gaspero, J Grimplet, A Fennell, Jp Londo, P Kersey, F Mattivi, S Naithani, Pascal Neveu, M Nikolski, M Pezzotti, Bi Reisch, R Töpfer, Ma Vivier, D Ware, Hadi Quesneville
article
Horticulture research, 2016, 3, pp.16056. ⟨10.1038/hortres.2016.56⟩
resume
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the framework of the International Grapevine Genome Program (www.vitaceae.org), to construct a coordinated federation of information systems holding grapevine data distributed around the world, providing an integrated set of interfaces supporting advanced data modeling, rich semantic integration and the next generation of data mining tools. To achieve this goal, it will be critical to develop, implement and adopt appropriate standards for data annotation and formatting. The development of this system, the GrapeIS, linking genotypes to phenotypes, and scientific research to agronomical and oeneological data, should provide new insights into grape biology, and allow the development of new varieties to meet the challenges of biotic and abiotic stress, environmental change, and consumer demand.
DOI
DOI : 10.1038/hortres.2016.56
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https://hal.science/hal-01404714/file/hortres201656_%7B73DC1FD1-E6BB-473F-9061-7F1125790324%7D.pdf BibTex
titre
Reconciling the evolutionary origin of bread wheat (Triticum aestivum)
auteur
Moaine El Baidouri, Florent Murat, Maeva Veyssière, Mélanie Molinier, Raphaël-Gauthier Flores, Laura Burlot, Michael Alaux, Hadi Quesneville, Caroline Pont, Jerome Salse
article
New Phytologist, 2016, 213 (3), ⟨10.1111/nph.14113⟩
resume
The origin of bread wheat (Triticum aestivum; AABBDD) has been a subject of controversy and of intense debate in the scientific community over the last few decades. In 2015, three articles published in New Phytologist discussed the origin of hexaploid bread wheat (AABBDD) from the diploid progenitors Triticum urartu (AA), a relative of Aegilops speltoides (BB) and Triticum tauschii (DD). Access to new genomic resources since 2013 has offered the opportunity to gain novel insights into the paleohistory of modern bread wheat, allowing characterization of its origin from its diploid progenitors at unprecedented resolution. We propose a reconciled evolutionary scenario for the modern bread wheat genome based on the complementary investigation of transposable element and mutation dynamics between diploid, tetraploid and hexaploid wheat. In this scenario, the structural asymmetry observed between the A, B and D subgenomes in hexaploid bread wheat derives from the cumulative effect of diploid progenitor divergence, the hybrid origin of the D subgenome, and subgenome partitioning following the polyploidization events.
DOI
DOI : 10.1111/nph.14113
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titre
Measures for interoperability of phenotypic data: minimum information requirements and formatting
auteur
Thomas Altmann, Daniel Arend, Elizabeth Arnaud, Dijun Chen, Guillaume Cornut, Fabio Fiorani, Wojciech Frohmberg, Astrid Junker, Christian Klukas, Matthias Lange, Cezary Mazurek, Anahita Nafissi, Pascal Neveu, Jan van Oeveren, Cyril Pommier, Hendrik Poorter, Philippe Rocca-Serra, Susanna-Assunta Sansone, Uwe Scholz, Marco van Schriek, Björn Usadel, Stephan Weise, Paul Kersey, Paweł Krajewski
article
Plant Methods, 2016, 12, pp.1-18. ⟨10.1186/s13007-016-0144-4⟩
resume
BACKGROUND: Plant phenotypic data shrouds a wealth of information which, when accurately analysed and linked to other data types, brings to light the knowledge about the mechanisms of life. As phenotyping is a field of research comprising manifold, diverse and time-consuming experiments, the findings can be fostered by reusing and combining existing datasets. Their correct interpretation, and thus replicability, comparability and interoperability, is possible provided that the collected observations are equipped with an adequate set of metadata. So far there have been no common standards governing phenotypic data description, which hampered data exchange and reuse. RESULTS: In this paper we propose the guidelines for proper handling of the information about plant phenotyping experiments, in terms of both the recommended content of the description and its formatting. We provide a document called "Minimum Information About a Plant Phenotyping Experiment", which specifies what information about each experiment should be given, and a Phenotyping Configuration for the ISA-Tab format, which allows to practically organise this information within a dataset. We provide examples of ISA-Tab-formatted phenotypic data, and a general description of a few systems where the recommendations have been implemented. CONCLUSIONS: Acceptance of the rules described in this paper by the plant phenotyping community will help to achieve findable, accessible, interoperable and reusable data.
DOI
DOI : 10.1186/s13007-016-0144-4
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https://hal.inrae.fr/hal-02640958/file/Publis16-mistea-014_cwiek-measures_1.pdf BibTex
titre
The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes
auteur
Anne M. Molitor, David Latrasse, Matthias Zytnicki, Philippe P. Andrey, Nicole Houba Hérin, Mélanie Hachet, Christophe Battail, Stefania del Prete, Adriana A. Alberti, Hadi Quesneville, Valérie Gaudin
article
The Plant cell, 2016, 28 (9), ⟨10.1105/tpc.16.00244⟩
resume
LHP1-INTERACTING FACTOR2 (LIF2), a heterogeneous nuclear ribonucleoprotein involved in Arabidopsis thaliana cell fate and stress responses, interacts with LIKE HETEROCHROMATIN PROTEIN1 (LHP1), a Polycomb Repressive Complex1 (PRC1) subunit. To investigate LIF2-LHP1 functional interplay, we mapped their genome-wide distributions in wild-type, lif2, and lhp1 backgrounds, under standard and stress conditions. Interestingly, LHP1-targeted regions form local clusters, suggesting an underlying functional organization of the plant genome. Regions targeted by both LIF2 and LHP1 were enriched in stress-responsive genes, the H2A.Z histone variant, and antagonistic histone marks. We identified specific motifs within the targeted regions, including a G-box-like motif, a GAGA motif, and a telo-box. LIF2 and LHP1 can operate both antagonistically and synergistically. In response to methyl jasmonate treatment, LIF2 was rapidly recruited to chromatin, where it mediated transcriptional gene activation. Thus, LIF2 and LHP1 participate in transcriptional switches in stress-response pathways.
DOI
DOI : 10.1105/tpc.16.00244
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https://hal.inrae.fr/hal-02633928/file/2016_Molitor_Plant%20Cell_1.pdf BibTex
titre
Study of gene trafficking between Acanthamoeba and giant viruses suggests an undiscovered family of Amoeba-infecting viruses
auteur
Florian Maumus, Guillaume Blanc
article
Genome Biology and Evolution, 2016, 8 (11), pp.3351-3363. ⟨10.1093/gbe/evw260⟩
resume
The nucleocytoplasmic large DNA viruses (NCLDV) are a group of extremely complex double-stranded DNA viruses, which are major parasites of a variety of eukaryotes. Recent studies showed that certain unicellular eukaryotes contain fragments of NCLDV DNA integrated in their genome, when surprisingly many of these organisms were not previously shown to be infected by NCLDVs. These findings prompted us to search the genome of Acanthamoeba castellanii strain Neff (Neff), one of the most prolific hosts in the discovery of giant NCLDVs, for possible DNA inserts of viral origin. We report the identification of 267 markers of lateral gene transfer with viruses, approximately half of which are clustered in Neff genome regions of viral origins, transcriptionally inactive or exhibit nucleotide-composition signatures suggestive of a foreign origin. The integrated viral genes had diverse origin among relatives of viruses that infect Neff, including Mollivirus, Pandoravirus, Marseillevirus, Pithovirus, and Mimivirus However, phylogenetic analysis suggests the existence of a yet-undiscovered family of amoeba-infecting NCLDV in addition to the five already characterized. The active transcription of some apparently anciently integrated virus-like genes suggests that some viral genes might have been domesticated during the amoeba evolution. These insights confirm that genomic insertion of NCLDV DNA is a common theme in eukaryotes. This gene flow contributed fertilizing the eukaryotic gene repertoire and participated in the occurrence of orphan genes, a long standing issue in genomics. Search for viral inserts in eukaryotic genomes followed by environmental screening of the original viruses should be used to isolate radically new NCLDVs.
DOI
DOI : 10.1093/gbe/evw260
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https://hal.science/hal-01604735/file/2016_Maumus_Genome%20Biology%20and%20Evolution_1.pdf BibTex
titre
Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening
auteur
Ophélie Jouffroy, Surya Saha, Lukas Mueller, Hadi Quesneville, Florian Maumus
article
BMC Genomics, 2016, 17 (1), pp.1-15. ⟨10.1186/s12864-016-2980-z⟩
resume
Background: Plant genomes are populated by different types of repetitive elements including transposable elements (TEs) and simple sequence repeats (SSRs) that can have a strong impact on genome size and dynamic as well as on the regulation of gene transcription. At least two-thirds of the tomato genome is composed of repeats. While their bulk impact on genome organization has been recently revealed by whole genome assembly, their influence on tomato biology and phenotype remains largely unaddressed. More specifically, the effects and roles of DNA repeats on the maturation of fleshy fruits, which is a complex process of key agro-economic interest, still needs to be investigated comprehensively and tomato is arguably an excellent model for such study. Results: We have performed a comprehensive annotation of the tomato repeatome to explore its potential impact on tomato genome composition and gene transcription. Our results show that the tomato genome can be fractioned into three compartments with different gene and repeat density, each compartment presenting contrasting repeat and gene composition, repeat-gene associations and different gene transcriptional levels. In the context of fruit ripening, we found that repeats are present in the majority of differentially methylated regions (DMRs) and thousands of repeat-associated DMRs are found in gene proximity including hundreds that are differentially regulated. Furthermore, we found that repeats are also present in the proximity of binding sites of the key ripening protein RIN. We also observed that some repeat families are present at unexpected high frequency in the proximity of genes that are differentially expressed during tomato ripening. Conclusion: Altogether, our study emphasizes the fractionation as defined by repeat content in the tomato genome and enables to further characterize the specificities of each genomic compartment. Additionally, our results present strong associations between differentially regulated genes, differentially methylated regions and repeats, suggesting a potential adaptive function of repeats in tomato ripening. Our work therefore provides significant perspectives for the understanding of the impact of repeats on the maturation of fleshy fruits.
DOI
DOI : 10.1186/s12864-016-2980-z
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https://hal.inrae.fr/hal-02631886/file/2016_%20Jouffroy_BMC%20Genomics_1.pdf BibTex
titre
Erratum to :"Understanding Brassicaceae evolution through ancestral genome reconstruction" (vol 16, 262, 2015)
auteur
Florent Murat, Alexandra Louis, Florian Maumus, Alix Armero, Richard Cooke, Hadi Quesneville, Hugues Roest Crollius, Jerome J. Salse
article
Genome Biology, 2016, 17 (64), ⟨10.1186/s13059-016-0887-2⟩
DOI
DOI : 10.1186/s13059-016-0887-2
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https://hal.inrae.fr/hal-02630062/file/2016_Murat_Genome%20Biology_1.pdf BibTex
titre
Giant viruses at the core of microscopic wars with global impacts
auteur
Adrien Villain, Lucie Gallot-Lavallee, Guillaume Blanc, Florian Maumus
article
Current Opinion in Virology, 2016, 17, pp.130-137. ⟨10.1016/j.coviro.2016.03.007⟩
resume
The unicellular eukaryotes (also called protists) that inhabit the contemporary oceans have large impacts on major biogeochemical cycles. Populations of oceanic protists are to a large extent regulated by their viral parasites, especially nucleocytoplasmic large DNA viruses (NCLDVs). NCLDVs can themselves be the prey of smaller viruses called virophages and can also be infected by transposable elements termed transpovirons. These entangled parasitisms have fostered the emergence of sophisticated infection and defence strategies. In addition persistent contact has facilitated the exchange of genes between different parties. Recent advances shed light on the strategies that govern such microbial wars. Endogenous virophage-like elements found in the genome of a marine alga could for instance provide the host acquired immunity against NCLDVs. In return, it was recently speculated that virophage sequences can be hijacked by NCLDVs and used as genetic weapons against virophages.
DOI
DOI : 10.1016/j.coviro.2016.03.007
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titre
Impact and insights from ancient repetitive elements in plant genomes
auteur
Florian Maumus, Hadi Quesneville
article
Current Opinion in Plant Biology, 2016, 30, pp.41-46. ⟨10.1016/j.pbi.2016.01.003⟩
DOI
DOI : 10.1016/j.pbi.2016.01.003
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2015

