Publications HAL du labo/EPI 104665;1002240

2024

Conference papers

titre
FAIR Plant Phenomics Data Management Tools and Guidelines.
auteur
Cyril Pommier
article
Plant and Animal Genome, Jan 2024, San Diego, United States
resume
Plant phenomics data has been greatly facilitated those past ten years at several levels: data standards to organize and describe data, databases for the management of the experiments, data repositories to ensure long term accessibility supplemented by data portals to maximise findability and finally guidelines to ease their usage. We will review the recent advances from joint initiatives involving two European infrastructures: ELIXIR (Life science data) and EMPHASIS (Plant phenomics). First we will update the current status of MIAPPE (www.miappe.org), a data standard interoperable with the Breeding API that enables not only phenoytping experiment formalisation but also their linking with genotyping. We will also give an overview of its usage in generic data repositories such as Dataverse or Zenodo and their relation with experimental database such as PHIS. Finding the right documentation to use those tools and standard is not always straightforward. The RDMKit (https://rdmkit.elixir-europe.org/) is a guidelines portal that has been build to help researchers finding the information subset they need. Through dedicated section, such as the plant domain page (https://rdmkit.elixir-europe.org/), it shows the complementarity between standard and tools and provide the guidances needed for data management. Finally, we will also update the status of FAIDARE (https://urgi.versailles.inrae.fr/faidare/), a global data portal that indexes 30 databases using either BrAPI or a generic minimal format.
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titre
Evolutionary Dynamics of Transposable Elements in Brachypodium distachyon Based on a Pangenomic Approach
auteur
Somia Saidi, Johann Confais, Hadi Quesneville
article
International Plant & Animal Genome (PAG 31), Jan 2024, San Diego, United States
resume
The impact of Transposable Elements (TEs) in a genome can be explored by searching for their insertions. Individuals of the same species independently undergo TE insertions, causing inter-individual genetic variability. This variability between individuals is the basis of the natural selection that leads to an increased adaptation of individuals to their environment. A way to search for the potential role of TEs in host adaptation is through a pangenomic approach. The TE pangenome can be described by (i) TE insertions present in all individuals of the species (core-genome), (ii) insertions present only among a subset of individuals (dispensable-genome) or (iii) ecogenome when the individuals share the same environment, and finally (iv) individual-specific insertions. A majority of current pangenome analysis methods are based on the alignment of reads from different genomes of the species to an assembled reference genome. But with the advent of third-generation sequencing, this question can now be better addressed by using multiple de novo assembled genomes of the same species to avoid the bias introduced by a single reference genome. We have developed a new pipeline, called panREPET, to handle this type of data. This pipeline identifies copies shared by a group of individuals by comparing individuals pairwise. We have described the pangenome in TEs of 54 de novo assembled genomes of Brachypodium distachyon. This pangenomic approach improves the description of the evolutionary history of TE families and enables us to date insertion events more accurately. We also looked for factors affecting the evolutionary dynamics of TE families: we found that climate is a factor that can explain certain TE dynamics.
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titre
Long Term Plant Phenomic Data Sharing in Generic Data Repositories (Zenodo, Dataverse, e!Dale) Using MIAPPE
auteur
Cyril Pommier, Erwan Le Floch, Daniel Arend, Flora D Anna
article
Plant and Animal Genome (PAG), Jan 2024, San Diego (CA), United States
resume
FAIR Phenomics data description and exchange is easier thanks to several standards such as MIAPPE and BrAPI which are implemented in several tools enabling data management along the data lifecycle. Furthermore, long term data access is complicated by the fact that there are currently no central data repository for this data type, like EBI and NCBI for omics data. As a consequence, plant phenomic data get shared either in specialized tools (Breedbase, PHIS, GnpIS, ...) or in file based data repositories such as Dataverse, Dryad or Zenodo. Those latter generic data repositories have several advantages, such as the capacity to cope with any new technology or scientific approach and presenting a rather low data submission barrier. The downside of this flexibility is that data can be ill described, making it poorly findable, reusable, interoperable according to the FAIR principles. To solve that, general guidelines have been developed to help plant researchers format and document their data following the Minimum Information About Plant Phenotyping Experiments (MIAPPE). They are available on the FAIR Cookbook, using the RDM Kit as an entry point. The present demonstration, based on a recent training (https://tess.elixir-europe.org/materials/workshop-on-resources-for-plant-sciences-2023), will briefly introduce MIAPPE and the RDM Kit before demonstrating the approach with a Dataverse instance, recherche data gouv (https://doi.org/10.15454/IASSTN ). Following this demonstration, attendees will have the necessary leads and information to prepare plant phenomics FAIR data submission into any file based data repository.
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Book sections

