Publications HAL du labo/EPI 104665;1002240

2022

Journal articles

titre
CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes
auteur
Héléna Vassilieff, Sana Haddad, Véronique Jamilloux, Nathalie Choisne, Vikas Sharma, Delphine Giraud, Mariène Wan, Saad Serfraz, Andrew D. W. Geering, Pierre-Yves Teycheney, Florian Maumus
article
Mobile DNA, 2022, 13, pp.31. ⟨10.1186/s13100-022-00288-w⟩
resume
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae . We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.
DOI
DOI : 10.1186/s13100-022-00288-w
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https://hal.inrae.fr/hal-03883611/file/s13100-022-00288-w.pdf BibTex
titre
Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative
auteur
Peter Langridge, Michael Alaux, Nuno Felipe Almeida, Karim Ammar, Michael Baum, Faouzi Bekkaoui, Alison R Bentley, Brian L Beres, Bettina Berger, Hans-Joachim Braun, Gina Brown-Guedira, Christopher James Burt, Mario Jose Caccamo, Luigi Cattivelli, Gilles Charmet, Peter Civan, Sylvie Cloutier, Jean-Pierre Cohan, Pierre J Devaux, Fiona M Doohan, M. Fernanda Dreccer, Moha Ferrahi, Silvia E Germán, Stephen B Goodwin, Simon Griffiths, Carlos Guzmán, Hirokazu Handa, Malcolm John Hawkesford, Zhonghu He, Eric Huttner, Tatsuya M Ikeda, Benjamin Kilian, Ian Philip King, Julie King, John A Kirkegaard, Jacob Lage, Jacques Le Gouis, Suchismita Mondal, Ewen Mullins, Frank Ordon, Jose Ivan Ortiz-Monasterio, Hakan Özkan, İrfan Öztürk, Silvia A Pereyra, Curtis J Pozniak, Hadi Quesneville, Martín C Quincke, Greg John Rebetzke, Jochen Christoph Reif, Teresa Saavedra-Bravo, Ulrich Schurr, Shivali Sharma, Sanjay Kumar Singh, Ravi P Singh, John W Snape, Wuletaw Tadesse, Hisashi Tsujimoto, Roberto Tuberosa, Tim G Willis, Xueyong Zhang
article
Agronomy, 2022, 12 (11), pp.2767. ⟨10.3390/agronomy12112767⟩
resume
Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper.
DOI
DOI : 10.3390/agronomy12112767
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https://hal.inrae.fr/hal-03942478/file/2022_Langridge-P_agronomy-12-02767%20%281%29.pdf BibTex
titre
Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci
auteur
Clément Gilbert, Florian Maumus
article
Genome Biology and Evolution, 2022, 14 (10), ⟨10.1093/gbe/evac141⟩
resume
Abstract The extent to which horizontal gene transfer (HGT) has shaped eukaryote evolution remains an open question. Two recent studies reported four plant-like genes acquired through two HGT events by the whitefly Bemisia tabaci, a major agricultural pest (Lapadula WJ, Mascotti ML, Juri Ayub M. 2020. Whitefly genomes contain ribotoxin coding genes acquired from plants. Sci Rep. 10(1):15503; Xia J, et al. 2021. Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell 184(7):1693–1705 e1617.). Here, we uncovered a total of 49 plant-like genes deriving from at least 24 independent HGT events in the genome of the Middle East Asia Minor 1 (MEAM1) whitefly. Orthologs of these genes are present in three cryptic B. tabaci species, they are phylogenetically nested within plant sequences, they are expressed and have evolved under purifying selection. The predicted functions of these genes suggest that most of them are involved in plant–insect interactions. Thus, substantial plant-to-insect HGT may have facilitated the evolution of B. tabaci toward adaptation to a large host spectrum. Our study shows that eukaryote-to-eukaryote HGT may be relatively common in some lineages and it provides new candidate genes that may be targeted to improve current control strategies against whiteflies.