Journal articles

titre
Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses
auteur
Nahid Shamandi, Matthias Zytnicki, Cyril Charbonnel, Emilie Elvira-Matelot, Aurore Bochnakian, Pascale Comella, Allison Mallory, Gersende Lepère, Julio Sáez-Vasquez, Herve H. Vaucheret, Robert Martienssen
article
PLoS Biology, 2015, 13 (12), pp.e1002326. ⟨10.1371/journal.pbio.1002326⟩
resume
Small RNAs play essential regulatory roles in genome stability, development, and responses to biotic and abiotic stresses in most eukaryotes. In plants, the RNaseIII enzyme DICER-LIKE1 (DCL1) produces miRNAs, whereas DCL2, DCL3, and DCL4 produce various size classes of siRNAs. Plants also encode RNASE THREE-LIKE (RTL) enzymes that lack DCL-specific domains and whose function is largely unknown. We found that virus infection induces RTL1 expression, suggesting that this enzyme could play a role in plant-virus interaction. To first investigate the biochemical activity of RTL1 independent of virus infection, small RNAs were sequenced from transgenic plants constitutively expressing RTL1. These plants lacked almost all DCL2-, DCL3-, and DCL4-dependent small RNAs, indicating that RTL1 is a general suppressor of plant siRNA pathways. In vivo and in vitro assays revealed that RTL1 prevents siRNA production by cleaving dsRNA prior to DCL2-, DCL3-, and DCL4-processing. The substrate of RTL1 cleavage is likely long-perfect (or near-perfect) dsRNA, consistent with the RTL1-insensitivity of miRNAs, which derive from DCL1-processing of short-imperfect dsRNA. Virus infection induces RTL1 mRNA accumulation, but viral proteins that suppress RNA silencing inhibit RTL1 activity, suggesting that RTL1 has evolved as an inducible antiviral defense that could target dsRNA intermediates of viral replication, but that a broad range of viruses counteract RTL1 using the same protein toolbox used to inhibit antiviral RNA silencing. Together, these results reveal yet another level of complexity in the evolutionary battle between viruses and plant defenses.
DOI
DOI : 10.1371/journal.pbio.1002326
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https://hal.science/hal-02116033/file/2015_Shamandi_Plos%20Biology_1.pdf BibTex
titre
A new approach for annotation of transposable elements using small RNA mapping.
auteur
Moaine El Baidouri, Kyung Do Kim, Brian Abernathy, Siwaret Arikit, Florian Maumus, Blake C Meyers, Scott A Jackson, Olivier Panaud
article
Nucleic Acids Research, 2015, 43 (13), pp.e84. ⟨10.1093/nar/gkv257⟩
resume
Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants.Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/.
DOI
DOI : 10.1093/nar/gkv257
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https://hal.science/hal-01215276/file/2015_El%20Baidouri_Nucleic%20Acids%20Research_1.pdf BibTex
titre
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
auteur
Guillaume Morel, Lieven Sterck, Dominique Swennen, Marina Marcet-Houben, Djamila Onesime, Anthony Levasseur, Noémie Jacques, Sandrine Mallet, Arnaud Couloux, Karine Labadie, Joelle Amselem, Jean-Marie Beckerich, Bernard Henrissat, Yves van de Peer, Patrick Wincker, Jean-Luc Souciet, Toni Gabaldón, Colin R. Tinsley, Serge Casaregola
article
Scientific Reports, 2015, 5, ⟨10.1038/srep11571⟩
resume
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi– yeasts split concomitant with the yeasts' genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts, and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
DOI
DOI : 10.1038/srep11571
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https://amu.hal.science/hal-01201920/file/srep11571.pdf BibTex
titre
Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.
auteur
Christophe Plomion, Jean-Marc Aury, Joëlle Amselem, Tina Alaeitabar, Valérie Barbe, Caroline Belser, Hélène Bergès, Catherine Bodénès, Nathalie Boudet, Christophe Boury, Aurélie Canaguier, Arnaud Couloux, Corinne da Silva, Sébastien Duplessis, François Ehrenmann, Barbara Estrada-Mairey, Stéphanie Fouteau, Nicolas Francillonne, Christine Gaspin, Cécile Guichard, Christophe C. Klopp, Karine Labadie, Céline Lalanne, Isabelle Le Clainche, Jean-Charles Leplé, Grégoire Le Provost, Thibault Leroy, Isabelle Lesur, Francis Martin, Jonathan Mercier, Célia Michotey, Florent Murat, Franck Salin, Delphine Steinbach, Patricia Faivre-Rampant, Patrick Wincker, Jérôme Salse, Hadi Quesneville, Antoine Kremer
article
Molecular Ecology Resources, 2015, 16 (1), pp.254-265. ⟨10.1111/1755-0998.12425⟩
resume
The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
DOI
DOI : 10.1111/1755-0998.12425
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titre
Deciphering genome content and evolutionary relationships of isolates from the fungus Magnaporthe oryzae attacking different host plants
auteur
Helene Chiapello, Ludovic Mallet, Cyprien Guerin, Gabriela Aguileta, Joelle J. Amselem, Thomas Kroj, Enrique Ortega-Abboud, Marc-Henri Lebrun, Bernard Henrissat, Annie Gendrault, François Rodolphe, Didier Tharreau, Elisabeth Fournier
article
Genome Biology and Evolution, 2015, 7 (10), pp.2896-2912. ⟨10.1093/gbe/evv187⟩
resume
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes [39-43 Mb] and gene content [12,283-14,781 genes] between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the 9 M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but reticulate inside the rice lineage. We detected traces of introgression from a non-rice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in non-rice lineages, whereas the rice lineage possessed 86 specific families absent from the non-rice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).
DOI
DOI : 10.1093/gbe/evv187
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https://hal.science/hal-01222884/file/2015_Chiapello_GBE_%7B20D019B5-2493-4780-978D-E9A1135F8A9E%7D.pdf BibTex
titre
A social–ecological approach to managing multiple agro-ecosystem services
auteur
Francoise Lescourret, Daniele Magda, Guy Richard, Anne-Francoise Adam-Blondon, Jacques Baudry, Marion Bardy, Isabelle Doussan, Bertrand Dumont, Francois Lefèvre, Isabelle Litrico, Roger Martin-Clouaire, Bernard Montuelle, Sylvain Pellerin, Manuel Plantegenest, Elise Tancoigne, Alban Thomas, Herve Guyomard, Jean-François Soussana
article
Current Opinion in Environmental Sustainability, 2015, 14, pp.68-75. ⟨10.1016/j.cosust.2015.04.001⟩
resume
The sustainability of agro-ecosystems depends on their ability to deliver an entire package of multiple ecosystem services, rather than provisioning services alone. New social and ecological dimensions of agricultural management must be explored in agricultural landscapes, to foster this ability. We propose a social–ecological framework for the service-based management of agro-ecosystems, specified through an explicit and symmetric representation of the ecosystem and the social system, and the dynamic links between them. It highlights how management practices, with their multiple effects, could drive the provision of multiple services. Based on this framework, we have identified the design of collective multiservice management as a key research issue. It requires innovations in stakeholder organizations and tools to foster synergy between ecosystem functioning and social dynamics, given the complexity and uncertainties of ecological systems.
DOI
DOI : 10.1016/j.cosust.2015.04.001
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https://hal.science/hal-01594893/file/Lescourret_etal2015_%7BA00782EA-17CB-461B-8B5F-DC6E9ACC9B7B%7D.pdf BibTex
titre
Impact of transposable elements on insect genomes and biology
auteur
Florian Maumus, Anna-Sophie Fiston-Lavier, Hadi Quesneville
article
Current Opinion in Insect Science, 2015, 7, pp.30-36. ⟨10.1016/j.cois.2015.01.001⟩
DOI
DOI : 10.1016/j.cois.2015.01.001
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titre
The BioMart community portal: an innovative alternative to large, centralized data repositories
auteur
Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah Burge, Cédric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Genova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David Goodstein, Kristian Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dong-Jin Han, Byung Woo Han, Todd Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah A. Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe C. Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Lió, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jérôme J. Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, François Moreews, Ibounyamine Nabihoudine, Nelson Ndegwa, Celine Noirot, Cristian Perez-Llamas, Alessandro Quattrone, Michael Primig, Davide Rambaldi, Olivier Sallou, James Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Hadi Quesneville, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk
article
Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩
resume
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
DOI
DOI : 10.1093/nar/gkv350
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https://univ-rennes.hal.science/hal-01146849/file/THe%20BioMart%20community%20portal%20an%20innovative%20alternative%20to%20large%2C%20centralized%20data%20repositories_CK-JM_1.pdf BibTex
titre
Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes
auteur
Jean Sebastien Parent, Vincent V. Jauvion, Nicolas N. Bouche, Christophe Beclin, Mélanie Hachet, Matthias Zytnicki, Herve H. Vaucheret
article
Nucleic Acids Research, 2015, 43 (17), pp.8464-8475. ⟨10.1093/nar/gkv753⟩
resume
Although post-transcriptional gene silencing (PTGS) has been studied for more than a decade, there is still a gap in our understanding of how de novo silencing is initiated against genetic elements that are not supposed to produce double-stranded (ds)RNA. Given the pervasive transcription occurring throughout eukaryote genomes, we tested the hypothesis that unintended transcription could produce antisense (as)RNA molecules that participate to the initiation of PTGS triggered by sense transgenes (S-PTGS). Our results reveal a higher level of asRNA in Arabidopsis thaliana lines that spontaneously trigger S-PTGS than in lines that do not. However, PTGS triggered by antisense transgenes (AS-PTGS) differs from S-PTGS. In particular, a hypomorphic ago1 mutation that suppresses S-PTGS prevents the degradation of asRNA but not sense RNA during AS-PTGS, suggesting a different treatment of coding and non-coding RNA by AGO1, likely because of AGO1 association to polysomes. Moreover, the intended asRNA produced during AS-PTGS is capped whereas the asRNA produced during S-PTGS derives from 3' maturation of a read-through transcript and is uncapped. Thus, we propose that uncapped asRNA corresponds to the aberrant RNA molecule that is converted to dsRNA by RNA-DEPENDENT RNA POLYMERASE 6 in siRNA-bodies to initiate S-PTGS, whereas capped asRNA must anneal with sense RNA to produce dsRNA that initiate AS-PTGS.
DOI
DOI : 10.1093/nar/gkv753
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https://hal.inrae.fr/hal-02630366/file/2015_Parent_Nucleic%20Acids%20Research_1.pdf BibTex
titre
Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation
auteur
Eva-Maria Willing, Vimal Rawat, Terezie Mandáková, Florian Maumus, Geo Velikkakam James, Karl J.V. Nordström, Claude Becker, Norman Warthmann, Claudia Chica, Bogna Szarzynska, Matthias Zytnicki, Maria C. Albani, Christiane Kiefer, Sara Bergonzi, Loren Castaings, Julieta L. Mateos, Markus C. Berns, Nora Bujdoso, Thomas Piofczyk, Laura de Lorenzo, Cristina Barrero-Sicilia, Isabel Mateos, Mathieu Piednoël, Jörg Hagmann, Romy Chen-Min-Tao, Raquel Iglesias-Fernández, Stephan C. Schuster, Carlos Alonso-Blanco, François Roudier, Pilar Carbonero, Javier Paz-Ares, Seth J. Davis, Ales Pecinka, Hadi Quesneville, Vincent Colot, Martin A. Lysak, Detlef Weigel, George Coupland, Korbinian Schneeberger
article
Nature Plants, 2015, 1 (2), pp.14023-14028. ⟨10.1038/nplants.2014.23⟩
resume
Despite evolutionary conserved mechanisms to silence transposable element activity, there are drastic differences in the abundance of transposable elements even among closely related plant species. We conducted a de novo assembly for the 375 Mb genome of the perennial model plant, Arabis alpina. Analysing this genome revealed long-lasting and recent transposable element activity predominately driven by Gypsy long terminal repeat retrotransposons, which extended the lowrecombining pericentromeres and transformed large formerly euchromatic regions into repeat-rich pericentromeric regions. This reduced capacity for long terminal repeat retrotransposon silencing and removal in A. alpina co-occurs with unexpectedly low levels of DNA methylation. Most remarkably, the striking reduction of symmetrical CG and CHG methylation suggests weakened DNA methylation maintenance in A. alpina compared with Arabidopsis thaliana. Phylogenetic analyses indicate a highly dynamic evolution of some components of methylation maintenance machinery that might be related to the unique methylation in A. alpina.
DOI
DOI : 10.1038/nplants.2014.23
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titre
The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release
auteur
Isabelle Lesur, Grégoire G. Le Provost, Pascal Bento, Corinne da Silva, Jean-Charles Leplé, Florent Murat, Saneyoshi S. Ueno, Jérôme Bartholome, Céline Lalanne, François Ehrenmann, Celine Noirot, Christian Burban, Valérie Léger, Joelle J. Amselem, Caroline Belser, Hadi Quesneville, Michael Stierschneider, Silvia Fluch, Lasse Feldhahn, Mika Tarkka, Sylvie Herrmann, Francois Buscot, Christophe C. Klopp, Antoine Kremer, Jérôme Salse, Jean-Marc Aury, Christophe Plomion
article
BMC Genomics, 2015, 16 (1), pp.112. ⟨10.1186/s12864-015-1331-9⟩
resume
Background Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. Results The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. Conclusion In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
DOI
DOI : 10.1186/s12864-015-1331-9
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https://hal.science/hal-02285504/file/s12864-015-1331-9_1.pdf BibTex
titre
Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses
auteur
Guillaume Blanc, Lucie Gallot-Lavallee, Florian Maumus