titre
Wheat Data Integration and FAIRification: IWGSC, GrainGenes, Ensembl and Other Data Repositories
auteur
Michael Alaux, Sarah Dyer, Taner Z Sen
article
The Wheat Genome, Springer International Publishing, pp.13-25, In press, Compendium of Plant Genomes, ⟨10.1007/978-3-031-38294-9_2⟩
resume
Wheat data integration and FAIRification are key to tackling the challenge of wheat improvement. The data repositories presented in this chapter play a central role in generating knowledge and allow data exchange and reuse. These repositories rely on international initiatives such as (i) the International Wheat Genome Sequencing Consortium (IWGSC), which delivers common genomics resources such as reference sequences, communal Web-based seminars and (ii) the Wheat Information System (WheatIS) of the Wheat Initiative ( http://www.wheatis.org ), which improves the interoperability and findability of the wheat data across the repositories.
DOI
DOI : 10.1007/978-3-031-38294-9_2
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https://hal.science/hal-04316553/file/Wheat_data_integration_and_FAIRification_Chapter.pdf BibTex

2023

Journal articles

titre
A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
auteur
Elodie Rey, Peter Maughan, Florian Maumus, Daniel Lewis, Leanne Wilson, Juliana Fuller, Sandra Schmöckel, Eric Jellen, Mark Tester, David Jarvis
article
Communications Biology, 2023, 6 (1), pp.1263. ⟨10.1038/s42003-023-05613-4⟩
resume
Abstract Quinoa ( Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use it, together with the A-genome diploid C. pallidicaule , to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.2%, 48.6%, and 57.9% of the quinoa, C. pallidicaule , and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.
DOI
DOI : 10.1038/s42003-023-05613-4
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titre
SNP discovery by exome capture and resequencing in a pea genetic resource collection
auteur
Grégoire Aubert, Jonathan Kreplak, Magalie Leveugle, Hervé Duborjal, Anthony Klein, Karen Boucherot, Emilie Vieille, Marianne Chabert-Martinello, Corinne Cruaud, Virginie Bourion, Isabelle Lejeune-Hénaut, Marie-Laure Pilet-Nayel, Yanis Bouchenak-Khelladi, Nicolas Francillonne, Nadim Tayeh, Jean-Philippe Pichon, Nathalie Rivière, Judith Burstin
article
Peer Community In Genomics, 2023, 3, pp.art. e100. ⟨10.24072/pci.genomics.100237⟩
resume
Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tool
DOI
DOI : 10.24072/pci.genomics.100237
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https://hal.inrae.fr/hal-04267953/file/2023-270.pdf BibTex
titre
Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
auteur
Baptiste Imbert, Jonathan Kreplak, Raphaël-Gauthier Flores, Grégoire Aubert, Judith Burstin, Nadim Tayeh
article
Frontiers in Artificial Intelligence, 2023, 6, pp.art. 1191122. ⟨10.3389/frai.2023.1191122⟩
resume
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for di erent traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities o ered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
DOI
DOI : 10.3389/frai.2023.1191122
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https://hal.inrae.fr/hal-04191716/file/2023-196.pdf BibTex
titre
Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes
auteur
Héléna Vassilieff, Andrew Geering, Nathalie Choisne, Pierre-Yves Teycheney, Florian Maumus
article
Biomolecules, 2023, 13 (7), pp.1069. ⟨10.3390/biom13071069⟩
resume
The Caulimoviridae is a family of double-stranded DNA viruses that infect plants. The genomes of most vascular plants contain endogenous caulimovirids (ECVs), a class of repetitive DNA elements that is abundant in some plant genomes, resulting from the integration of viral DNA in the chromosomes of germline cells during episodes of infection that have sometimes occurred millions of years ago. In this review, we reflect on 25 years of research on ECVs that has shown that members of the Caulimoviridae have occupied an unprecedented range of ecological niches over time and shed light on their diversity and macroevolution. We highlight gaps in knowledge and prospects of future research fueled by increased access to plant genome sequence data and new tools for genome annotation for addressing the extent, impact, and role of ECVs on plant biology and the origin and evolutionary trajectories of the Caulimoviridae.
DOI
DOI : 10.3390/biom13071069
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titre