DOI
DOI : 10.1093/gbe/evac141
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https://hal.inrae.fr/hal-03846467/file/Gilbert_2022_HGTbemisia.pdf BibTex
titre
Capturing Wheat Phenotypes at the Genome Level
auteur
Babar Hussain, Bala A Akpınar, Michael Alaux, Ahmed M Algharib, Deepmala Sehgal, Zulfiqar Ali, Gudbjorg I Aradottir, Jacqueline Batley, Arnaud Bellec, Alison R Bentley, Halise B Cagirici, Luigi Cattivelli, Frédéric Choulet, James Cockram, Francesca Desiderio, Pierre Devaux, Munevver Dogramaci, Gabriel Dorado, Susanne Dreisigacker, David Edwards, Khaoula El-Hassouni, Kellye Eversole, Tzion Fahima, Melania Figueroa, Sergio Gálvez, Kulvinder S Gill, Liubov Govta, Alvina Gul, Goetz Hensel, Pilar Hernandez, Leonardo Abdiel Crespo-Herrera, Amir Ibrahim, Benjamin Kilian, Viktor Korzun, Tamar Krugman, Yinghui Li, Shuyu Liu, Amer F Mahmoud, Alexey Morgounov, Tugdem Muslu, Faiza Naseer, Frank Ordon, Etienne Paux, Dragan Perovic, Gadi V P Reddy, Jochen Christoph Reif, Matthew Reynolds, Rajib Roychowdhury, Jackie Rudd, Taner Z Sen, Sivakumar Sukumaran, Bahar Sogutmaz Ozdemir, Vijay Kumar Tiwari, Naimat Ullah, Turgay Unver, Selami Yazar, Rudi Appels, Hikmet Budak
article
Frontiers in Plant Science, 2022, 13, ⟨10.3389/fpls.2022.851079⟩
resume
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat ( Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
DOI
DOI : 10.3389/fpls.2022.851079
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https://hal.inrae.fr/hal-03740520/file/2022_Hussain_fpls-13-851079.pdf BibTex
titre
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
auteur
Gabriel Rech, Santiago Radío, Sara Guirao-Rico, Laura Aguilera, Vivien Horvath, Llewellyn Green, Hannah Lindstadt, Véronique Jamilloux, Hadi Quesneville, Josefa González
article
Nature Communications, 2022, 13 (1), pp.1948
resume
Abstract High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.
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titre
The era of reference genomes in conservation genomics
auteur
Florian Maumus, Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah Oomen, Sadye Paez, Per Palsbøll, Christophe Pampoulie, María Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila Mazzoni, Erich Jarvis, Miklós Bálint, Fedor Čiampor, María José Ruiz-López, Goujie Zhang, Sargis Aghayan, Tyler Alioto, Isabel Almudi, Nadir Alvarez, Paulo Alves, Isabel Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit Boštjančić, Bastien Boussau, Catherine Breton, Elena Buzan, Paula Campos, Carlos Carreras, L. Filipe Castro, Luis Chueca, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica Cunha, Frédéric Delsuc, Alice Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean-François Flot, Toni Gabaldón, Dolores Galea Agius, Guido Gallo, Alice Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill Jakobsen, Sissel Jentoft, Peter Klinga, Agnieszka Kloch, Claudius Kratochwil, Henrik Kusche, Kara K.S. Layton, Jennifer Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Ann Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael Monaghan, Matteo Montagna, Robert Mysłajek, Marco Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Simona Secomandi, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja Vernes, Cristiano Vernesi, David Vieites, Robert Waterhouse, Christopher Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit
article
Trends in Ecology & Evolution, 2022, ⟨10.1016/j.tree.2021.11.008⟩
DOI
DOI : 10.1016/j.tree.2021.11.008
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titre
Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection
auteur
Etienne Paux, Stéphane Lafarge, François Balfourier, Jérémy Derory, Gilles Charmet, Michael Alaux, Geoffrey Perchet, Marion Bondoux, Frédéric Baret, Romain Barillot, Catherine Ravel, Pierre Sourdille, Jacques Le Gouis
article
Biology, 2022, 11 (1), pp.1-28. ⟨10.3390/biology11010149⟩
resume
There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker–trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years.