article
Proceedings of the National Academy of Sciences of the United States of America, 2015, 112 (38), pp.E5318-E5326. ⟨10.1073/pnas.1506469112⟩
resume
Virophages are recently discovered double-stranded DNA virus satellites that prey on giant viruses (nucleocytoplasmic large DNA viruses; NCLDVs), which are themselves parasites of unicellular eukaryotes. This coupled parasitism can result in the indirect control of eukaryotic cell mortality by virophages. However, the details of such tripartite relationships remain largely unexplored. We have discovered similar to 300 predicted genes of putative virophage origin in the nuclear genome of the unicellular alga Bigelowiella natans. Physical clustering of these genes indicates that virophage genomes are integrated into the B. natans genome. Virophage inserts show high levels of similarity and synteny between each other, indicating that they are closely related. Virophage genes are transcribed not only in the sequenced B. natans strain but also in other Bigelowiella isolates, suggesting that transcriptionally active virophage inserts are widespread in Bigelowiella populations. Evidence that B. natans is also a host to NCLDV members is provided by the identification of NCLDV inserts in its genome. These putative large DNA viruses may be infected by B. natans virophages. We also identify four repeated elements sharing structural and genetic similarities with transpovirons-a class of mobile elements first discovered in giant viruses-that were probably independently inserted in the B. natans genome. We argue that endogenized provirophages may be beneficial to both the virophage and B. natans by (i) increasing the chances for the virophage to coinfect the host cell with an NCLDV prey and (ii) defending the host cell against fatal NCLDV infections.
DOI
DOI : 10.1073/pnas.1506469112
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https://hal.inrae.fr/hal-02639645/file/2015_Blanc_PNAS_1.pdf BibTex
titre
Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon
auteur
Joelle J. Amselem, Marielle Vigouroux, Simone Oberhaensli, James K M Brown, Laurence V Bindschedler, Pari Skamnioti, Thomas Wicker, Pietro D Spanu, Hadi Quesneville, Soledad Sacristán
article
BMC Genomics, 2015, 16 (1), pp.917. ⟨10.1186/s12864-015-2185-x⟩
resume
BACKGROUND: The Avrk1 and Avra10 avirulence (AVR) genes encode effectors that increase the pathogenicity of the fungus Blumeria graminis f.sp. hordei (Bgh), the powdery mildew pathogen, in susceptible barley plants. In resistant barley, MLK1 and MLA10 resistance proteins recognize the presence of AVRK1 and AVRA10, eliciting the hypersensitive response typical of gene for gene interactions. Avrk1 and Avra10 have more than 1350 homologues in Bgh genome, forming the EKA (Effectors homologous to Avr k 1 and Avr a 10) gene family. RESULTS: We tested the hypothesis that the EKA family originated from degenerate copies of Class I LINE retrotransposons by analysing the EKA family in the genome of Bgh isolate DH14 with bioinformatic tools specially developed for the analysis of Transposable Elements (TE) in genomes. The Class I LINE retrotransposon copies homologous to Avrk1 and Avra10 represent 6.5% of the Bgh annotated genome and, among them, we identified 293 AVR/effector candidate genes. We also experimentally identified peptides that indicated the translation of several predicted proteins from EKA family members, which had higher relative abundance in haustoria than in hyphae. CONCLUSIONS: Our analyses indicate that Avrk1 and Avra10 have evolved from part of the ORF1 gene of Class I LINE retrotransposons. The co-option of Avra10 and Avrk1 as effectors from truncated copies of retrotransposons explains the huge number of homologues in Bgh genome that could act as dynamic reservoirs from which new effector genes may evolve. These data provide further evidence for recruitment of retrotransposons in the evolution of new biological functions.
DOI
DOI : 10.1186/s12864-015-2185-x
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https://hal.science/hal-01264935/file/2015_Amselem_BMC%20Genomic_%7B349C9477-B0C0-4015-80F6-916C99F2AC70%7D.pdf BibTex
titre
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus
auteur
Michael H Perlin, Joelle J. Amselem, Eric Fontanillas, Su San Toh, Zehua Chen, Jonathan Goldberg, Sébastien Duplessis, Bernard Henrissat, Sarah Young, Qiandong Zeng, Gabriela Aguileta, Elsa Petit, Helene Badouin, Jared Andrews, Dominique Razeeq, Toni Gabaldón, Hadi Quesneville, Tatiana Giraud, Michael E Hood, David J Schultz, Christina A Cuomo
article
BMC Genomics, 2015, 16 (461), ⟨10.1186/s12864-015-1660-8⟩
resume
Abstract Background: The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development. Results: We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14 % of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions. Conclusions: The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.
DOI
DOI : 10.1186/s12864-015-1660-8
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https://hal.science/hal-01186421/file/2015_BMC%20Genomics_Perlin_%7B398BC7AB-CBD3-4ED6-B5C4-BBC99384EA11%7D.pdf BibTex
titre
Towards recommendations for metadata and data handling in plant phenotyping
auteur
Pawel Krajewski, Dijun Chen, Hanna Cwiek, Aalt D. J. van Dijk, Fabio Fiorani, Paul Kersey, Christian Klukas, Matthias Lange, Augustyn Markiewicz, Jan Peter Nap, Jan van Oeveren, Cyril Pommier, Uwe Scholz, Marco van Schriek, Björn Usadel, Stephan Weise
article
Journal of Experimental Botany, 2015, 66 (18), pp.5417-5427. ⟨10.1093/jxb/erv271⟩
resume
Recent methodological developments in plant phenotyping, as well as the growing importance of its applications in plant science and breeding, are resulting in a fast accumulation of multidimensional data. There is great potential for expediting both discovery and application if these data are made publicly available for analysis. However, collection and storage of phenotypic observations is not yet sufficiently governed by standards that would ensure interoperability among data providers and precisely link specific phenotypes and associated genomic sequence information. This lack of standards is mainly a result of a large variability of phenotyping protocols, the multitude of phenotypic traits that are measured, and the dependence of these traits on the environment. This paper discusses the current situation of standardization in the area of phenomics, points out the problems and shortages, and presents the areas that would benefit from improvement in this field. In addition, the foundations of the work that could revise the situation are proposed, and practical solutions developed by the authors are introduced.
DOI
DOI : 10.1093/jxb/erv271
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titre
Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes
auteur
Joelle J. Amselem, Marc-Henri Lebrun, Hadi Quesneville
article
BMC Genomics, 2015, 16 (1), pp.141. ⟨10.1186/s12864-015-1347-1⟩
resume
We identified fungal genomes containing large numbers of TEs with many C to T mutations associated with species-specific dinucleotide signatures. This bias suggests that a basic defense mechanism against TE invasion similar to RIP is widespread in fungi, although the efficiency and specificity of this mechanism differs between species. Our analysis revealed that dinucleotide signatures are associated with the presence/absence of specific Dnmt1 subfamilies. In particular, an RID1-dependent RIP mechanism was found only in Ascomycota.
DOI
DOI : 10.1186/s12864-015-1347-1
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https://hal.science/hal-01142763/file/s12864-015-1347-1_%7B33366C96-F519-435C-847C-04DE73C5B5A8%7D.pdf BibTex
titre
High-throughput physical map anchoring via BAC-pool sequencing
auteur
Katerina Cvikova, Federica Cattonaro, Michael M. Alaux, Nils Stein, Klaus F. X. Mayer, Jaroslav Dolezel, Jan Bartos
article
BMC Plant Biology, 2015, 15, ⟨10.1186/s12870-015-0429-1⟩
resume
Background: Physical maps created from large insert DNA libraries, typically cloned in BAC vector, are valuable resources for map-based cloning and de novo genome sequencing. The maps are most useful if contigs of overlapping DNA clones are anchored to chromosome(s), and ordered along them using molecular markers. Here we present a novel approach for anchoring physical maps, based on sequencing three-dimensional pools of BAC clones from minimum tilling path. Results: We used physical map of wheat chromosome arm 3DS to validate the method with two different DNA sequence datasets. The first comprised 567 genes ordered along the chromosome arm based on syntenic relationship of wheat with the sequenced genomes of Brachypodium, rice and sorghum. The second dataset consisted of 7,136 SNP-containing sequences, which were mapped genetically in Aegilops tauschii, the donor of the wheat D genome. Mapping of sequence reads from individual BAC pools to the first and the second datasets enabled unambiguous anchoring 447 and 311 3DS-specific sequences, respectively, or 758 in total. Conclusions: We demonstrate the utility of the novel approach for BAC contig anchoring based on mass parallel sequencing of three-dimensional pools prepared from minimum tilling path of physical map. The existing genetic markers as well as any other DNA sequence could be mapped to BAC clones in a single in silico experiment. The approach reduces significantly the cost and time needed for anchoring and is applicable to any genomic project involving the construction of anchored physical map.
DOI
DOI : 10.1186/s12870-015-0429-1
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https://hal.inrae.fr/hal-02630859/file/2015_Cvikova_BMC%20Plant%20Biology_1.pdf BibTex
titre
Understanding Brassicaceae evolution through ancestral genome reconstruction
auteur
Florent Murat, Alexandra Louis, Florian Maumus, Alix Armero Villanueva, Richard Cooke, Hadi Quesneville, Hugues Roest Crollius, Jerome Salse
article
Genome Biology, 2015, 16 (262), ⟨10.1186/s13059-015-0814-y⟩
resume
Brassicaceae is a family of green plants of high scientific and economic interest, including thale cress (Arabidopsis thaliana), cruciferous vegetables (cabbages) and rapeseed.We reconstruct an evolutionary framework of Brassicaceae composed of high-resolution ancestral karyotypes using the genomes of modern A. thaliana, Arabidopsis lyrata, Capsella rubella, Brassica rapa and Thellungiella parvula. The ancestral Brassicaceae karyotype (Brassicaceae lineages I and II) is composed of eight protochromosomes and 20,037 ordered and oriented protogenes. After speciation, it evolved into the ancestral Camelineae karyotype (eight protochromosomes and 22,085 ordered protogenes) and the proto-Calepineae karyotype (seven protochromosomes and 21,035 ordered protogenes) genomes.The three inferred ancestral karyotype genomes are shown here to be powerful tools to unravel the reticulated evolutionary history of extant Brassicaceae genomes regarding the fate of ancestral genes and genomic compartments, particularly centromeres and evolutionary breakpoints. This new resource should accelerate research in comparative genomics and translational research by facilitating the transfer of genomic information from model systems to species of agronomic interest.
DOI
DOI : 10.1186/s13059-015-0814-y
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https://hal.science/hal-01281832/file/2015_Murat_Genome%20Biology_%7BE3266011-5AC6-478A-AA7E-C7C054BE6E66%7D.pdf BibTex
titre
Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts
auteur
Guillaume Morel, Lieven Sterck, Dominique Swennen, Marina Marcet-Houben, Djamila Onesime, Anthony Levasseur, Noémie Jacques, Sandrine Mallet, Arnaux Couloux, Karine Labadie, Joëlle Amselem, Jean-Marie Beckerich, Bernard Henrissat, Yves van de Peer, Patrick Wincker, Jean-Luc Souciet, Toni Gabaldón, Colin R. Tinsley, Serge Casaregola
article
Scientific Reports, 2015, 5 (1), pp.11571. ⟨10.1038/srep11571⟩
resume
The evolutionary history of the characters underlying the adaptation of microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics to investigate evolutionary relationships of the dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion of genes showed discordant phylogenies, clustering with the filamentous fungus subphylum (Pezizomycotina), rather than the yeast subphylum (Saccharomycotina), of the Ascomycota. These genes appear not to be the result of Horizontal Gene Transfer (HGT), but to have been specifically retained by G. candidum after the filamentous fungi–yeasts split concomitant with the yeasts’ genome contraction. We refer to these genes as SRAGs (Specifically Retained Ancestral Genes), having been lost by all or nearly all other yeasts and thus contributing to the phenotypic specificity of lineages. SRAG functions include lipases consistent with a role in cheese making and novel endoglucanases associated with degradation of plant material. Similar gene retention was observed in three other distantly related yeasts representative of this ecologically diverse subphylum. The phenomenon thus appears to be widespread in the Saccharomycotina and argues that, alongside neo-functionalization following gene duplication and HGT, specific gene retention must be recognized as an important mechanism for generation of biodiversity and adaptation in yeasts.
DOI
DOI : 10.1038/srep11571
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https://agroparistech.hal.science/hal-03665128/file/Morel2015.pdf BibTex
titre
Karyotype and Gene Order Evolution from ReconstructedExtinct Ancestors Highlight Contrasts in Genome Plasticity ofModern Rosid Crops
auteur
Florent Murat, Rongzhi R. Zhang, Sébastien Guizard, Haris Gavranovic, Raphael Flores, Delphine Steinbach, Hadi Quesneville, Eric Tannier, Jérôme Salse
article
Genome Biology and Evolution, 2015, 7 (3), pp.735-749. ⟨10.1093/gbe/evv014⟩
resume
We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, “DicotSyntenyViewer” (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids.
DOI
DOI : 10.1093/gbe/evv014
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https://hal.science/hal-01133906/file/2015_Murat_Genome%20Biology%20and%20Evolution_1.pdf BibTex