A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat
auteur
Reda Amezrou, Colette Audéon, Jérôme Compain, Sandrine Gélisse, Aurélie Ducasse, Cyrille Saintenac, Nicolas Lapalu, Clémentine Louet, Simon Orford, Daniel Croll, Joëlle Amselem, Sabine Fillinger, Thierry Marcel
article
PLoS Pathogens, 2023, 19 (5), pp.e1011376. ⟨10.1371/journal.ppat.1011376⟩
resume
Zymoseptoria tritici is the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping AvrStb9 transgenic strains on Stb9 cultivars, near isogenic lines and wheat mapping populations, showed that AvrStb9 interacts with Stb9 resistance gene, triggering an immune response. AvrStb9 encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector. AvrStb9 is also conserved among a global Z . tritici population and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an ‘atypical’ conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.
DOI
DOI : 10.1371/journal.ppat.1011376
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https://hal.inrae.fr/hal-04102220/file/journal.ppat.1011376.pdf BibTex
titre
SyntenyViewer: a comparative genomics-driven translational research tool
auteur
Raphael Flores, Cécile Huneau, Laura Burlot, Mathilde Lainé, Erik Kimmel, Cyril Pommier, Michael Alaux, Anne-Françoise Adam-Blondon, Caroline Pont, Hadi Quesneville, Jerome Salse
article
Database - The journal of Biological Databases and Curation, 2023, 2023, ⟨10.1093/database/baad027⟩
resume
SyntenyViewer is a public web-based tool relying on a relational database available at https://urgi.versailles.inrae.fr/synteny delivering comparative genomics data and associated reservoir of conserved genes between angiosperm species for both fundamental (evolutionary studies) and applied (translational research) applications. SyntenyViewer is made available for (i) providing comparative genomics data for seven major botanical families of flowering plants, (ii) delivering a robust catalog of 103 465 conserved genes between 44 species and inferred ancestral genomes, (iii) allowing us to investigate the evolutionary fate of ancestral genes and genomic regions in modern species through duplications, inversions, deletions, fusions, fissions and translocations, (iv) use as a tool to conduct translational research of key trait-related genes from model species to crops and (v) offering to host any comparative genomics data following simplified procedures and formats Database URL: https://urgi.versailles.inrae.fr/synteny
DOI
DOI : 10.1093/database/baad027
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https://hal.inrae.fr/hal-04099923/file/baad027.pdf BibTex
titre
Sidestepping Darwin: horizontal gene transfer from plants to insects
auteur
Clément Gilbert, Florian Maumus
article
Current Opinion in Insect Science, 2023, 57, pp.101035. ⟨10.1016/j.cois.2023.101035⟩
DOI
DOI : 10.1016/j.cois.2023.101035
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https://hal.inrae.fr/hal-04072018/file/MS_COIS_07-11-2023%20-%20HAL.pdf BibTex
titre
How genomics can help biodiversity conservation
auteur
Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido Gallo, José Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah Oomen, Sadye Paez, Per Palsbøll, Christophe Pampoulie, María Ruiz-López, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich Jarvis, Miklós Bálint, Claudio Ciofi, Robert Waterhouse, Camila Mazzoni, Jacob Höglund, Sargis Aghayan, Tyler Alioto, Isabel Almudi, Nadir Alvarez, Paulo Alves, Isabel Amorim Do Rosario, Agostinho Antunes, Paula Arribas, Petr Baldrian, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit Boštjančić, Bastien Boussau, Catherine Breton, Elena Buzan, Paula Campos, Carlos Carreras, L. Filipe C. Castro, Luis Chueca, Fedor Čiampor, 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 Agius, 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, 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, Florian Maumus, 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, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja Vernes, Cristiano Vernesi, David Vieites, Christopher Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit
article
Trends in Genetics, 2023, ⟨10.1016/j.tig.2023.01.005⟩
resume
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
DOI
DOI : 10.1016/j.tig.2023.01.005
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https://hal.inrae.fr/hal-04082874/file/How%2520genomics%2520can%2520help%2520biodiversity%2520conservation%25202023.pdf BibTex