DOI
DOI : 10.3390/biology11010149
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https://hal.inrae.fr/hal-03529813/file/2022_Paux_biology-11-00149.pdf BibTex
titre
Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation
auteur
Francesco Dal Grande, Véronique Jamilloux, Nathalie Choisne, Anjuli Calchera, Gregor Rolshausen, Malte Petersen, Meike Schulz, Maria Nilsson, Imke Schmitt
article
Biology, 2022, 11 (1), pp.24. ⟨10.3390/biology11010024⟩
resume
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host’s ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
DOI
DOI : 10.3390/biology11010024
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titre
Survival and growth of 711 forest tree taxa in eight French arbore-tums from three different climate regions
auteur
Catherine Ducatillion, Thierry Lamant, Richard Bellanger, Valentin Bouttier, Jean-Charles Bastien, Célia Michotey, Gautier Laurent, Bruno Fady, Brigitte Musch
article
Annals of Sylviculture Research, 2022, 47 (1), pp.30-38. ⟨10.12899/asr-2325⟩
resume
Arboretums have been used for decades for scientific, educational, horticultural and aesthetic purposes. Recently, climate change concerns have renewed the interest of the scientific community for these invaluable experimental forest systems. Here, we report a dataset from eight scientific arboretums planted in three contrasted French metropolitan bioclimates: Oceanic, Mountain and Mediterranean. In total, 92,236 trees were planted in 3,678 different plots. Originating from a worldwide range of ha-bitats, from sea-level up to 3,670 m in elevation, the collection spans 711 forest tree taxa (species, subspecies and varieties) from 177 genera. Taxa often include several geographic sources (so-called provenances), often simultaneously in different arboretums, making within species analyses possible. Cool-climate temperate Pinaceae (pines, firs, spruces, hemlocks, etc.) are well represented in the Atlantic and Mountain arboretums while Mediterranean arboretums are particularly rich with genera from the Myrtaceae (mostly eucalypts) and the Pinaceae (mostly pines). Data include survival, growth (height and diameter) and health status. Planted between 1969 and 1976, 338 taxa had survived at time of assessment and occurred as at least one individual in one plot. Data can be used to assess species suitability for ecological restoration and afforestation, and to help improve functional niche modelin
DOI
DOI : 10.12899/asr-2325
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titre
Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
auteur
Gabriel Rech, Santiago Radío, Sara Guirao-Rico, Laura Aguilera, Vivien Horvath, Llewellyn Green, Hannah Lindstadt, Véronique Jamilloux, Hadi Quesneville, Josefa González
article
Nature Communications, 2022, 13 (1), pp.1-16. ⟨10.1038/s41467-022-29518-8⟩
resume
Abstract High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.
DOI
DOI : 10.1038/s41467-022-29518-8
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titre
Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks
auteur
Agnès Baud, Mariène Wan, Danielle Nouaud, Nicolas Francillonne, Dominique Anxolabéhère, Hadi Quesneville
article
Peer Community Journal, 2022, 2, pp.e14. ⟨10.24072/pcjournal.68⟩
DOI
DOI : 10.24072/pcjournal.68
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titre
Genome-Wide Screening of Transposable Elements in the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), Revealed Insertions with Potential Insecticide Resistance Implications
auteur
Marwa Zidi, Khouloud Klai, Johann Confais, Benoît Chénais, Aurore Caruso, Françoise Denis, Maha Khemakhem, Nathalie Casse
article
Insects, 2022, 13, pp.1-13. ⟨10.3390/insects13050396⟩
resume
Transposable elements (TEs) are genetically mobile units that move from one site to another within a genome. These units can mediate regulatory changes that can result in massive changes in genes expression. In fact, a precise identification of TEs can allow the detection of the mechanisms involving these elements in gene regulation and genome evolution. In the present study, a genome- wide analysis of the Hemipteran pest Bemisia tabaci was conducted using bioinformatics tools to identify, annotate and estimate the age of TEs, in addition to their insertion sites, within or near of the defensome genes involved in insecticide resistance. Overall, 1,292,393 TE copies were identified in the B. tabaci genome grouped into 4872 lineages. A total of 699 lineages were found to belong to Class I of TEs, 1348 belong to Class II, and 2825 were uncategorized and form the largest part of TEs (28.81%). The TE age estimation revealed that the oldest TEs invasion happened 14 million years ago (MYA) and the most recent occurred 0.2 MYA with the insertion of Class II TE elements. The analysis of TE insertion sites in defensome genes revealed 94 insertions. Six of these TE insertions were found within or near previously identified differentially expressed insecticide resistance genes. These insertions may have a potential role in the observed insecticide resistance in these pests.