2014

Journal articles

titre
The coffee genome provides insight into the convergent evolution of caffeine biosynthesis
auteur
France Denoeud, Lorenzo Carretero-Paulet, Alexis Dereeper, Gaëtan Droc, Romain Guyot, Marco Pietrella, Chunfang Zheng, Adriana A. Alberti, François Anthony, Giuseppe Aprea, Jean-Marc Aury, Pascal Bento, Maria Bernard, Stephanie Bocs, Claudine Campa, Alberto Cenci, Marie-Christine Combes, Dominique Crouzillat, Corinne da Silva, Loretta Daddiego, Fabien de Bellis, Stéphane Dussert, Olivier Garsmeur, Thomas Gayraud, Valentin Guignon, Katharina Jahn, Véronique Jamilloux, Thierry Joet, Karine Labadie, Tianying Lan, Julie Leclercq, Maud Lepelley, Thierry Leroy, Lei-Ting Li, Pablo Librado, Loredana Lopez, Adriana Muñoz, Benjamin Noel, Alberto Pallavicini, Gaetano Perrotta, Valérie Poncet, David Pot, - Priyono, Michel Rigoreau, Mathieu Rouard, Julio Rozas, Christine Tranchant-Dubreuil, Robert Vanburen, Qiong Zhang, Alan C Andrade, Xavier Argout, Benoit Bertrand, Alexandre de Kochko, Giorgio Graziosi, Robert J Henry, - Jayarama, Ray Ming, Chifumi Nagai, Steve Rounsley, David Sankoff, Giovanni Giuliano, Victor A Albert, Patrick Wincker, Philippe Lashermes
article
Science, 2014, 345 (6201), pp.1181-1184. ⟨10.1126/science.1255274⟩
resume
Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
DOI
DOI : 10.1126/science.1255274
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titre
Ancient hybridizations among the ancestral genomes of bread wheat
auteur
T. Marcussen, S. Sandve, L. Heier, M. Spannagl, M. Pfeifer, K. Jakobsen, B. Wulff, B. Steuernagel, K. Mayer, O.-A. Olsen, J. Rogers, J. Dole el, C. Pozniak, K. Eversole, C. Feuillet, B. Gill, B. Friebe, A. Lukaszewski, Pierre Sourdille, T. Endo, M. Kubalakova, J.  ihalikova, Z. Dubska, J. Vrana, R.  perkova, H.  imkova, M. Febrer, L. Clissold, K. Mclay, K. Singh, P. Chhuneja, N. Singh, J. Khurana, E. Akhunov, F. Choulet, A. Alberti, Valérie Barbe, P. Wincker, H. Kanamori, F. Kobayashi, T. Itoh, T. Matsumoto, H. Sakai, T. Tanaka, J. Wu, Y. Ogihara, H. Handa, P. Maclachlan, A. Sharpe, D. Klassen, D. Edwards, J. Batley, S. Lien, M. Caccamo, S. Ayling, R. Ramirez-Gonzalez, B. Clavijo, J. Wright, M. Martis, M. Mascher, J. Chapman, J. Poland, U. Scholz, K. Barry, R. Waugh, D. Rokhsar, G. Muehlbauer, N. Stein, H. Gundlach, M. Zytnicki, Véronique Jamilloux, H. Quesneville, T. Wicker, P. Faccioli, M. Colaiacovo, A. Stanca, H. Budak, L. Cattivelli, N. Glover, L. Pingault, E. Paux, S. Sharma, R. Appels, M. M. Bellgard, B. Chapman, T. Nussbaumer, K. Bader, H. Rimbert, S. Wang, R. Knox, A. Kilian, M. Alaux, F. Alfama, L. Couderc, N. Guilhot, C. Viseux, M. Loaec, B. Keller, S. Praud
article
Science, 2014, 345 (6194), pp.1250092-1250092. ⟨10.1126/science.1250092⟩
resume
The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor similar to 7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.
DOI
DOI : 10.1126/science.1250092
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PASTEC: an automatic transposable element classification tool
auteur
Claire Hoede, Sandie Arnoux, Mark Moissette, Timothée Chaumier, Olivier Inizan, Véronique Jamilloux, Hadi Quesneville
article
PLoS ONE, 2014, 9 (5), pp.e91929. ⟨10.1371/journal.pone.0091929⟩
resume
The classification of transposable elements (TEs) is key step towards deciphering their potential impact on the genome. However, this process is often based on manual sequence inspection by TE experts. With the wealth of genomic sequences now available, this task requires automation, making it accessible to most scientists. We propose a new tool, PASTEC, which classifies TEs by searching for structural features and similarities. This tool outperforms currently available software for TE classification. The main innovation of PASTEC is the search for HMM profiles, which is useful for inferring the classification of unknown TE on the basis of conserved functional domains of the proteins. In addition, PASTEC is the only tool providing an exhaustive spectrum of possible classifications to the order level of the Wicker hierarchical TE classification system. It can also automatically classify other repeated elements, such as SSR (Simple Sequence Repeats), rDNA or potential repeated host genes. Finally, the output of this new tool is designed to facilitate manual curation by providing to biologists with all the evidence accumulated for each TE consensus. PASTEC is available as a REPET module or standalone software (http://urgi.versailles.inra.fr/download/repet/REPET_linux-x64-2.2.tar.gz). It requires a Unix-like system. There are two standalone versions: one of which is parallelized (requiring Sun grid Engine or Torque), and the other of which is not.
DOI
DOI : 10.1371/journal.pone.0091929
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titre
The genome of the stress-tolerant wild tomato species Solanum pennellii
auteur
Anthony Bolger, Federico Scossa, Marie E Bolger, Christa Lanz, Florian Maumus, Takayuki Tohge, Hadi Quesneville, Saleh Alseekh, Iben Sørensen, Gabriel Lichtenstein, Eric A Fich, Mariana Conte, Heike Keller, Korbinian Schneeberger, Rainer Schwacke, Itai Ofner, Julia Vrebalov, Yimin Xu, Sonia Osorio, Saulo Alves Aflitos, Elio Schijlen, José Jimenez-Gomez, Malgorzata Ryngajllo, Seisuke Kimura, Ravi Kumar, Daniel Koenig, Lauren R Headland, Julin N Maloof, Neelima Sinha, Roeland C H J van Ham, René Klein Lankhorst, Linyong Mao, Alexander Vogel, Borjana Arsova, Ralph Panstruga, Zhangjun Fei, Jocelyn K C Rose, Dani Zamir, Fernando Carrari, James J Giovannoni, Detlef Weigel, Björn Usadel, Alisdair R Fernie
article
Nature Genetics, 2014, 46 (9), pp.1034-1038. ⟨10.1038/ng.3046⟩
resume
Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.
DOI
DOI : 10.1038/ng.3046
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Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution
auteur
Andrew D W Geering, Florian Maumus, Dario Copetti, Nathalie Choisne, Derrick J Zwickl, Matthias Zytnicki, Alistair R Mctaggart, Simone Scalabrin, Silvia Vezzulli, Rod A Wing, Hadi Quesneville, Pierre-Yves Teycheney
article
Nature Communications, 2014, 5, ⟨10.1038/ncomms6269⟩
resume
The extent and importance of endogenous viral elements have been extensively described in animals but are much less well understood in plants. Here we describe a new genus of Caulimoviridae called 'Florendovirus', members of which have colonized the genomes of a large diversity of flowering plants, sometimes at very high copy numbers (>0.5% total genome content). The genome invasion of Oryza is dated to over 1.8 million years ago (MYA) but phylogeographic evidence points to an even older age of 20-34 MYA for this virus group. Some appear to have had a bipartite genome organization, a unique characteristic among viral retroelements. In Vitis vinifera, 9% of the endogenous florendovirus loci are located within introns and therefore may influence host gene expression. The frequent colocation of endogenous florendovirus loci with TA simple sequence repeats, which are associated with chromosome fragility, suggests sequence capture during repair of double-stranded DNA breaks.
DOI
DOI : 10.1038/ncomms6269
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https://hal.inrae.fr/hal-02631214/file/2014_Geering_Nature%20Communications_1.pdf BibTex
titre
Tedna: a transposable element de novo assembler
auteur
Matthias Zytnicki, Eduard Akhunov, Hadi Quesneville
article
Bioinformatics, 2014, (on-line), pp.1-3. ⟨10.1093/bioinformatics/btu365⟩
resume
Recent technological advances are allowing many laboratories to sequence their research organisms. Available de novo assemblers leave repetitive portions of the genome poorly assembled. Some genomes contain high proportions of transposable elements, and transposable elements appear to be a major force behind diversity and adaptation. Few de novo assemblers for transposable elements exist, and most have either been designed for small genomes or 454 reads. In this article, we present a new transposable element de novo assembler, Tedna, which assembles a set of transposable elements directly from the reads. Tedna uses Illumina paired-end reads, the most widely used sequencing technology for de novo assembly, and forms full-length transposable elements. Availability and implementation: Tedna is available at http://urgi.versailles.inra.fr/Tools/Tedna, under the GPLv3 license. It is written in C++11 and only requires the Sparsehash Package, freely available under the New BSD License. Tedna can be used on standard computers with limited RAM resources, although it may also use large memory for better results. Most of the code is parallelized and thus ready for large infrastructures.
DOI
DOI : 10.1093/bioinformatics/btu365
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Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana
auteur
Florian Maumus, Hadi Quesneville
article
Nature Communications, 2014, 5, 9 p. ⟨10.1038/ncomms5104⟩
resume
Little is known about the evolution of repeated sequences over long periods of time. Using two independent approaches, we show that the majority of the repeats found in the Arabidopsis thaliana genome are ancient and likely to derive from the retention of fragments deposited during ancestral bursts that occurred early in the Brassicaceae evolution. We determine that the majority of young repeats are found in pericentromeric domains, while older copies are frequent in the gene-rich regions. Our results further suggest that the DNA methylation of repeats through small RNA-mediated pathways can last over prolonged periods of time. We also illustrate the way repeated sequences are composted by mutations towards genomic dark matter over time, probably driven by the deamination of methylcytosines, which also have an impact on epigenomic landscapes. Overall, we show that the ancient proliferation of repeat families has long-term consequences on A. thaliana biology and genome composition.
DOI
DOI : 10.1038/ncomms5104
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https://hal.inrae.fr/hal-02633174/file/2014_Maumus_NatureComm_1.pdf BibTex
titre
Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome
auteur
Y. Pauchet, C. A. Saski, F. A. Feltus, Isabelle I. Luyten, Hadi Quesneville, D. G. Heckel
article
Insect Molecular Biology, 2014, 23 (3), pp.286-300. ⟨10.1111/imb.12081⟩
resume
The ability of herbivorous beetles from the superfamilies Chrysomeloidea and Curculionoidea to degrade plant cell wall polysaccharides has only recently begun to be appreciated. The presence of plant cell wall degrading enzymes (PCWDEs) in the beetle's digestive tract makes this degradation possible. Sequences encoding these beetle-derived PCWDEs were originally identified from transcriptomes and strikingly resemble those of saprophytic and phytopathogenic microorganisms, raising questions about their origin; e.g. are they insect- or microorganism-derived? To demonstrate unambiguously that the genes encoding PCWDEs found in beetle transcriptomes are indeed of insect origin, we generated a bacterial artificial chromosome library from the genome of the leaf beetle Chrysomela tremula, containing 18432 clones with an average size of 143kb. After hybridizing this library with probes derived from 12 C.tremulaPCWDE-encoding genes and sequencing the positive clones, we demonstrated that the latter genes are encoded by the insect's genome and are surrounded by genes possessing orthologues in the genome of Tribolium castaneum as well as in three other beetle genomes. Our analyses showed that although the level of overall synteny between C.tremula and T.castaneum seems high, the degree of microsynteny between both species is relatively low, in contrast to the more closely related Colorado potato beetle.
DOI
DOI : 10.1111/imb.12081
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Structural and Functional Partitioning of Bread Wheat Chromosome 3B
auteur
Frédéric Choulet, Adriana A. Alberti, Sébastien Theil, Natasha Marie Glover, Valérie Barbe, Josquin Daron, Lise Pingault, Pierre Sourdille, Arnaud Couloux, Etienne Paux, Philippe Leroy, Sophie Mangenot, Nicolas N. Guilhot, Jacques Le Gouis, François Balfourier, Michael M. Alaux, Véronique Jamilloux, Poulain Julie, Celine Durand, Arnaud A. Bellec, Christine Gaspin, Jaroslav Dolezel, Jane Rogers, Klaas Vandepoele, Jean-Marc Aury, Klaus Mayer, Helene H. Berges, Hadi Quesneville, Patrick Wincker, Catherine C. Feuillet
article
Science, 2014, 345 (6194), ⟨10.1126/science.1249721⟩
resume
We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.
DOI
DOI : 10.1126/science.1249721
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The first set of expressed sequence tags (EST) from the medicinal mushroom Agaricus subrufescens delivers resource for gene discovery and marker development
auteur
Marie Foulongne-Oriol, Nicolas Lapalu, Cyril Férandon, Cathy Spataro, Nathalie Ferrer, Joelle J. Amselem, Jean-Michel Savoie
article
Applied Microbiology and Biotechnology, 2014, 98 (18), pp.7879-92. ⟨10.1007/s00253-014-5844-y⟩
resume
Agaricus subrufescens is one of the most important culinary-medicinal cultivable mushrooms with potentially high-added-value products and extended agronomical valorization. The development of A. subrufescens-related technologies is hampered by, among others, the lack of suitable molecular tools. Thus, this mushroom is considered as a genomic orphan species with a very limited number of available molecular markers or sequences. To fill this gap, this study reports the generation and analysis of the first set of expressed sequence tags (EST) for A. subrufescens. cDNA fragments obtained from young sporophores (SP) and vegetative mycelium in liquid culture (CL) were sequenced using 454 pyrosequencing technology. After assembly process, 4,989 and 5,125 sequences were obtained in SP and CL libraries, respectively. About 87 % of the EST had significant similarity with Agaricus bisporus-predicted proteins, and 79 % correspond to known proteins. Functional categorization according to Gene Ontology could be assigned to 49 % of the sequences. Some gene families potentially involved in bioactive compound biosynthesis could be identified. A total of 232 simple sequence repeats (SSRs) were identified, and a set of 40 EST-SSR polymorphic markers were successfully developed. This EST dataset provides a new resource for gene discovery and molecular marker development. It constitutes a solid basis for further genetic and genomic studies in A. subrufescens.
DOI
DOI : 10.1007/s00253-014-5844-y
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titre
Genome interplay in the grain transcriptome of hexaploid bread wheat
auteur
Matthias Pfeifer, Karl G. Kugler, Simen R. Sandve, Bujie Zhan, Heidi Rudi, Torgeir R. Hvidsten, Klaus F. X. Mayer, Jane Rogers, Jaroslav Doležel, Curtis Pozniak, Kellye Eversole, Catherine Feuillet, Bikram B. Gill, Bernd Friebe, Adam J. Lukaszewski, Pierre Sourdille, Takashi R. Endo, Marie Kubaláková, Jarmila Číhalíková, Zdeňka Dubská, Jan Vrána, Romana Šperková, Hana Šimková, Melanie Febrer, Leah Clissold, Kirsten Mclay, Kuldeep Singh, Parveen Chhuneja, Nagendra K Singh, Jitendra Khurana, Eduard Akhunov, Frédéric Choulet, Adriana A. Alberti, Valérie Barbe, Patrick Wincker, Hiroyuki Kanamori, Fuminori Kobayashi, Takeshi Itoh, Takashi Matsumoto, Hiroaki Sakai, Tsuyoshi Tanaka, Jianzhong Wu, Yasunari Ogihara, Hirokazu Handa, P Ron Maclachlan, Andrew Sharpe, Darrin Klassen, David Edwards, Jacqueline Batley, Odd-Arne Olsen, Sigbjørn Lien, Burkhard Steuernagel, Brande Wulff, Mario Caccamo, Sarah Ayling, Ricardo H Ramirez-Gonzalez, Bernardo J Clavijo, Jonathan Wright, Manuel Spannagl, Mihaela M Martis, Martin Mascher, Jarrod Chapman, Jesse A Poland, Uwe Scholz, Kerrie Barry, Robbie Waugh, Daniel S Rokhsar, Gary J Muehlbauer, Nils Stein, Heidrun H. Gundlach, Matthias Zytnicki, Véronique Jamilloux, Hadi Quesneville, Thomas Wicker, Primetta Faccioli, Moreno Colaiacovo, Antonio Michele Stanca, Hikmet Budak, Luigi Cattivelli, Natasha Glover, Lise Pingault, Etienne Paux, Sapna Sharma, Rudi Appels, Matthew Bellgard, Brett Chapman, Thomas Nussbaumer, Kai Christian Bader, Hélène Rimbert, Shichen Wang, Ron Knox, Andrzej Kilian, Michael M. Alaux, Françoise Alfama, Loïc Couderc, Nicolas N. Guilhot, Claire Viseux, Mikael Loaec, Beat Keller, Sébastien Praud
article
Science, 2014, 345 (6194), pp.287-287. ⟨10.1126/science.1250091⟩
resume
Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.
DOI
DOI : 10.1126/science.1250091
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Changes in the benthic algal flora of lake Ganzirri, north-eastern Sicily (Italy)
auteur
Clara Bertuccio, Giuseppa Genovese, Antonio Manghisi, Corinne Cruaud, Arnaud Couloux, Line Le Gall, Marina Morabito
article
Natura Rerum, 2014, 3 (2013/2014), pp.79-91
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Plant genomes enclose footprints of past infections by giant virus relatives
auteur
Florian Maumus, Aline Epert, Fabien Nogué, Guillaume Blanc
article
Nature Communications, 2014, 5, ⟨10.1038/ncomms5268⟩
resume
Nucleocytoplasmic large DNA viruses (NCLDVs) are eukaryotic viruses with large genomes (100 kb-2.5 Mb), which include giant Mimivirus, Megavirus and Pandoravirus. NCLDVs are known to infect animals, protists and phytoplankton but were never described as pathogens of land plants. Here, we show that the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii have open reading frames (ORFs) with high phylogenetic affinities to NCLDV homologues. The P. patens genes are clustered in DNA stretches (up to 13 kb) containing up to 16 NCLDV-like ORFs. Molecular evolution analysis suggests that the NCLDV-like regions were acquired by horizontal gene transfer from distinct but closely related viruses that possibly define a new family of NCLDVs. Transcriptomics and DNA methylation data indicate that the NCLDV-like regions are transcriptionally inactive and are highly cytosine methylated through a mechanism not relying on small RNAs. Altogether, our data show that members of NCLDV have infected land plants.
DOI
DOI : 10.1038/ncomms5268
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https://hal.science/hal-01204072/file/ncomms5268.pdf BibTex
titre
A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome
auteur
. International Wheat Genome Sequencing Consortium (iwgsc), Michael M. Alaux, Françoise F. Alfama-Depauw, Frédéric Choulet, Loïc Couderc, Natasha Marie Glover, Claire Guerche, Nicolas N. Guilhot, Véronique Jamilloux, Mikael Loaec, Etienne Paux, Lise Pingault, Hadi Quesneville, Pierre Sourdille, Matthias Zytnicki
article
Science, 2014, 345 (6194), pp.1251788. ⟨10.1126/science.1251788⟩
resume
An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.
DOI
DOI : 10.1126/science.1251788
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Organization and evolution of transposable elements along the bread wheat chromosome 3B
auteur
Josquin Daron, Natasha Glover, Lise Pingault, Sébastien Theil, Véronique Jamilloux, Etienne Paux, Valérie Barbe, Sophie Mangenot, Adriana A. Alberti, Patrick Wincker, Hadi Quesneville, Catherine C. Feuillet, Frédéric Choulet
article
Genome Biology, 2014, 15 (12), pp.1-15. ⟨10.1186/s13059-014-0546-4⟩
resume
Background The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements and two recent rounds of polyploidization. The assembly of a 774 Mb reference sequence of wheat chromosome 3B provided us with the opportunity to explore the impact of transposable elements (TEs) on the complex wheat genome structure and evolution at a resolution and scale never reached so far. Results We develop an automated workflow, CLARI-TE, for TE modeling in complex genomes. We delineate precisely 56,488 intact and 196,391 fragmented TEs along the 3B pseudomolecule, accounting for 85% of the sequence, and reconstruct 30,199 nested insertions. TEs have been mostly silent for the last one million years, and the 3B chromosome has been shaped by a succession of bursts that occurred between 1 to 3 million years ago. Accelerated TE elimination in the high-recombination distal regions is a driving force towards chromosome partitioning. CACTAs overrepresented in the high-recombination distal regions are significantly associated with recently duplicated genes. In addition, we identify 140 CACTA-mediated gene capture events with 17 genes potentially created by exon shuffling and show that 19 captured genes are transcribed and under selection pressure, suggesting the important role of CACTAs in the recent wheat adaptation. Conclusion Accurate TE modeling uncovers the dynamics of TEs in a highly complex and polyploid genome. It provides novel insights into chromosome partitioning and highlights the role of CACTA transposons in the high level of gene duplication in wheat.
DOI
DOI : 10.1186/s13059-014-0546-4
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https://hal.inrae.fr/hal-02630315/file/2014_Daron_Genome%20Biology_1.pdf BibTex
titre
Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter
auteur
Florian Maumus, Hadi Quesneville
article
PLoS ONE, 2014, 9 (4), ⟨10.1371/journal.pone.0094101⟩
resume
Eukaryotic genomes contain highly variable amounts of DNA with no apparent function. This so- called junk DNA is composed of two components: repeated and repeat- derived sequences ( together referred to as the repeatome), and nonannotated sequences also known as genomic dark matter. Because of their high duplication rates as compared to other genomic features, transposable elements are predominant contributors to the repeatome and the products of their decay is thought to be a major source of genomic dark matter. Determining the origin and composition of junk DNA is thus important to help understanding genome evolution as well as host biology. In this study, we have used a combination of tools enabling to show that the repeatome from the small and reducing A. thaliana genome is significantly larger than previously thought. Furthermore, we present the concepts and results from a series of innovative approaches suggesting that a significant amount of the A. thaliana dark matter is of repetitive origin. As a tentative standard for the community, we propose a deep compendium annotation of the A. thaliana repeatome that may help addressing farther genome evolution as well as transcriptional and epigenetic regulation in this model plant.
DOI
DOI : 10.1371/journal.pone.0094101
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https://hal.inrae.fr/hal-02636753/file/Maumus-2014-plos-one_1 BibTex
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Global discovery and characterization of small non-coding RNAs in marine microalgae
auteur
Sara López-Gomollón, Matthew Beckers, Tina Rathjen, Simon Moxon, Florian Maumus, Irina Mohorianu, Vincent Moulton, Tamas Dalmay, Thomas Mock
article
BMC Genomics, 2014, 15, ⟨10.1186/1471-2164-15-697⟩
resume
Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results: Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions: This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and maybe used for acclimation to environmental conditions.
DOI
DOI : 10.1186/1471-2164-15-697
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https://hal.inrae.fr/hal-02640460/file/2014_Lopez%20Gomollon_BMC%20Genomics_1.pdf BibTex
titre
The grapevine gene nomenclature system
auteur
Jérôme Grimplet, Anne-Francoise Adam-Blondon, Pierre-François Bert, Olivier Bitz, Dario Cantu, Christopher Davies, Serge Delrot, Mario Pezzotti, Stéphane Rombauts, Grant R Cramer
article
BMC Genomics, 2014, 15 (1077), ⟨10.1186/1471-2164-15-1077⟩
resume
Background Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, data on structural and functional characterization of grape genes accumulated exponentially. To better exploit the results obtained by the international community, we think that a coordinated nomenclature for gene naming in species with sequenced genomes is essential. It will pave the way for the accumulation of functional data that will enable effective scientific discussion and discovery. The exploitation of data that were generated independently of the genome release is hampered by their heterogeneous nature and by often incompatible and decentralized storage. Classically, large amounts of data describing gene functions are only available in printed articles and therefore remain hardly accessible for automatic text mining. On the other hand, high throughput “Omics” data are typically stored in public repositories, but should be arranged in compendia to better contribute to the annotation and functional characterization of the genes. Results With the objective of providing a high quality and highly accessible annotation of grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Super-Nomenclature Committee for Grape Gene Annotation (sNCGGa) to coordinate the effort of experts to annotate the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define conventions for a gene naming system in this paper. Conclusions Learning from similar initiatives in other plant species such as Arabidopsis, rice and tomato, a versatile nomenclature system has been developed in anticipation of future genomic developments and annotation issues. The sNCGGa’s first outreach to the grape community has been focused on implementing recommended guidelines for the expert annotators by: (i) providing a common annotation platform that enables community-based gene curation, (ii) developing a gene nomenclature scheme reflecting the biological features of gene products that is consistent with that used in other organisms in order to facilitate comparative analyses.
DOI
DOI : 10.1186/1471-2164-15-1077
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2013

Journal articles

titre
Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes.
auteur
Florent Murat, Rongzhi Zhang, Sébastien Guizard, Raphael Flores, Alix Armero, Caroline Pont, Delphine Steinbach, Hadi Quesneville, Richard Cooke, Jerome Salse
article
Genome Biology and Evolution, 2013, 6 (1), pp.12-33
resume
Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted, and shuffled, defining dominant (bias toward duplicate retention) and sensitive (bias toward duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in seven protochromosomes containing 16,464 protogenes and following evolutionary rules where 1) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) subgenomes, 2) subgenome dominance is revealed by both gene deletion and shuffling from the S blocks, 3) duplicate deletion/movement may have been mediated by single-/double-stranded illegitimate recombination mechanisms, 4) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, 5) the fusion of two dominant blocks leads to supradominant neochromosomes (D + D = D) with higher ancestral gene retention compared with D + S = D (i.e., fusion of blocks with opposite sensitivity) or even S + S = S (i.e., fusion of two sensitive ancestral blocks). A new user-friendly online tool named "PlantSyntenyViewer," available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
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titre
Pan genome of the phytoplankton Emiliania underpins its global distribution
auteur
Betsy A Read, Jessica Kegel, Mary J Klute, Alan Kuo, Stephane C Lefebvre, Florian Maumus, Christoph Mayer, John Miller, Adam Monier, Asaf Salamov, Jeremy Young, Maria Aguilar, Jean-Michel Claverie, Stephan Frickenhaus, Karina Gonzalez, Emily K Herman, Yao-Cheng Lin, Johnathan Napier, Hiroyuki Ogata, Analissa F Sarno, Jeremy Shmutz, Declan Schroeder, Frederic Verret, Peter von Dassow, Klaus Valentin, Yves van de Peer, Glen Wheeler, Emiliana Huxleyi, Joel B Dacks, Charles F. Delwiche, Sonya T. Dyhrman, Gernot Glöckner, Uwe John, Thomas Richards, Alexandra Z Worden, Xiaoyu Zhang, Igor V. Grigoriev, J. Mark Cock
article
Nature, 2013, 499 (7457), pp.209-213. ⟨10.1038/nature12221⟩
resume
Coccolithophores have influenced the global climate for over 200 million years1. These marine phytoplankton can account for 20 per cent of total carbon fixation in some systems2. They form blooms that can occupy hundreds of thousands of square kilometres and are distinguished by their elegantly sculpted calcium carbonate exoskeletons (coccoliths), rendering them visible from space3. Although coccolithophores export carbon in the form of organic matter and calcite to the sea floor, they also release CO2 in the calcification process. Hence, they have a complex influence on the carbon cycle, driving either CO2 production or uptake, sequestration and export to the deep ocean4. Here we report the first haptophyte reference genome, from the coccolithophore Emiliania huxleyi strain CCMP1516, and sequences from 13 additional isolates. Our analyses reveal a pan genome (core genes plus genes distributed variably between strains) probably supported by an atypical complement of repetitive sequence in the genome. Comparisons across strains demonstrate that E. huxleyi, which has long been considered a single species, harbours extensive genome variability reflected in different metabolic repertoires. Genome variability within this species complex seems to underpin its capacity both to thrive in habitats ranging from the equator to the subarctic and to form large-scale episodic blooms under a wide variety of environmental conditions.
DOI
DOI : 10.1038/nature12221
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https://hal.science/hal-01074841/file/Read%20Ehux%20genome%20Nature%2013.pdf BibTex
titre
GnpIS: an information system to integrate genetic and genomic data from plants and fungi
auteur
Delphine D. Steinbach, Michael M. Alaux, Joelle J. Amselem, Nathalie Choisne, Sophie S. Durand, Raphaël-Gauthier R.-G. Flores, Aminah A. Keliet, Erik Kimmel, Nicolas Lapalu, Isabelle I. Luyten, Célia Michotey, Nacer Mohellibi, Cyril Pommier, Sebastien S. Reboux, Dorothée Valdenaire, Daphné Verdelet, Hadi Quesneville
article
Database - The journal of Biological Databases and Curation, 2013, 2013, pp.1-9. ⟨10.1093/database/bat058⟩
resume
Data integration is a key challenge for modern bioinformatics. It aims to provide biologists with tools to explore relevant data produced by different studies. Large-scale international projects can generate lots of heterogeneous and unrelated data. The challenge is to integrate this information with other publicly available data. Nucleotide sequencing throughput has been improved with new technologies; this increases the need for powerful information systems able to store, manage and explore data. GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. Here, we illustrate its use. Database URL: http://urgi.versailles.inra.fr/gnpis.
DOI
DOI : 10.1093/database/bat058
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https://hal.inrae.fr/hal-02648084/file/Database-2013-Steinbach-database-bat058_1.pdf BibTex
titre
A statistical framework for joint eQTL analysis in multiple tissues
auteur
Timothée Flutre, Xiaoquan Wen, Jonathan Pritchard, Matthew Stephens
article
PLoS Genetics, 2013, 9 (5), ⟨10.1371/journal.pgen.1003486⟩
resume
Mapping expression Quantitative Trait Loci (eQTLs) represents a powerful and widely adopted approach to identifying putative regulatory variants and linking them to specific genes. Up to now eQTL studies have been conducted in a relatively narrow range of tissues or cell types. However, understanding the biology of organismal phenotypes will involve understanding regulation in multiple tissues, and ongoing studies are collecting eQTL data in dozens of cell types. Here we present a statistical framework for powerfully detecting eQTLs in multiple tissues or cell types (or, more generally, multiple subgroups). The framework explicitly models the potential for each eQTL to be active in some tissues and inactive in others. By modeling the sharing of active eQTLs among tissues, this framework increases power to detect eQTLs that are present in more than one tissue compared with "tissue-by-tissue" analyses that examine each tissue separately. Conversely, by modeling the inactivity of eQTLs in some tissues, the framework allows the proportion of eQTLs shared across different tissues to be formally estimated as parameters of a model, addressing the difficulties of accounting for incomplete power when comparing overlaps of eQTLs identified by tissue-by-tissue analyses. Applying our framework to re-analyze data from transformed B cells, T cells, and fibroblasts, we find that it substantially increases power compared with tissue-by-tissue analysis, identifying 63% more genes with eQTLs (at FDR = 0.05). Further, the results suggest that, in contrast to previous analyses of the same data, the majority of eQTLs detectable in these data are shared among all three tissues.
DOI
DOI : 10.1371/journal.pgen.1003486
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https://hal.science/hal-01190566/file/2013_Flutre_Plos%20Gen_1.pdf BibTex
titre
The wheat powdery mildew genome shows the unique evolution of an obligate biotroph
auteur
Thomas Wicker, Simone Oberhaensli, Francis Parlange, Jan P Buchmann, Margarita Shatalina, Stefan Roffler, Roi Ben-David, Jaroslav Dolezel, Paul Schulze-Lefert, Pietro D Spanu, Remy Bruggmann, Joelle J. Amselem, Hadi Quesneville, Emiel Ver Loren van Themaat, Timothy Paape, Kentaro K Shimizu, Beat Keller
article
Nature Genetics, 2013, 45 (9), pp.1092-1098. ⟨10.1038/ng.2704⟩
resume
Wheat powdery mildew, Blumeria graminis forma specialis tritici, is a devastating fungal pathogen with a poorly understood evolutionary history. Here we report the draft genome sequence of wheat powdery mildew, the resequencing of three additional isolates from different geographic regions and comparative analyses with the barley powdery mildew genome. Our comparative genomic analyses identified 602 candidate effector genes, with many showing evidence of positive selection. We characterize patterns of genetic diversity and suggest that mildew genomes are mosaics of ancient haplogroups that existed before wheat domestication. The patterns of diversity in modern isolates suggest that there was no pronounced loss of genetic diversity upon formation of the new host bread wheat 10,000 years ago. We conclude that the ready adaptation of B. graminis f.sp. tritici to the new host species was based on a diverse haplotype pool that provided great genetic potential for pathogen variation.
DOI
DOI : 10.1038/ng.2704
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titre
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
auteur
Tanja Slotte, Khaled M Hazzouri, J Arvid Agren, Daniel Koenig, Florian Maumus, Ya-Long Guo, Kim Steige, Adrian E Platts, Juan S Escobar, L Killian Newman, Wei Wang, Terezie Mandáková, Emilio Vello, Lisa M Smith, Stefan R Henz, Joshua Steffen, Shohei Takuno, Yaniv Brandvain, Graham Coop, Peter Andolfatto, Tina T Hu, Mathieu Blanchette, Richard M Clark, Hadi Quesneville, Magnus Nordborg, Brandon S Gaut, Martin A Lysak, Jerry Jenkins, Jane Grimwood, Jarrod Chapman, Simon Prochnik, Shengqiang Shu, Daniel Rokhsar, Jeremy Schmutz, Detlef Weigel, Stephen I Wright
article
Nature Genetics, 2013, 45 (7), pp.831-835. ⟨10.1038/ng.2669⟩
resume
The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
DOI
DOI : 10.1038/ng.2669
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titre
Efficient comparison of sets of intervals with NC-lists
auteur
Matthias Zytnicki, Yufei Luo, Hadi Quesneville
article
Bioinformatics, 2013, 29 (7), pp.933-939. ⟨10.1093/bioinformatics/btt070⟩
resume
Motivation: High-throughput sequencing produces in a small amount of time a large amount of data, which are usually difficult to analyze. Mapping the reads to the transcripts they originate from, to quantify the expression of the genes, is a simple, yet time demanding, example of analysis. Fast genomic comparison algorithms are thus crucial for the analysis of the ever-expanding number of reads sequenced. Results: We used NC-lists to implement an algorithm that compares a set of query intervals with a set of reference intervals in two steps. The first step, a pre-processing done once for all, requires time O½#Rlogð#RÞ þ #Qlogð#QÞ , where Q and R are the sets of query and reference intervals. The search phase requires constant space, and time Oð#R þ #Q þ #MÞ, where M is the set of overlaps. We showed that our algorithm compares favorably with five other algorithms, especially when several comparisons are performed. Availability: The algorithm has been included to S–MART, a versatile tool box for RNA-Seq analysis, freely available at http://urgi.versailles. inra.fr/Tools/S-Mart. The algorithm can be used for many kinds of data (sequencing reads, annotations, etc.) in many formats (GFF3, BED, SAM, etc.), on any operating system. It is thus readily useable for the analysis of next-generation sequencing data.
DOI
DOI : 10.1093/bioinformatics/btt070
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titre
Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes
auteur
Caroline C. Pont, Florent Murat, Sébastien S. Guizard, Raphaël-Gauthier R.-G. Flores, Séverine S. Foucrier, Yannick Y. Bidet, Umar Masood Quraishi Masood-Quraishi, Michael M. Alaux, Jaroslav J. Doležel, Tzion T. Fahima, Hikmet H. Budak, Beat B. Keller, Silvio S. Salvi, Marco M. Maccaferri, Delphine D. Steinbach, Catherine C. Feuillet, Hadi H. Quesneville, Jerome J. Salse
article
Plant Journal, 2013, pp.1-29. ⟨10.1111/tpj.12366⟩
resume
Bread wheat derives from a grass ancestor structured in 7 protochromosomes followed by a paleotetraploidization to reach a 12 chromosomes intermediate and a neohexaploidization (involving subgenomes A, B and D) event that finally shaped the 21 modern chromosomes. Insights into wheat syntenome in sequencing COS (Conserved Orthologous Set) genes unravelled differences in genomic structure (such as gene conservation and diversity) and genetical landscape (such as recombination pattern) between ancestral as well as recent duplicated blocks. Contrasted evolutionary plasticity is observed where the B subgenome appears more sensitive (i.e. plastic) in contrast to A as dominant (i.e. stable) in response to the neotetraploidization and D subgenome as supradominant (i.e. pivotal) in response to the neohexaploidization event. Finally, the wheat syntenome, delivered through a public web interface PlantSyntenyViewer at http://urgi.versailles.inra.fr/synteny-wheat, can be considered as a guide for accelerated dissection of major agronomical traits in wheat. This article is protected by copyright. All rights reserved.
DOI
DOI : 10.1111/tpj.12366
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titre
Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance.
auteur
Sonia Campo, Cristina Peris-Peris, Christelle Siré, Ana Beatriz Moreno, Livia Donaire, Matthias Zytnicki, Cedric Notredame, César Llave, Blanca San Segundo
article
New Phytologist, 2013, 199 (1), pp.212-27. ⟨10.1111/nph.12292⟩
resume
Plants have evolved efficient defence mechanisms to defend themselves from pathogen attack. Although many studies have focused on the transcriptional regulation of defence responses, less is known about the involvement of microRNAs (miRNAs) as post-transcriptional regulators of gene expression in plant immunity. This work investigates miRNAs that are regulated by elicitors from the blast fungus Magnaporthe oryzae in rice (Oryza sativa). Small RNA libraries were constructed from rice tissues and subjected to high-throughput sequencing for the identification of elicitor-responsive miRNAs. Target gene expression was examined by microarray analysis. Transgenic lines were used for the analysis of miRNA functioning in disease resistance. Elicitor treatment is accompanied by dynamic alterations in the expression of a significant number of miRNAs, including new members of annotated miRNAs. Novel miRNAs from rice are proposed. We report a new rice miRNA, osa-miR7695, which negatively regulates an alternatively spliced transcript of OsNramp6 (Natural resistance-associated macrophage protein 6). This novel miRNA experienced natural and domestication selection events during evolution, and its overexpression in rice confers pathogen resistance. This study highlights an miRNA-mediated regulation of OsNramp6 in disease resistance, whilst illustrating the existence of a novel regulatory network that integrates miRNA function and mRNA processing in plant immunity.
DOI
DOI : 10.1111/nph.12292
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titre
Shared sub-genome dominance following polyploidization explains grass genome evolutionary plasticity from a 7 protochromosome ancestor with 16K protogenes
auteur
Florent Murat, Rongzhi R. Zhang, Sébastien S. Guizard, Raphaël-Gauthier R.-G. Flores, Alix A. Armero Villanueva, Caroline C. Pont, Delphine D. Steinbach, Hadi H. Quesneville, Richard R. Cooke, Jerome J. Salse
article
Genome Biology and Evolution, 2013, 6 (1), pp.12-33. ⟨10.1093/gbe/evt200⟩
resume
Modern plant genomes are diploidized paleopolyploids. We revisited grass genome paleohistory in response to the diploidization process through a detailed investigation of the evolutionary fate of duplicated blocks. Ancestrally duplicated genes can be conserved, deleted and shuffled, defining dominant (bias towards duplicate retention) and sensitive (bias towards duplicate erosion) chromosomal fragments. We propose a new grass genome paleohistory deriving from an ancestral karyotype structured in 7 protochromosomes containing 16,464 protogenes and following evolutionary rules where (i) ancestral shared polyploidizations shaped conserved dominant (D) and sensitive (S) sub-genomes, (ii) sub-genome dominance is revealed by both gene deletion and shuffling from the S blocks, (iii) duplicate deletion/movement may have been mediated by single/double stranded illegitimate recombination mechanisms, (iv) modern genomes arose through centromeric fusion of protochromosomes, leading to functional monocentric neochromosomes, (v) the fusion of two dominant blocks leads to supradominant neochromosomes (D+D=D) with higher ancestral gene retention compared to D+S=D (i.e. fusion of blocks with opposite sensitivity) or even S+S=S (i.e. fusion of two sensitive ancestral blocks). A new user friendly online tool named 'PlantSyntenyViewer', available at http://urgi.versailles.inra.fr/synteny-cereal, presents the refined comparative genomics data.
DOI
DOI : 10.1093/gbe/evt200
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titre
Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters
auteur
Vanessa Zanni, Angéline Eymery, Michael Coiffet, Matthias Zytnicki, Isabelle Luyten, Hadi Quesneville, Chantal Vaury, Silke Jensen
article
Proceedings of the National Academy of Sciences of the United States of America, 2013, ⟨10.1073/pnas.1313677110⟩
resume
Most of our understanding of Drosophila heterochromatin structure and evolution has come from the annotation of heterochromatin from the isogenic y; cn bw sp strain. However, almost nothing is known about the heterochromatin's structural dynamics and evolution. Here, we focus on a 180-kb heterochromatic locus producing Piwi-interacting RNAs (piRNA cluster), the flamenco (flam) locus, known to be responsible for the control of at least three transposable elements (TEs). We report its detailed structure in three different Drosophila lines chosen according to their capacity to repress or not to repress the expression of two retrotransposons named ZAM and Idefix, and we show that they display high structural diversity. Numerous rearrangements due to homologous and nonhomologous recombination, deletions and segmental duplications, and loss and gain of TEs are diverse sources of active genomic variation at this locus. Notably, we evidence a correlation between the presence of ZAM and Idefix in this piRNA cluster and their silencing. They are absent from flam in the strain where they are derepressed. We show that, unexpectedly, more than half of the flam locus results from recent TE insertions and that most of the elements concerned are prone to horizontal transfer between species of the melanogaster subgroup. We build a model showing how such high and constant dynamics of a piRNA master locus open the way to continual emergence of new patterns of piRNA biogenesis leading to changes in the level of transposition control.
DOI
DOI : 10.1073/pnas.1313677110
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https://hal.science/hal-01189713/file/2013_Zanni_PNAS_1.pdf BibTex
titre
Management and dissemination of MS proteomic data with PROTICdb: Example of a quantitative comparison between methods of protein extraction
auteur
Olivier Langella, Benoit B. Valot, Daniel Jacob, Thierry T. Balliau, Raphaël-Gauthier Flores, Christine Hoogland, Johann J. Joets, Michel M. Zivy
article
Proteomics, 2013, 13 (9), pp.1457-1466. ⟨10.1002/pmic.201200564⟩
resume
High throughput MS-based proteomic experiments generate large volumes of complex data and necessitate bioinformatics tools to facilitate their handling. Needs include means to archive data, to disseminate them to the scientific communities, and to organize and annotate them to facilitate their interpretation. We present here an evolution of PROTICdb, a database software that now handles MS data, including quantification. PROTICdb has been developed to be as independent as possible from tools used to produce the data. Biological samples and proteomics data are described using ontology terms. A Taverna workflow is embedded, thus permitting to automatically retrieve information related to identified proteins by querying external databases. Stored data can be displayed graphically and a "Query Builder" allows users to make sophisticated queries without knowledge on the underlying database structure. All resources can be accessed programmatically using a Java client API or RESTful web services, allowing the integration of PROTICdb in any portal. An example of application is presented, where proteins extracted from a maize leaf sample by four different methods were compared using a label-free shotgun method. Data are available at http://moulon.inra.fr/protic/public. PROTICdb thus provides means for data storage, enrichment, and dissemination of proteomics data.
DOI
DOI : 10.1002/pmic.201200564
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titre
Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline
auteur
Claire Toffano-Nioche, Yufei Luo, Claire Kuchly, Claire Wallon, Delphine D. Steinbach, Matthias Zytnicki, Annick Jacq, Daniel Gautheret
article
Methods, 2013, 63 (1), pp.60 - 65. ⟨10.1016/j.ymeth.2013.06.003⟩
resume
RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR'PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coil. (C) 2013 The Authors. Published by Elsevier Inc. All rights reserved.
DOI
DOI : 10.1016/j.ymeth.2013.06.003
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2012