DOI
DOI : 10.3390/insects13050396
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https://hal-univ-lemans.archives-ouvertes.fr/hal-03658789/file/Zidi_2022.pdf BibTex

2021

Journal articles

titre
TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation
auteur
. The Te Hub Consortium, Tyler A. Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, Travis J. Wheeler
article
Mobile DNA, 2021, 12 (1), ⟨10.1186/s13100-021-00244-0⟩
resume
Transposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into their unique biology has driven the creation of a large collection of databases, software, classification systems, and annotation guidelines. The diversity of available TE-related methods and resources raises compatibility concerns and can be overwhelming to researchers and communicators seeking straightforward guidance or materials. To address these challenges, we have initiated a new resource, TE Hub, that provides a space where members of the TE community can collaborate to document and create resources and methods. The space consists of (1) a website organized with an open wiki framework, https://tehub.org , (2) a conversation framework via a Twitter account and a Slack channel, and (3) bi-monthly Hub Update video chats on the platform’s development. In addition to serving as a centralized repository and communication platform, TE Hub lays the foundation for improved integration, standardization, and effectiveness of diverse tools and protocols. We invite the TE community, both novices and experts in TE identification and analysis, to join us in expanding our community-oriented resource.
DOI
DOI : 10.1186/s13100-021-00244-0
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https://hal.inrae.fr/hal-03400275/file/2021_Elliott_Mobile_DNA.pdf BibTex
titre
Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp
auteur
Sarah Farhat, Phuong Le, Ehsan Kayal, Benjamin Noel, Estelle Bigeard, Erwan Corre, Florian Maumus, Isabelle Florent, Adriana A. Alberti, Jean-Marc Aury, Tristan Barbeyron, Ruibo Cai, Corinne da Silva, Benjamin Istace, Karine Labadie, Dominique Marie, Jonathan Mercier, Tsinda Rukwavu, Jeremy Szymczak, Thierry Tonon, Catharina Alves-De-Souza, Pierre Rouzé, Yves van de Peer, Patrick Wincker, Stephane Rombauts, Betina Porcel, Laure Guillou
article
BMC Biology, 2021, 19 (1), ⟨10.1186/s12915-020-00927-9⟩
resume
Background: Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. Results: We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. Conclusion: These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
DOI
DOI : 10.1186/s12915-020-00927-9
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https://hal.inrae.fr/hal-03114990/file/Farhat_2021_genomes%20Amoebophrya.pdf BibTex
titre
Grapevine and Wine Metabolomics-Based Guidelines for FAIR Data and Metadata Management
auteur
Stefania Savoi, Panagiotis Arapitsas, Éric Duchêne, Maria Nikolantonaki, Ignacio Ontañón, Silvia Carlin, Florian Schwander, Regis Gougeon, António Ferreira, Georgios Theodoridis, Reinhard Töpfer, Urska Vrhovsek, Anne-Françoise Adam-Blondon, Mario Pezzotti, Fulvio Mattivi
article
Metabolites, 2021, 11 (11), ⟨10.3390/metabo11110757⟩
resume
In the era of big and omics data, good organization, management, and description of experimental data are crucial for achieving high-quality datasets. This, in turn, is essential for the export of robust results, to publish reliable papers, make data more easily available, and unlock the huge potential of data reuse. Lately, more and more journals now require authors to share data and metadata according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles. This work aims to provide a step-by-step guideline for the FAIR data and metadata management specific to grapevine and wine science. In detail, the guidelines include recommendations for the organization of data and metadata regarding (i) meaningful information on experimental design and phenotyping, (ii) sample collection, (iii) sample preparation, (iv) chemotype analysis, (v) data analysis (vi) metabolite annotation, and (vii) basic ontologies. We hope that these guidelines will be helpful for the grapevine and wine metabolomics community and that it will benefit from the true potential of data usage in creating new knowledge being revealed.
DOI
DOI : 10.3390/metabo11110757
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https://hal.inrae.fr/hal-03602686/file/2021_Savoi_metabolites.pdf BibTex
titre
A Genomic Survey of Mayetiola destructor Mobilome Provides New Insights into the Evolutionary History of Transposable Elements in the Cecidomyiid Midges
auteur
Wiem Ben Amara, Hadi Quesneville, Maha Mezghani Khemakhem
article
PLoS ONE, 2021, 16 (10), pp.e0257996. ⟨10.1371/journal.pone.0257996⟩
resume
The availability of the Whole-Genome Sequence of the wheat pest Mayetiola destructor offers the opportunity to investigate the Transposable Elements (TEs) content and their relationship with the genes involved in the insect virulence. In this study, de novo annotation carried out using REPET pipeline showed that TEs occupy approximately 16% of the genome and are represented by 1038 lineages. Class II elements were the most frequent and most TEs were inactive due to the deletions they have accumulated. The analyses of TEs ages revealed a first burst at 20% of divergence from present that mobilized many TE families including mostly Tc1/mariner and Gypsy superfamilies and a second burst at 2% of divergence, which involved mainly the class II elements suggesting new TEs invasions. Additionally, 86 TEs insertions involving recently transposed elements were identified. Among them, several MITEs and Gypsy retrotransposons were inserted in the vicinity of SSGP and chemosensory genes. The findings represent a valuable resource for more in-depth investigation of the TE impact onto M . destructor genome and their possible influence on the expression of the virulence and chemosensory genes and consequently the behavior of this pest towards its host plants.