Journal articles

titre
International Congress on Transposable Elements (ICTE) 2012 in Saint Malo and the sea of TE stories.
auteur
Abdelkader Aïnouche, Mireille Bétermier, Mick Chandler, Richard Cordaux, Gaël Cristofari, Jean-Marc Deragon, Pascale Lesage, Olivier Panaud, Hadi Quesneville, Chantal Vaury, Cristina Vieira, Clémentine Vitte
article
Mobile DNA, 2012, 3 (1), pp.17. ⟨10.1186/1759-8753-3-17⟩
resume
ABSTRACT: An international conference on Transposable Elements (TEs) was held 21--24 April 2012 in Saint Malo, France. Organized by the French Transposition Community (GDR Elements Genetiques Mobiles et Genomes, CNRS) and the French Society of Genetics, the conference's goal was to bring together researchers from around the world who study transposition in diverse organisms using multiple experimental approaches. The meeting drew more than 217 attendees and most contributed through poster presentations (117), invited talks and short talks selected from poster abstracts (48 in total). The talks were organized into four scientific sessions, focused on: impact of TEs on genomes, control of transposition, evolution of TEs and mechanisms of transposition. Here, we present highlights from the talks given during the platform sessions. The conference was sponsored by Alliance pour les sciences de la vie et de la sante (Aviesan), Centre national de la recherche scientifique (CNRS), Institut national de la sante et de la recherche medicale (INSERM), Institut de recherche pour le developpement (IRD), Institut national de la recherche agronomique (INRA), Universite de Perpignan, Universite de Rennes 1, Region Bretagne and Mobile DNA. Chair of the organization committee Jean-Marc Deragon Organizers Abdelkader Ainouche, Mireille Betermier, Mick Chandler, Richard Cordaux, Gael Cristofari, Jean-Marc Deragon, Pascale Lesage, Didier Mazel, Olivier Panaud, Hadi Quesneville, Chantal Vaury, Cristina Vieira and Clementine Vitte.
DOI
DOI : 10.1186/1759-8753-3-17
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https://inserm.hal.science/inserm-00764323/file/1759-8753-3-17.pdf BibTex
titre
Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis
auteur
Sophie S. Schbath, Veronique V. Martin, Matthias Zytnicki, Julien Fayolle, Valentin Loux, Jean-François Gibrat
article
Journal of Computational Biology, 2012, 19 (6), pp.796-813. ⟨10.1089/cmb.2012.0022⟩
resume
Mapping short reads against a reference genome is classically the first step of many next-generation sequencing data analyses, and it should be as accurate as possible. Because of the large number of reads to handle, numerous sophisticated algorithms have been developped in the last 3 years to tackle this problem. In this article, we first review the underlying algorithms used in most of the existing mapping tools, and then we compare the performance of nine of these tools on a well controled benchmark built for this purpose. We built a set of reads that exist in single or multiple copies in a reference genome and for which there is no mismatch, and a set of reads with three mismatches. We considered as reference genome both the human genome and a concatenation of all complete bacterial genomes. On each dataset, we quantified the capacity of the different tools to retrieve all the occurrences of the reads in the reference genome. Special attention was paid to reads uniquely reported and to reads with multiple hits.
DOI
DOI : 10.1089/cmb.2012.0022
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https://hal.inrae.fr/hal-02645697/file/mapping_1.pdf BibTex
titre
MetaBase-the wiki-database of biological databases
auteur
Dan M. Bolser, Pierre-Yves Chibon, Sungsam Gong, Daniel Jacob, Victoria Fabia Dominguez del Angel, Dan Swan, Sebastian Bassi, Virginia Gonzalez, Prashanth Suravajhala, Seungwoo Hwang, Paolo Romano, Rob Edwards, Bryan Bishop, John Eargle, Timur Shtatland, Nicholas J. Provart, Dave Clements, Daniel P. Renfro, Daeui Bhak, Jong Bhak
article
Nucleic Acids Research, 2012, 40 (1), pp.D1250-D1254. ⟨10.1093/nar/gkr1099⟩
resume
Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.
DOI
DOI : 10.1093/nar/gkr1099
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https://hal.inrae.fr/hal-02648461/file/2012_Bolser_Nucleic%20Acids%20Research_1.pdf BibTex
titre
Highly Dynamic Exon Shuffling in Candidate Pathogen Receptors ... What if Brown Algae Were Capable of Adaptive Immunity?
auteur
Antonios Zambounis, Marek Elias, Lieven Sterck, Florian Maumus, Claire M. M. Gachon
article
Molecular Biology and Evolution, 2012, 29 (4), pp.1263 - 1276. ⟨10.1093/molbev/msr296⟩
resume
Pathogen recognition is the first step of immune reactions. In animals and plants, direct or indirect pathogen recognition is often mediated by a wealth of fast-evolving receptors, many of which contain ligand-binding and signal transduction domains, such as leucine-rich or tetratricopeptide repeat (LRR/TPR) and NB-ARC domains, respectively. In order to identify candidates potentially involved in algal defense, we mined the genome of the brown alga Ectocarpus siliculosus for homologues of these genes and assessed the evolutionary pressures acting upon them. We thus annotated all Ectocarpus LRR-containing genes, in particular an original group of LRR-containing GTPases of the ROCO family, and 24 NB-ARC-TPR proteins. They exhibit high birth and death rates, while a diversifying selection is acting on their LRR (respectively TPR) domain, probably affecting the ligand-binding specificities. Remarkably, each repeat is encoded by an exon, and the intense exon shuffling underpins the variability of LRR and TPR domains. We conclude that the Ectocarpus ROCO and NB-ARC-TPR families are excellent candidates for being involved in recognition/transduction events linked to immunity. We further hypothesize that brown algae may generate their immune repertoire via controlled somatic recombination, so far only known from the vertebrate adaptive immune systems.
DOI
DOI : 10.1093/molbev/msr296
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titre
TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.
auteur
Philippe Leroy, Nicolas Guilhot, Hiroaki Sakai, Aurélien Bernard, Frédéric Choulet, Sébastien Theil, Sébastien Reboux, Naoki Amano, Timothée Flutre, Céline Pelegrin, Hajime Ohyanagi, Michael Seidel, Franck Giacomoni, Matthieu Matthieu.Reichstadt@inrae.Fr Reichstadt, Michael Alaux, Emmanuelle Gicquello, Fabrice Legeai, Lorenzo Cerutti, Hisataka Numa, Tsuyoshi Tanaka, Klaus Mayer, Takeshi Itoh, Hadi Quesneville, Catherine Feuillet
article
Frontiers in Plant Science, 2012, 3, pp.5. ⟨10.3389/fpls.2012.00005⟩
resume
In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future.
DOI
DOI : 10.3389/fpls.2012.00005
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https://inria.hal.science/hal-00753407/file/2013_Leroy_Frontiers%20in%20Plant%20Science_1 BibTex
titre
Linkage to the mating-type locus across the genus microbotryum: insights into nonrecombining chromosomes
auteur
Elsa Petit, Tatiana Giraud, Damien M. de Vienne, Marco A Coelho, Gabriela Aguileta, Joelle J. Amselem, Jonathan Kreplak, Julie Poulain, Frédérick F. Gavory, Patrick Wincker, Sarah K Young, Christina Cuomo, Michael Perlin, Michael E Hood
article
Evolution - International Journal of Organic Evolution, 2012, 66 (11), pp.3519-3533. ⟨10.1111/j.1558-5646.2012.01703.x⟩
resume
Parallels have been drawn between the evolution of nonrecombining regions in fungal mating-type chromosomes and animal and plant sex chromosomes, particularly regarding the stages of recombination cessation forming evolutionary strata of allelic divergence. Currently, evidence and explanations for recombination cessation in fungi are sparse, and the presence of evolutionary strata has been examined in a minimal number of fungal taxa. Here, the basidiomycete genus Microbotryum was used to determine the history of recombination cessation for loci on the mating-type chromosomes. Ancestry of linkage with mating type for 13 loci was assessed across 20 species by a phylogenetic method. No locus was found to exhibit trans-specific polymorphism for alternate alleles as old as the mating pheromone receptor, indicating that ages of linkage to mating type varied among the loci. The ordering of loci in the ancestry of linkage to mating type does not agree with their previously proposed assignments to evolutionary strata. This study suggests that processes capable of influencing divergence between alternate alleles may act at loci in the nonrecombining regions (e.g., gene conversion) and encourages further work to dissect the evolutionary processes acting upon genomic regions that determine mating compatibility.
DOI
DOI : 10.1111/j.1558-5646.2012.01703.x
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https://hal.science/hal-01190628/file/Petit%20-%202012%20-%20Evolution%20-%20Wiley_1.htm BibTex
titre
Chado controller: advanced annotation management with a community annotation system
auteur
Valention Guignon, Gaëtan Droc, Michael M. Alaux, Franc-Christophe Baurens, Olivier Garsmeur, Claire Poiron, Tim Carver, Mathieu Rouard, Stephanie Bocs
article
Bioinformatics, 2012, 28 (7), pp.1054-1056. ⟨10.1093/bioinformatics/bts046⟩
resume
We developed a controller that is compliant with the Chado database schema, GBrowse and genome annotation-editing tools such as Artemis and Apollo. It enables the management of public and private data, monitors manual annotation ( with controlled vocabularies, structural and functional annotation controls) and stores versions of annotation for all modified features. The Chado controller uses PostgreSQL and Perl.
DOI
DOI : 10.1093/bioinformatics/bts046
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https://hal.inrae.fr/hal-02651830/file/Bioinformatics-2012-Guignon-1054-6_1.pdf BibTex
titre
Alcohol and wine in relation to cancer and other diseases
auteur
Attilio Giacosa, Anne-Francoise A.-F. Adam-Blondon, Sara Baer-Sinnott, Roberto Barale, Luigi Bavaresco, Gabriele Di Gaspero, Laura Dugo, Robert Curtis Ellison, Vincenzo Gerbi, Dun Gifford, Jaak Janssens, Carlo La Vecchia, Eva Negri, Mario Pezzotti, Leonardo Santi, Luca Santi, Mariangela Rondanelli
article
European Journal of Cancer Prevention, 2012, 21 (1), pp.103-108. ⟨10.1097/CEJ.0b013e32834761d3⟩
resume
Heavy alcohol consumption is associated with increased overall mortality, cancer, liver, and cardiovascular diseases; but low doses of alcohol (up to one drink per day) are not associated with the risk of any cancer site with the exception of breast cancer and possibly of oral and pharyngeal cancers. Moreover, recent evidence indicates that moderate alcohol and specifically wine intake provides cardioprotection and neuroprotection and may increase longevity. Various experimental data hypothesize a potential cancer chemopreventive role of some grape extracts, and complete sequencing of the grapevine genome has revealed genes responsible for the synthesis of health-promoting compounds (resveratrol and other polyphenols), thus advocating the development of future potential nutraceutical strategies. This focuses on the pros and cons of moderate alcohol and wine consumption and opens a debate on this topic.
DOI
DOI : 10.1097/CEJ.0b013e32834761d3
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titre
The ABO blood group is a trans-species polymorphism in primates
auteur
Laure L. Segurel, Emma E. E. E. Thompson, Timothée T. Flutre, Jessica J. Lovstad, Aarti A. Venkat, Susan W. S. W. Margulis, Jill J. Moyse, Steve S. Ross, Kathryn K. Gamble, Guy G. Sella, Carole C. Ober, Molly M. Przeworski
article
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (45), pp.18493 - 18498. ⟨10.1073/pnas.1210603109⟩
resume
The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multiallelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the A and B blood groups result from a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years-to date, the only such example in hominoids and Old World monkeys outside of the major histocompatibility complex.
DOI
DOI : 10.1073/pnas.1210603109
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https://hal.science/hal-00956369/file/18493.full.pdf BibTex