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DOI : 10.1371/journal.pone.0257996
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titre
Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)
auteur
Saad Serfraz, Vikas Sharma, Florian Maumus, Xavier Aubriot, Andrew D W Geering, Pierre-Yves Teycheney
article
Frontiers in Plant Science, 2021, 12, ⟨10.3389/fpls.2021.683681⟩
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Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene ( R1 ) of brinjal eggplant ( Solanum melongena ) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena , whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum , the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum .
DOI
DOI : 10.3389/fpls.2021.683681
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https://hal.inrae.fr/hal-03328857/file/2021_Serfraz_Frontiers-in-Plant-Science.pdf BibTex
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The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species
auteur
Lars Opgenoorth, B. Dauphin, Raquel Benavides, Katrin Heer, Paraskevi Alizoti, Elisabet Martínez-Sancho, Ricardo Alía, Olivier Ambrosio, Albet Audrey, Francisco Auñón, Camilla Avanzi, Evangelia Avramidou, Francesca Bagnoli, Evangelos Barbas, Cristina C Bastias, Catherine Bastien, Eduardo Ballesteros, Giorgia Beffa, Frédéric Bernier, Henri Bignalet, Guillaume Bodineau, Damien Bouic, Sabine Brodbeck, William Brunetto, Jurata Buchovska, Melanie Buy, Ana M Cabanillas-Saldaña, Bárbara Carvalho, Nicolas Cheval, José M Climent, Marianne Correard, Eva Cremer, Darius Danusevičius, Fernando Del Caño, Jean-Luc Denou, Nicolas Di Gerardi, Bernard Dokhelar, Alexis Ducousso, Anne Eskild Nilsen, Anna-Maria Farsakoglou, Patrick Fonti, Ioannis Ganopoulos, José M García Del Barrio, Olivier Gilg, Santiago C González-Martínez, René Graf, Alan Gray, Delphine Grivet, Felix Gugerli, Christoph Hartleitner, Enja Hollenbach, Agathe Hurel, Bernard Issehut, Florence Jean, Veronique Jorge, Arnaud Jouineau, Jan-Philipp Kappner, Katri Kärkkäinen, Robert Kesälahti, Florian Knutzen, Sonja T Kujala, Timo A Kumpula, Mariaceleste Labriola, Celine Lalanne, Johannes Lambertz, Martin Lascoux, Vincent Lejeune, Gregoire Le-Provost, Joseph Levillain, Mirko Liesebach, David López-Quiroga, Benjamin Meier, Ermioni Malliarou, Jérémy Marchon, Nicolas Mariotte, Antonio Mas, Silvia Matesanz, Helge Meischner, Célia Michotey, Pascal Milesi, Sandro Morganti, Daniel Nievergelt, Eduardo Notivol, Geir Ostreng, Birte Pakull, Annika Perry, Andrea Piotti, Christophe Plomion, Nicolas Poinot, Mehdi Pringarbe, Luc Puzos, Tanja Pyhäjärvi, Annie Raffin, José A Ramírez-Valiente, Christian Rellstab, Dourthe Remi, Sebastian Richter, Juan J Robledo-Arnuncio, Sergio San Segundo, Outi Savolainen, Silvio Schueler, Volker Schneck, Ivan Scotti, Vladimir Semerikov, Lenka Slámová, Jørn Henrik Sønstebø, Ilaria Spanu, Jean Thevenet, Mari Mette Tollefsrud, Norbert Turion, Giovanni Giuseppe Vendramin, Marc Villar, Georg Von Arx, Johan Westin, Bruno Fady, Tor Myking, Fernando Valladares, Filippos A Aravanopoulos, Stephen Cavers
article
GigaScience, 2021, 10 (3), pp.giab010. ⟨10.1093/gigascience/giab010⟩
resume
Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information;The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.