2011

Journal articles

titre
Cabomba as a model for studies of early angiosperm evolution.
auteur
Aurelie C M Vialette-Guiraud, Michael Alaux, Fabrice Legeai, Cedric Finet, Pierre Chambrier, Spencer C Brown, Aurelie Chauvet, Carlos Magdalena, Paula J Rudall, C.P. Scutt
article
Annals of Botany, 2011, 108 (4), pp.589-98. ⟨10.1093/aob/mcr088⟩
resume
BACKGROUND: The angiosperms, or flowering plants, diversified in the Cretaceous to dominate almost all terrestrial environments. Molecular phylogenetic studies indicate that the orders Amborellales, Nymphaeales and Austrobaileyales, collectively termed the ANA grade, diverged as separate lineages from a remaining angiosperm clade at a very early stage in flowering plant evolution. By comparing these early diverging lineages, it is possible to infer the possible morphology and ecology of the last common ancestor of the extant angiosperms, and this analysis can now be extended to try to deduce the developmental mechanisms that were present in early flowering plants. However, not all species in the ANA grade form convenient molecular-genetic models. SCOPE: The present study reviews the genus Cabomba (Nymphaeales), which shows a range of features that make it potentially useful as a genetic model. We focus on characters that have probably been conserved since the last common ancestor of the extant flowering plants. To facilitate the use of Cabomba as a molecular model, we describe methods for its cultivation to flowering in the laboratory, a novel Cabomba flower expressed sequence tag database, a well-adapted in situ hybridization protocol and a measurement of the nuclear genome size of C. caroliniana. We discuss the features required for species to become tractable models, and discuss the relative merits of Cabomba and other ANA-grade angiosperms in molecular-genetic studies aimed at understanding the origin of the flowering plants.
DOI
DOI : 10.1093/aob/mcr088
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https://hal.science/hal-00855948/file/Ann%20Bot-2011-Vialette-Guiraud-589-98_1.pdf BibTex
titre
The gypsy database (GyDB) of mobile genetic elements: release 2.0
auteur
Carlos Llorens, Ricardo Futami, Laura Covelli, Laura Dominguez-Escriba, Jose M. Viu, Daniel Tamarit, Jose Aguilar-Rodriguez, Miguel Vicente-Ripolles, Gonzalo Fuster, Guillermo P. Bernet, Florian Maumus, Alfonso Munoz-Pomer, Jose M. Sempere, Amparo Latorre, Andrès Moya
article
Nucleic Acids Research, 2011, 39 (S1), pp.D70-D74. ⟨10.1093/nar/gkq1061⟩
resume
This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.
DOI
DOI : 10.1093/nar/gkq1061
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https://hal.inrae.fr/hal-02648997/file/Nucl.%20Acids%20Res.-2011-Llorens-D70-4_1.pdf BibTex
titre
S-MART, a software toolbox to aid RNA-seq data analysis
auteur
Matthias Zytnicki, Hadi Quesneville
article
PLoS ONE, 2011, 6 (10), pp.1-3. ⟨10.1371/journal.pone.0025988⟩
resume
High-throughput sequencing is now routinely performed in many experiments. But the analysis of the millions of sequences generated, is often beyond the expertise of the wet labs who have no personnel specializing in bioinformatics. Whereas several tools are now available to map high-throughput sequencing data on a genome, few of these can extract biological knowledge from the mapped reads. We have developed a toolbox called S-MART, which handles mapped RNA-Seq data. SMART is an intuitive and lightweight tool which performs many of the tasks usually required for the analysis of mapped RNA-Seq reads. S-MART does not require any computer science background and thus can be used by all of the biologist community through a graphical interface. S-MART can run on any personal computer, yielding results within an hour even for Gb of data for most queries. S-MART may perform the entire analysis of the mapped reads, without any need for other ad hoc scripts. With this tool, biologists can easily perform most of the analyses on their computer for their RNA-Seq data, from the mapped data to the discovery of important loci.
DOI
DOI : 10.1371/journal.pone.0025988
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https://hal.inrae.fr/hal-02645963/file/journal.pone.0025988_1.pdf BibTex
titre
Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis
auteur
Ikhlak Ahmed, Alexis Sarazin, Chris Bowler, Vincent Colot, Hadi Quesneville
article
Nucleic Acids Research, 2011, 39 (16), pp.6919-6931. ⟨10.1093/nar/gkr324⟩
resume
Transposable elements (TEs) and their relics play major roles in genome evolution. However, mobilization of TEs is usually deleterious and strongly repressed. In plants and mammals, this repression is typically associated with DNA methylation, but the relationship between this epigenetic mark and TE sequences has not been investigated systematically. Here, we present an improved annotation of TE sequences and use it to analyze genome-wide DNA methylation maps obtained at single-nucleotide resolution in Arabidopsis. We show that although the majority of TE sequences are methylated, similar to 26% are not. Moreover, a significant fraction of TE sequences densely methylated at CG, CHG and CHH sites (where H = A, T or C) have no or few matching small interfering RNA (siRNAs) and are therefore unlikely to be targeted by the RNA-directed DNA methylation (RdDM) machinery. We provide evidence that these TE sequences acquire DNA methylation through spreading from adjacent siRNA-targeted regions. Further, we show that although both methylated and unmethylated TE sequences located in euchromatin tend to be more abundant closer to genes, this trend is least pronounced for methylated, siRNA-targeted TE sequences located 5' to genes. Based on these and other findings, we propose that spreading of DNA methylation through promoter regions explains at least in part the negative impact of siRNA-targeted TE sequences on neighboring gene expression.
DOI
DOI : 10.1093/nar/gkr324
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https://hal.inrae.fr/hal-02647005/file/Nucl.%20Acids%20Res.-2011-Ahmed-6919-31_1.pdf BibTex
titre
In search of lost trajectories: recovering the diversification of transposable elements
auteur
Timothée T. Flutre, Emmanuelle E. Permal, Hadi H. Quesneville
article
Mobile Genetic Elements, 2011, 1 (2), pp.151-154. ⟨10.4161/mge.1.2.17094⟩
resume
Transposable elements (TEs) are DNA sequences that have the capacity to move and duplicate within genomes, and occasionally between them. They are present in almost all species and are especially prevalent in eukaryotes where they can account for most of the genomic content. As a result of their dynamics and their mere presence, TEs can profoundly shape genomes and gene expression. With the current pace of sequencing technology improvement, a rapidly increasing number of genomes, particularly from non-model species, are being sequenced. However, the complete annotation of these genomes and especially of the TEs they contain, still poses fundamental difficulties. In a recent article, we presented a combined method that automatically annotates TEs with accuracy and sensitivity, and takes their diversification dynamics into account in the de novo annotation process. Here, we further discuss several additional aspects of our results, notably in the light of our knowledge of TE dynamics and the conceptual model behind the TE detection algorithms currently in use. In addition, we propose a new approach that uses simulations to improve algorithm performance.
DOI
DOI : 10.4161/mge.1.2.17094
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titre
Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea
auteur
Joelle J. Amselem, Christina A. Cuomo, Jan A. L. van Kan, Muriel Viaud, Ernesto P. Benito, Arnaud Couloux, Pedro M Coutinho, Ronald P. de Vries, Paul S. Dyer, Sabine, Helma Fillinger-David, Elisabeth Fournier, Lilian Gout, Matthias Hahn, Linda Kohn, Nicolas Lapalu, Kim M. Plummer, Jean-Marc Pradier, Emmanuel Quevillon, Amir Sharon, Adeline Simon, Arjen ten Have, Bettina Tudzynski, Paul Tudzynski, Patrick Wincker, Marion Andrew, Véronique Anthouard, Ross E. Beever, Rolland Beffa, Isabelle Benoit, Ourdia Bouzid, Baptiste Brault, Zehua Chen, Mathias Choquer, Jerome Collemare, Pascale Cotton, Etienne Danchin, Corinne da Silva, Angelique Gautier, Corinne Giraud-Delville, Tatiana Giraud, Celedonio Gonzalez, Sandrine Grossetete, Ulrich Gueldener, Bernard Henrissat, Barbara J. Howlett, Chinnappa Kodira, Matthias Kretschmer, Anne Lappartient, Michaela Leroch, Caroline Levis, Evan Mauceli, Cécile Neuvéglise, Birgitt Oeser, Matthew Pearson, Julie Poulain, Nathalie Poussereau, Hadi Quesneville, Christine Rascle, Julia Schumacher, Béatrice Segurens, Adrienne Sexton, Evelyn Silva, Catherine Sirven, Darren M. Soanes, Nicholas J. Talbot, Matt Templeton, Chandri Yandava, Oded Yarden, Qiandong Zeng, Jeffrey A. Rollins, Marc-Henri Lebrun, Marty Dickman
article
PLoS Genetics, 2011, 7 (8), ⟨10.1371/journal.pgen.1002230⟩
resume
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.
DOI
DOI : 10.1371/journal.pgen.1002230
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https://hal.science/hal-01190236/file/journal.pgen.1002230.PDF BibTex
titre
Stemming epigenetics in marine stramenopiles
auteur
Florian Maumus, Pablo Rabinowicz, Chris Bowler, Máximo Rivarola
article
Current Genomics, 2011, 12 (5), pp.357-370
resume
Epigenetics include DNA methylation, the modification of histone tails that affect chromatin states, and small RNAs that are involved in the setting and maintenance of chromatin modifications. Marine stramenopiles (MAS), which are a diverse assemblage of algae that acquired photosynthesis from secondary endosymbiosis, include single-celled organisms such as diatoms as well as multicellular forms such as brown algae. The recent publication of two diatom genomes that diverged similar to 90 million years ago (mya), as well as the one of a brown algae that diverged from diatoms similar to 250 Mya, provide a great system of related, yet diverged set of organisms to compare epigenetic marks and their relationships. For example, putative DNA methyltransferase homologues were found in diatoms while none could be identified in the brown algal genome. On the other hand, no canonical DICER-like protein was found in diatoms in contrast to what is observed in brown algae. A key interest relies in understanding the adaptive nature of epigenetics and its inheritability. In contrast to yeast that lack DNA methylation, homogeneous cultures of diatoms constitute an attractive system to study epigenetic changes in response to environmental conditions such as nutrient-rich to nutrient-poor transitions which is especially relevant because of their ecological importance. P. tricornutum is also of outstanding interest because it is observed as three different morphotypes and thus constitutes a simple and promising model for the study of the epigenetic phenomena that accompany cellular differentiation. In this review we focus on the insights obtained from MAS comparative genomics and epigenomic analyses.
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https://hal.inrae.fr/hal-02644011/file/Maumus_1.pdf BibTex
titre
Considering transposable element diversification in de novo annotation approaches
auteur
Timothée T. Flutre, Elodie E. Duprat, Catherine C. Feuillet, Hadi H. Quesneville
article
PLoS ONE, 2011, 6 (1), pp.1-15. ⟨10.1371/journal.pone.0016526⟩
resume
Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species.
DOI
DOI : 10.1371/journal.pone.0016526
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https://hal.science/hal-00956366/file/journal.pone.0016526_1.pdf BibTex
titre
Obligate biotrophy features unraveled by the genomic analysis of rust fungi
auteur
Sébastien Duplessis, Christina A C. A. Cuomo, Yao-Cheng Y.-C. Lin, Andrea Aerts, Emilie Tisserant, Claire Veneault-Fourrey, David L. Joly, Stéphane S. Hacquard, Joelle Amselem, Brandi B. Cantarel, Readman R. Chin, Pedro M Coutinho, Nicolas N. Feau, Matthew M. Field, Pascal Frey, Éric Gelhaye, Jonathan J. Goldberg, Manfred G M. G. Grabherr, Chimappa D C. D. Kodira, Annegret Kohler, Ursula U. Kues, Erika A E. A. Lindquist, Susan S. Lucas, Rohit R. Mago, Evan E. Mauceli, Emmanuelle Morin, Claude C. Murat, Jasmyn J. J. J. Pangilinan, Robert R. Park, Matthew M. Pearson, Hadi H. Quesneville, Nicolas Rouhier, Sharadha Sakthikumar, Asaf A A. A. Salamov, Jeremy J. Schmutz, Benjamin B. Selles, Harris Shapiro, Philippe P. Tanguay, Gerald A G. A. Tuskan, Bernard Henrissat, Yves Y. van de Peer, Pierre P. Rouze, Jeffrey G. J. G. Ellis, Peter N P. N. Dodds, Jacqueline E. J. E. Schein, Shaobin S. Zhong, Richard C R. C. Hamelin, Igor V I. V. Grigoriev, Les J L. J. Szabo, Francis Martin
article
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (22), pp.9166-9171. ⟨10.1073/pnas.1019315108⟩
resume
Rust fungi are some of the most devastating pathogens of crop plants. They are obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart from their hosts. Their lifestyle has slowed the dissection of molecular mechanisms underlying host invasion and avoidance or suppression of plant innate immunity. We sequenced the 101-Mb genome of Melampsora larici-populina, the causal agent of poplar leaf rust, and the 89-Mb genome of Puccinia graminis f. sp. tritici, the causal agent of wheat and barley stem rust. We then compared the 16,399 predicted proteins of M. larici-populina with the 17,773 predicted proteins of P. graminis f. sp tritici. Genomic features related to their obligate biotrophic lifestyle include expanded lineage-specific gene families, a large repertoire of effector-like small secreted proteins, impaired nitrogen and sulfur assimilation pathways, and expanded families of amino acid and oligopeptide membrane transporters. The dramatic up-regulation of transcripts coding for small secreted proteins, secreted hydrolytic enzymes, and transporters in planta suggests that they play a role in host infection and nutrient acquisition. Some of these genomic hallmarks are mirrored in the genomes of other microbial eukaryotes that have independently evolved to infect plants, indicating convergent adaptation to a biotrophic existence inside plant cells.
DOI
DOI : 10.1073/pnas.1019315108
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https://hal.science/hal-01000169/file/43777_20110621115023025_1.pdf BibTex
titre
Formation of plant metabolic gene clusters within dynamic chromosomal regions
auteur
Ben Field, Anna-Sophie Lavier-Fiston, Ariane Kemen, Katrin Geisler, Hadi Quesneville, Anne E. Osbourn
article
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (38), pp.16116-16121. ⟨10.1073/pnas.1109273108⟩
resume
In bacteria, genes with related functions often are grouped together in operons and are cotranscribed as a single polycistronic mRNA. In eukaryotes, functionally related genes generally are scattered across the genome. Notable exceptions include gene clusters for catabolic pathways in yeast, synthesis of secondary metabolites in filamentous fungi, and the major histocompatibility complex in animals. Until quite recently it was thought that gene clusters in plants were restricted to tandem duplicates (for example, arrays of leucine-rich repeat disease-resistance genes). However, operon-like clusters of coregulated nonhomologous genes are an emerging theme in plant biology, where they may be involved in the synthesis of certain defense compounds. These clusters are unlikely to have arisen by horizontal gene transfer, and the mechanisms behind their formation are poorly understood. Previously in thale cress (Arabidopsis thaliana) we identified an operon-like gene cluster that is required for the synthesis and modification of the triterpene thalianol. Here we characterize a second operon-like triterpene cluster (the marneral cluster) from A. thaliana, compare the features of these two clusters, and investigate the evolutionary events that have led to cluster formation. We conclude that common mechanisms are likely to underlie the assembly and control of operon-like gene clusters in plants.
DOI
DOI : 10.1073/pnas.1109273108
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https://hal.inrae.fr/hal-02647681/file/2011_Field_Proceedings%20of%20the%20National%20Academy%20of%20Sciences%20of%20the%20United%20States%20of%20America_1.pdf BibTex
titre
Molecular, genetic and transcriptional evidence for a role of VvAGL11 in stenospermocarpic seedlessness in grapevine
auteur
Nilo Mejia, Braulio Soto, Marcos Guerrero, Ximena Casanueva, Cléa Houel, Maria de Los Angeles Miccono, Rodrigo Ramos, Loic L. Le Cunff, Jean-Michel Boursiquot, Patricio Hinrichsen, Anne-Francoise A.-F. Adam-Blondon
article
BMC Biology, 2011, 11, 18 p. ⟨10.1186/1471-2229-11-57⟩
resume
Background: Stenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level. Results: Genetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development. Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11’s regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation. For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site. Conclusion: We propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the Dlineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.
DOI
DOI : 10.1186/1471-2229-11-57
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https://hal.inrae.fr/hal-02644774/file/Publis011-agap-049_Mejia_BMC_Molecular%20genetic%20transcriptional%20grapevine_1.pdf BibTex
titre
Correlation of LNCR rasiRNAs expression with heterochromatin formation during development of the holocentric insect spodoptera frugiperda
auteur
Slavica Stanojcic, Sylvie Gimenez, Emmanuelle E. Permal, Francois F. Cousserans, Hadi Quesneville, Philippe Fournier, Emmanuelle d'Alençon
article
PLoS ONE, 2011, 6 (9), pp.1-14. ⟨10.1371/journal.pone.0024746⟩
resume
Repeat-associated small interfering RNAs (rasiRNAs) are derived from various genomic repetitive elements and ensure genomic stability by silencing endogenous transposable elements. Here we describe a novel subset of 46 rasiRNAs named LNCR rasiRNAs due to their homology with one long non-coding RNA (LNCR) of Spodoptera frugiperda. LNCR operates as the intermediate of an unclassified transposable element (TE-LNCR). TE-LNCR is a very invasive transposable element, present in high copy numbers in the S. frugiperda genome. LNCR rasiRNAs are single-stranded RNAs without a prominent nucleotide motif, which are organized in two distinct, strand-specific clusters. The expression of LNCR and LNCR rasiRNAs is developmentally regulated. Formation of heterochromatin in the genomic region where three copies of the TE-LNCR are embedded was followed by chromatin immunoprecipitation (ChIP) and we observed this chromatin undergo dynamic changes during development. In summary, increased LNCR expression in certain developmental stages is followed by the appearance of a variety of LNCR rasiRNAs which appears to correlate with subsequent accumulation of a heterochromatic histone mark and silencing of the genomic region with TE-LNCR. These results support the notion that a repeat-associated small interfering RNA pathway is linked to heterochromatin formation and/or maintenance during development to establish repression of the TE-LNCR transposable element. This study provides insights into the rasiRNA silencing pathway and its role in the formation of fluctuating heterochromatin during the development of one holocentric organism.
DOI
DOI : 10.1371/journal.pone.0024746
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https://hal.inrae.fr/hal-02651170/file/Slavica%20Stanojcic_1.pdf BibTex
titre
BlastR-fast and accurate database searches for non-coding RNAs
auteur
Giovanni Bussotti, Emanuele Raineri, Ionas Erb, Matthias Zytnicki, Andreas Wilm, Emmanuel Beaudoing, Philipp Bucher, Cedric Notredame
article
Nucleic Acids Research, 2011, 39 (16), pp.6886-6895. ⟨10.1093/nar/gkr335⟩
resume
We present and validate BlastR, a method for efficiently and accurately searching non-coding RNAs. Our approach relies on the comparison of di-nucleotides using BlosumR, a new log-odd substitution matrix. In order to use BlosumR for comparison, we recoded RNA sequences into protein-like sequences. We then showed that BlosumR can be used along with the BlastP algorithm in order to search non-coding RNA sequences. Using Rfam as a gold standard, we benchmarked this approach and show BlastR to be more sensitive than BlastN. We also show that BlastR is both faster and more sensitive than BlastP used with a single nucleotide log-odd substitution matrix. BlastR, when used in combination with WU-BlastP, is about 5% more accurate than WU-BlastN and about 50 times slower. The approach shown here is equally effective when combined with the NCBI-Blast package. The software is an open source freeware available from www.tcoffee.org/blastr.html.
DOI
DOI : 10.1093/nar/gkr335
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https://hal.inrae.fr/hal-02644812/file/Nucl.%20Acids%20Res.-2011-Bussotti-6886-95_1.pdf BibTex
titre
Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
auteur
T. Rouxel, J. Grandaubert, Jk. Hane, Claire Hoede, Angela P. van de Wouw, A. Couloux, V. Dominguez, Véronique Anthouard, P. Bally, S. Bourras, Anton J. Cozijnsen, Lynda M. Ciuffetti, Alexandre A. Degrave, A. Dilmaghani, L. Duret, I. Fudal, Stephen B. Goodwin, L. Gout, N. Glaser, J. Linglin, Gert H. J. Kema, Nicolas Lapalu, Christophe B. Lawrence, K. May, M. Meyer, B. Ollivier, J. Poulain, Conrad L. Schoch, A. Simon, Joseph W. Spatafora, A. Stachowiak, B. Gillian Turgeon, Brett M. Tyler, D. Vincent, J. Weissenbach, J. Amselem, H. Quesneville, Richard P. Oliver, P. Wincker, Marie-Hélène Balesdent, Barbara J. Howlett
article
Nature Communications, 2011, 2, pp.202. ⟨10.1038/ncomms1189⟩
resume
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints.
DOI
DOI : 10.1038/ncomms1189
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https://institut-agro-rennes-angers.hal.science/hal-00841751/file/ncomms1189.pdf BibTex