DOI
DOI : 10.1093/gigascience/giab010
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https://hal.inrae.fr/hal-03282821/file/giab010.pdf BibTex
titre
The GenTree Leaf Collection: Inter‐ and intraspecific leaf variation in seven forest tree species in Europe
auteur
Raquel Benavides, Bárbara Carvalho, Cristina Bastias, David López‐quiroga, Antonio Mas, Stephen Cavers, Alan Gray, Audrey Albet, Ricardo Alía, Olivier Ambrosio, Filippos Aravanopoulos, Francisco Auñón, Camilla Avanzi, Evangelia Avramidou, Francesca Bagnoli, Eduardo Ballesteros, Evangelos Barbas, Catherine Bastien, Frédéric Bernier, Henry Bignalet, Damien Bouic, William Brunetto, Jurata Buchovska, Ana Cabanillas‐saldaña, Nicolas Cheval, José Climent, Marianne Correard, Eva Cremer, Darius Danusevičius, B. Dauphin, Fernando del Caño, Jean‐luc Denou, Bernard Dokhelar, Rémi Dourthe, Anna‐maria Farsakoglou, Andreas Fera, Patrick Fonti, Ioannis Ganopoulos, José García del Barrio, Olivier Gilg, Santiago González‐martínez, René Graf, Delphine Grivet, Felix Gugerli, Christoph Hartleitner, Katrin Heer, Enja Hollenbach, Agathe Hurel, Bernard Issehuth, Florence Jean, Veronique Jorge, Arnaud Jouineau, Jan‐philipp Kappner, Katri Kärkkäinen, Robert Kesälahti, Florian Knutzen, Sonja Kujala, Timo Kumpula, Mariaceleste Labriola, Celine Lalanne, Johannes Lambertz, Martin Lascoux, Gregoire Le Provost, Mirko Liesebach, Ermioni Malliarou, Jérémy Marchon, Nicolas Mariotte, Elisabet Martínez‐sancho, Silvia Matesanz, Helge Meischner, Célia Michotey, Pascal Milesi, Sandro Morganti, Tor Myking, Anne Nilsen, Eduardo Notivol, Lars Opgenoorth, Geir Østreng, Birte Pakull, Andrea Piotti, Christophe Plomion, Nicolas Poinot, Mehdi Pringarbe, Luc Puzos, Tanja Pyhäjärvi, Annie Raffin, José Ramírez‐valiente, Christian Rellstab, Sebastian Richter, Juan Robledo‐arnuncio, Sergio San Segundo, Outi Savolainen, Volker Schneck, Silvio Schueler, Ivan Scotti, Vladimir Semerikov, Jørn Henrik Sønstebø, Ilaria Spanu, Jean Thevenet, Mari Mette Tollefsrud, Norbert Turion, Giovanni Giuseppe Vendramin, Marc Villar, Johan Westin, Bruno Fady, Fernando Valladares
article
Global Ecology and Biogeography, 2021, 30 (3), pp.590-597. ⟨10.1111/geb.13239⟩
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Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes.