2010

Journal articles

titre
Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements.
auteur
E. d'Alençon, H. Sezutsu, Fabrice Legeai, E. Permal, S. Bernard-Samain, S. Gimenez, C. Gagneur, F. Cousserans, M. Shimomura, A. Brun-Barale, T. Flutre, A. Couloux, P. East, K. Gordon, K. Mita, H. Quesneville, P. Fournier, R. Feyereisen
article
Proceedings of the National Academy of Sciences of the United States of America, 2010, 107 (17), pp.7680-5. ⟨10.1073/pnas.0910413107⟩
resume
The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera. We sequenced BACs from two major pests, the noctuid moths Helicoverpa armigera and Spodoptera frugiperda, corresponding to 15 regions distributed on 11 B. mori chromosomes, each BAC/region being anchored by known orthologous gene(s) to analyze syntenic relationships and genome rearrangements among the three species. Nearly 300 genes and numerous transposable elements were identified, with long interspersed nuclear elements and terminal inverted repeats the most abundant transposable element classes. There was a high degree of synteny conservation between B. mori and the two noctuid species. Conserved syntenic blocks of identified genes were very small, however, approximately 1.3 genes per block between B. mori and the two noctuid species and 2.0 genes per block between S. frugiperda and H. armigera. This corresponds to approximately two chromosome breaks per Mb DNA per My. This is a much higher evolution rate than among species of the Drosophila genus and may be related to the holocentric nature of the lepidopteran genomes. We report a large cluster of eight members of the aminopeptidase N gene family that we estimate to have been present since the Jurassic. In contrast, several clusters of cytochrome P450 genes showed multiple lineage-specific duplication events, in particular in the lepidopteran CYP9A subfamily. Our study highlights the value of the silkworm genome as a reference in lepidopteran comparative genomics.
DOI
DOI : 10.1073/pnas.0910413107
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https://inria.hal.science/inria-00537908/file/45295_20110131040726116_1.pdf BibTex
titre
Soft arc consistency revisited
auteur
Martin Cooper, Simon de Givry, Marti Sanchez, Thomas Schiex, Matthias Zytnicki, Tomas Werner
article
Artificial Intelligence, 2010, 174, pp.449-478. ⟨10.1016/j.artint.2010.02.001⟩
resume
The Valued Constraint Satisfaction Problem (VCSP) is a generic optimization problem defined by a network of local cost functions defined over discrete variables. It has applications in Artificial Intelligence, Operations Research, Bioinformatics and has been used to tackle optimization problems in other graphical models (including discrete Markov Random Fields and Bayesian Networks). The incremental lower bounds produced by local consistency filtering are used for pruning inside Branch and Bound search. In this paper, we extend the notion of arc consistency by allowing fractional weights and by allowing several arc consistency operations to be applied simultaneously. Over the rationals and allowing simultaneous operations, we show that an optimal arc consistency closure can theoretically be determined in polynomial time by reduction to linear programming. This defines Optimal Soft Arc Consistency (OSAC). To reach a more practical algorithm, we show that the existence of a sequence of arc consistency operations which increases the lower bound can be detected by establishing arc consistency in a classical Constraint Satisfaction Problem (CSP) derived from the original cost function network. This leads to a new soft arc consistency method, called, Virtual Arc Consistency which produces improved lower bounds compared with previous techniques and which can solve submodular cost functions. These algorithms have been implemented and evaluated on a variety of problems, including two difficult frequency assignment problems which are solved to optimality for the first time. Our implementation is available in the open source toulbar2 platform.
DOI
DOI : 10.1016/j.artint.2010.02.001
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titre
Genome expansion and gene loss in powdery mildew fungi reveal tradeoffs in extreme parasitism
auteur
Pietro D Spanu, James C Abbott, Joelle J. Amselem, Timothy A. Burgis, Darren M Soanes, Kurt Stueber, Emiel Ver Loren van Themaat, James K.M Brown, Sarah A Butcher, Sarah J Gurr, Marc-Henri M.-H. Lebrun, Christopher J Ridout, Paul Schulze-Lefert, Nicolas J. Talbot, Nahal Ahmadinejad, Christian Ametz, Geraint R Barton, Mariam Benjdia, Przemyslaw Bidzinski, Laurence V Bindschedler, Maike Both, Marin T Brewer, Lance Cadle-Davidson, Molly M Cadle-Davidson, Jérôme Collemare, Raimer Cramer, Omer Frenkel, Dale Godfrey, James J. Harriman, Claire Hoede, Brian C. King, Sven Klages, Jochen) Kleemann, Daniela Knoll, Prasanna S Kotis, Jonathan J. Kreplak, Francisco J Lopez-Ruiz, Xunli Lu, Takaki Maekawa, Siraprapa Mahanil, Cristina Micali, Michael G Milgroom, Giovanni Montana, Sandra Noir, Richard O'Connell, Simone Oberhaensli, Francis Parlange, Carsten Pedersen, Hadi Quesneville, Richard Reinhardt, Matthias Rott, Soledad Sacristán, Sarah M Schmidt, Moritz Schoen, Pari Skamnioti, Hans Sommer, Amber Stephens, Hiroyuki Takahara, Hans Thordal-Christensen, Marielle Vigouroux, Ralf Wessling, Thomas Wicker, Ralf Panstruga
article
Science, 2010, 330 (6010), pp.1543-1546. ⟨10.1126/science.1194573⟩
resume
Powdery mildews are phytopathogens whose growth and reproduction are entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis of barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well as a comparison with the analysis of two powdery mildews pathogenic on dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, and gene losses. The missing genes encode enzymes of primary and secondary metabolism, carbohydrate-active enzymes, and transporters, probably reflecting their redundancy in an exclusively biotrophic life-style. Among the 248 candidate effectors of pathogenesis identified in the Blumeria genome, very few (less than 10) define a core set conserved in all three mildews, suggesting that most effectors represent species-specific adaptations.
DOI
DOI : 10.1126/science.1194573
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titre
Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
auteur
Francis Martin, Annegret Kohler, Claude Murat, Raffaella Balestrini, Pedro M Coutinho, Olivier Jaillon, Barbara Montanini, Emmanuelle Morin, Benjamin Noel, Riccardo Percudani, Betina M Porcel, Andrea Rubini, Antonella Amicucci, Joelle Amselem, Véronique Anthouard, Sergio Arcioni, François Artiguenave, Jean-Marc Aury, Paola Ballario, Angelo Bolchi, Andrea Brenna, Annick Brun, Marc Buée, Brandi Cantarel, Gérard Chevalier, Arnaud Couloux, Corinne da Silva, France Denoeud, Sébastien Duplessis, Stefano Ghignone, Benoît Hilselberger, Mirco Iotti, Benoit Marçais, Antonietta Mello, Michele Miranda, Giovanni Pacioni, Hadi Quesneville, Claudia Riccioni, Roberta Ruotolo, Richard Splivallo, Vilberto Stocchi, Emilie Tisserant, Arturo Roberto Viscomi, Alessandra Zambonelli, Elisa Zampieri, Bernard Henrissat, Marc-Henri Lebrun, Francesco Paolocci, Paola Bonfante, Simone Ottonello, Patrick Wincker
article
Nature, 2010, 464 (7291), pp.1033-1038. ⟨10.1038/nature08867⟩
resume
The Périgord black truffle ($Tuber\ melanosporum$ Vittad.) and the Piedmont white truffle dominate today's truffle market. The hypogeous fruiting body of $T.\ melanosporum$ is a gastronomic delicacy produced by an ectomycorrhizal symbiont endemic to calcareous soils in southern Europe. The worldwide demand for this truffle has fuelled intense efforts at cultivation. Identification of processes that condition and trigger fruit body and symbiosis formation, ultimately leading to efficient crop production, will be facilitated by a thorough analysis of truffle genomic traits. In the ectomycorrhizal $Laccaria\ bicolor$, the expansion of gene families may have acted as a 'symbiosis toolbox'. This feature may however reflect evolution of this particular taxon and not a general trait shared by all ectomycorrhizal species. To get a better understanding of the biology and evolution of the ectomycorrhizal symbiosis, we report here the sequence of the haploid genome of $T.\ melanosporum$, which at $\sim$125 megabases is the largest and most complex fungal genome sequenced so far. This expansion results from a proliferation of transposable elements accounting for $\sim$58% of the genome. In contrast, this genome only contains $\sim$7,500 protein-coding genes with very rare multigene families. It lacks large sets of carbohydrate cleaving enzymes, but a few of them involved in degradation of plant cell walls are induced in symbiotic tissues. The latter feature and the upregulation of genes encoding for lipases and multicopper oxidases suggest that $T.\ melanosporum$ degrades its host cell walls during colonization. Symbiosis induces an increased expression of carbohydrate and amino acid transporters in both $L.\ bicolor$ and $T.\ melanosporum$, but the comparison of genomic traits in the two ectomycorrhizal fungi showed that genetic predispositions for symbiosis $-$'the symbiosis toolbox'$-$ evolved along different ways in ascomycetes and basidiomycetes
DOI
DOI : 10.1038/nature08867
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https://cea.hal.science/cea-00907731/file/mar.pdf BibTex
titre
The $Ectocarpus$ genome and the independent evolution of multicellularity in brown algae
auteur
J. Mark Cock, Lieven Sterck, Pierre Rouzé, Delphine Scornet, Andrew E. Allen, Grigoris Amoutzias, Véronique Anthouard, François Artiguenave, Jean-Marc Aury, Jonathan H Badger, Bank Beszteri, Kenny Billiau, Eric Bonnet, John H. Bothwell, Chris Bowler, Catherine Boyen, Colin Brownlee, Carl J Carrano, Bénédicte Charrier, Ga Youn Cho, Susana M Coelho, Jonas Collén, Erwan Corre, Corinne da Silva, Ludovic Delage, Nicolas Delaroque, Simon M. Dittami, Sylvie Doulbeau, Marek Elias, Garry Farnham, Claire M. M. Gachon, Bernhard Gschloessl, Svenja Heesch, Kamel Jabbari, Claire Jubin, Hiroshi Kawai, Kei Kimura, Bernard Kloareg, Frithjof C. Küpper, Daniel Lang, Aude Le Bail, Catherine Leblanc, Patrice Lerouge, Martin Lohr, Pascal J Lopez, Cindy Martens, Florian Maumus, Gurvan Michel, Diego Miranda-Saavedra, Julia Morales, Hervé Moreau, Taizo Motomura, Chikako Nagasato, Carolyn A Napoli, David R Nelson, Pi Nyvall-Collén, Akira F Peters, Cyril Pommier, Philippe Potin, Julie Poulain, Hadi Quesneville, Betsy Read, Stefan A. Rensing, Andrés Ritter, Sylvie Rousvoal, Manoj Samanta, Gaelle Samson, Declan C Schroeder, Béatrice Ségurens, Martina Strittmatter, Thierry Tonon, James W Tregear, Klaus Valentin, Peter von Dassow, Takahiro Yamagishi, Yves van de Peer, Patrick Wincker
article
Nature, 2010, 465 (7298), pp.617-621. ⟨10.1038/nature09016⟩
resume
Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related(1). These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae(2-5), closely related to the kelps(6,7) (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic(2) approaches to explore these and other(4,5) aspects of brown algal biology further.
DOI
DOI : 10.1038/nature09016
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https://cea.hal.science/cea-00906990/file/Coc.pdf BibTex
titre
Long noncoding RNAs with enhancer-like function in human cells
auteur
Thomas Derrien, Malte Beringer, Kiranmai Gumireddy, Alessandro Gardini, Giovanni Bussotti, Fan Lai, Matthias Zytnicki, Cedric Notredame, Qihong Huang, Roderic Guigo, Ramin Shiekhattar
article
Cell, 2010, 143 (1), pp.46-58. ⟨10.1016/j.cell.2010.09.001⟩
resume
While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation.
DOI
DOI : 10.1016/j.cell.2010.09.001
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https://hal.inrae.fr/hal-02668720/file/1-s2.0-S0092867410010111-main_1.pdf BibTex

Theses

titre
The annotation of transposable elements through the understanding of their diversification
auteur
Timothée Flutre
article
Sciences du Vivant [q-bio]. Université Paris-Diderot - Paris VII, 2010. Français. ⟨NNT : ⟩
resume
Any living organism is the result of complex interactions between its genome and its environment, interactions characterizedby transfers of matter and energy required for the survival of the organism and the transmission of its genome. Since the discovery in the years 1910 that the chromosome is the mechanical basis of the genetic information, the biologists study genomes in order to decipher the mecanisms and processes operating in the development of organisms and the evolution of populations. Thanks to the technological improvements of the last decades, several genomes were fully sequenced, their number increasing quickly, but they are far from being deciphered. Indeed, some of their components, the transposable elements, are still not well understood, although they were detected in almost every species studied so far, and they can account for up to 90% of their genome. Transposable elements are DNA sequences that can move and duplicate within genomes. They hence have a major impact on genome structure but also on the expression of neighbouring genes, notably via epigenetic mechanisms. Their evolution is also peculiar as they have a non-mendelian vertical transmission and as numerous cases of horizontal transfers were highlighted. However, except for some model organisms for which reference quences are available, the annotation of transposable elements often corresponds to a bottleneck in the analysis of genomic sequences. Moreover, comparative genomics studies have shown that genomes are much more dynamic than previously expected, particularly in plants, thus making even more difficult the precise annotation of transposable elements. During my PhD work, I started by comparing existing computer programs used in de novo approaches of transposable element identification. In this aim, I designed a test protocol on the genomes of Drosophila melanogaster and Arabidopsis thaliana. As a result, I proposed a de novo approach combining several tools, thus enabling the automatic recovery of a great numberof reference sequences. Moreover, I showed that our approach highlighted the structural variations present within well-known families, notably by distinguishing structural variants belonging to a same family of transposable elements, thus reflecting the diversification of such families during their evolution. This approach was implemented in a package (REPET) making possible the analysis of transposable elements in numerous genomes from plants, insects and fungi among others. This work lead to a roadmap describing, from a practical point of view, how to annotate the transposable element content of any newly sequenced genome. As a consequence, many questions about the impact of these elements on the evolution of genome structure can now be tackled using several genomes more or less related withe ach other. I also propose several perspectives, notably the simulation of the data required for the improvement of the tools, a way complementary to the modeling of transposable element dynamics.
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https://theses.hal.science/tel-00560242/file/TimFlutre_thesis_20101003.pdf BibTex
titre
The annotation of transposable elements through the understanding of their diversification
auteur
Timothée Flutre
article
Sciences du Vivant [q-bio]. Université Paris Diderot - Paris 7, 2010. Français. ⟨NNT : ⟩
resume
Tout organisme vivant est le produit d'interactions complexes entre son génome et son environnement, interactions caractérisées par des échanges de matière et d'énergie indispensables à la survie de l'organisme et la transmission de son génome. Depuis la découverte dans les années 1910 que le chromosome est le support de l'information génétique, les biologistes étudient les génomes afin de décrypter les mécanismes et processus à l’œuvre dans le développement des organismes et l'évolution des populations. Grâce aux améliorations technologiques des dernières décennies, plusieurs génomes ont été entièrement séquencés, leur nombre s'accroissant rapidement, mais ils sont loin d'être décryptés pour autant. En effet, certains de leurs composants, les éléments transposables, sont encore mal compris, bien qu'ils aient été détectés chez quasiment toutes les espèces étudiées, et qu'ils puissent représenter jusqu'à 90% du contenu total de leurs génomes. Les éléments transposables sont des fragments du génome possédant la particularité d'être mobiles. Ils ont donc un impact majeur sur la structure des génomes mais également sur l'expression des gènes avoisinants, notamment via des mécanismes épigénétiques. Leur évolution est aussi particulière étant donné qu'ils ont une transmission verticale non-mendélienne et que de nombreux cas de transferts horizontaux ont été mis en évidence. Mais, à part dans le cas de certains organismes modèles pour lesquels nous disposons de séquences de référence, l'annotation des éléments transposables représente souvent un goulot d'étranglement dans l'analyse des séquences génomiques. A cela s'ajoute le fait que les études de génomique comparée montrent que les génomes sont bien plus dynamiques qu'on ne le croyait, en particulier ceux des plantes, ce qui complique d'autant l'annotation précise des éléments transposables. Pendant mes travaux de thèse, j'ai commencé par comparer les programmes informatiques existants utilisés dans les approches d'annotation de novo des éléments transposables. Pour cela, j'ai mis au point un protocole de test sur les génomes de Drosophila melanogaster et Arabidopsis thaliana. Ceci m'a permis de proposer une approche de novo combinant plusieurs outils, capable ainsi de reconstruire automatiquement un grand nombre de séquences de référence. De plus, j'ai pu montrer que notre approche mettait en évidence les variations structurales au sein de familles bien connues, notamment en distinguant des variants structuraux appartenant à une même famille d'éléments transposables, reflétant ainsi la diversification de ces familles au cours de leur évolution. Cette approche a été implémentée dans une suite d'outils (REPET) rendant possible l'analyse des éléments transposables de nombreux génomes de plantes, insectes, champignons et autres. Ces travaux ont abouti à une feuille de route décrivant de manière pratique comment annoter le contenu en éléments transposables de tout génome nouvellement séquencé. Par conséquent, de nombreuses questions concernant l'impact de ces éléments sur l'évolution de la structure des génomes peuvent maintenant être abordées chez différents génomes plus ou moins proches. Je propose également plusieurs pistes de recherche, notamment la simulation des données nécessaires à l'amélioration des algorithmes de détection, démarche complémentaire de la modélisation de la dynamique des éléments transposables.
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https://hal.inrae.fr/tel-02824845/file/TFlutre_these_20101028_1.pdf BibTex