DOI
DOI : 10.1111/geb.13239
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https://hal.inrae.fr/hal-03282266/file/Global%20Ecology%20and%20Biogeography%20-%202021%20-%20Benavides%20-%20The%20GenTree%20Leaf%20Collection%20Inter%25u2010%20and%20intraspecific%20leaf%20variation.pdf BibTex
titre
Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization
auteur
Jérémy Gauthier, Hélène Boulain, Joke J F A van Vugt, Lyam Baudry, Emma Persyn, Jean-Marc Aury, Benjamin Noel, Anthony Bretaudeau, Fabrice Legeai, Sven Warris, Mohamed A Chebbi, Géraldine Dubreuil, Bernard Duvic, Natacha Kremer, Philippe Gayral, Karine Musset, Thibaut Josse, Diane Bigot, Christophe Bressac, Sébastien Moreau, Georges Périquet, Myriam Harry, Nicolas Montagne, Isabelle Boulogne, Mahnaz Sabeti-Azad, Martine Maïbèche, Thomas Chertemps, Frédérique Hilliou, David Siaussat, Joëlle Amselem, Isabelle Luyten, Claire Capdevielle-Dulac, Karine Labadie, Bruna Laís Merlin, Valérie Barbe, Jetske G de Boer, Martial Marbouty, Fernando Luis Cônsoli, Stéphane Dupas, Aurélie Hua-Van, Gaelle Le Goff, Annie Bézier, Emmanuelle Jacquin-Joly, James B Whitfield, Louise E M Vet, Hans M Smid, Laure Kaiser, Romain Koszul, Elisabeth Huguet, Elisabeth A. Herniou, Jean-Michel Drezen
article
Communications Biology, 2021, 4 (1), pp.1-15. ⟨10.1038/s42003-020-01623-8⟩
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Endogenous viruses form an important proportion of eukaryote genomes and a source of novel functions. How large DNA viruses integrated into a genome evolve when they confer a benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success of parasitoid wasps, into whose genomes they integrated similar to 103 million years ago. Here we show, from the assembly of a parasitoid wasp genome at a chromosomal scale, that bracovirus genes colonized all ten chromosomes of Cotesia congregata. Most form clusters of genes involved in particle production or parasitism success. Genomic comparison with another wasp, Microplitis demolitor, revealed that these clusters were already established similar to 53mya and thus belong to remarkably stable genomic structures, the architectures of which are evolutionary constrained. Transcriptomic analyses highlight temporal synchronization of viral gene expression without resulting in immune gene induction, suggesting that no conflicts remain between ancient symbiotic partners when benefits to them converge. Jeremy Gauthier et al. present the chromosome scale assembly of the genome of the parasitic wasp C. congregata and show that bracovirus genes have colonized all ten chromosomes. Comparison with genome scaffolds of another wasp reveals a striking stability of these regions over similar to 53 million years, suggesting strong evolutionary constraints.
DOI
DOI : 10.1038/s42003-020-01623-8
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https://hal.science/hal-03127732/file/Gauthier%20et%20al.%20commsbio%202021.pdf BibTex
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Aethionema arabicum genome annotation using PacBio full‐length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research
auteur
Noe Fernandez‐pozo, Timo Metz, Jake Chandler, Lydia Gramzow, Zsuzsanna Mérai, Florian Maumus, Ortrun Mittelsten Scheid, Günter Theissen, M. Eric Schranz, Gerhard Leubner‐metzger, Stefan Rensing
article
Plant Journal, 2021, pp.1-19. ⟨10.1111/tpj.15161⟩
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Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Isoseq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-a polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of fulllength transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-b and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).
DOI
DOI : 10.1111/tpj.15161
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https://hal.inrae.fr/hal-03135342/file/2021_Fernandez-Pozo_The%20Plant%20Journal.pdf BibTex
titre
Gene-rich UV sex chromosomes harbor conserved regulators of sexual development
auteur
Sarah Carey, Jerry Jenkins, John Lovell, Florian Maumus, Avinash Sreedasyam, Adam Payton, Shengqiang Shu, George Tiley, Noe Fernandez-Pozo, Adam Healey, Kerrie Barry, Cindy Chen, Mei Wang, Anna Lipzen, Chris Daum, Christopher Saski, Jordan Mcbreen, Roth Conrad, Leslie Kollar, Sanna Olsson, Sanna Huttunen, Jacob Landis, J. Gordon Burleigh, Norman Wickett, Matthew Johnson, Stefan Rensing, Jane Grimwood, Jeremy Schmutz, Stuart Mcdaniel
article
Science Advances , 2021, 7 (27), pp.1-12. ⟨10.1126/sciadv.abh2488⟩
resume
Nonrecombining sex chromosomes, like the mammalian Y, often lose genes and accumulate transposable elements, a process termed degeneration. The correlation between suppressed recombination and degeneration is clear in animal XY systems, but the absence of recombination is confounded with other asymmetries between the X and Y. In contrast, UV sex chromosomes, like those found in bryophytes, experience symmetrical population genetic conditions. Here, we generate nearly gapless female and male chromosome-scale reference genomes of the moss Ceratodon purpureus to test for degeneration in the bryophyte UV sex chromosomes. We show that the moss sex chromosomes evolved over 300 million years ago and expanded via two chromosomal fusions. Although the sex chromosomes exhibit weaker purifying selection than autosomes, we find that suppressed recombination alone is insufficient to drive degeneration. Instead, the U and V sex chromosomes harbor thousands of broadly expressed genes, including numerous key regulators of sexual development across land plants.
DOI
DOI : 10.1126/sciadv.abh2488
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