Conference papers

titre
Linking heterogeneous data from model plant species in a graph database
auteur
Johann Confais, Nicolas Francillonne
article
Séminaire résidentiel INRAE Semantic Linked Data édition 2023, réseau IN-OVIVE "Intégration de sources/masses de données hétérogènes et ontologies", Oct 2023, Agde, France
resume
More and more data are available nowadays due to emerging technology and tools to analyze genomes. In this situation, it is necessary to identify or develop tools to connect all these data together. In this context, graph database seems to be an appealing method to connect data as nodes and relation between them as edges or links. Graph NEO4J TE contains genomic data on two model plant species, one dicot and one monocot A.thaliana and B.distachyon. It puts into interaction genomic coordinates between entities like structural gene annotation, transposable elements, transcription factor binding site and other allowing to search possible positional relation between these entities. We enrich these information with functional annotation, phenotyping characterization data and localization data linked with our genomic data using pivotal node like accession or gene. Neo4J allows RDF importation into the database. We have been able to successfully import gene ontology into our database and to import AgroLD rice gene data from turtle files (zenodo repository) and bind these information with our own database with a simple query. Finally we can export our own dataset in RDF format. That RDF can be imported into other instance of neo4j database. The database has been developed in « Graph » working group of CATI GREP. In this group 3 project are in development on different species and thematic. We have commonly defined the modelisation of nodes and relationship to allow connections between graphs.
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titre
PlantBioinfoPF (URGI) et son offre de service d'annotation des éléments transposables dans les génomes
auteur
Johann Confais
article
Journées du PEPI IBIS 2023, PEPI Ingénierie Bio Informatique et Statistique pour les données haut-débit (IBIS), Sep 2023, Paris, France
resume
Les outils d'annotation des éléments transposables (ET) sont de plus en plus accessibles au grand public mais peuvent rester complexes dans le traitement de génomes de grandes tailles ou en trop grand nombre pour des non initiés. La plateforme PlantBioinfoPF hebergée par l'URGI propose l'accès à des ressources de calculs adaptées et un service d'annotation des ET dans les génomes. Illustration au travers de 2 projets et présentation de l'offre de service.
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titre
Characterization of Transposable Elements in Pangenomes
auteur
Somia Saidi, Johann Confais, Hadi Quesneville
article
Journées du PEPI IBIS 2023, PEPI Ingénierie Bio Informatique et Statistique pour les données haut-débit (IBIS), Sep 2023, Paris, France
resume
Transposable elements (TEs) are mobile DNA elements that can invade genomes by transposition. Despite their reputation as parasitic sequences, they can enrich the genomes with functional novelties that foster genome evolution. The impact of TEs in a genome can be explored by searching for their insertions. Individuals of the same species independently undergo TE insertions causing inter-individual genetic variability. This variability between individuals is the basis of the natural selection that leads to an increased adaptation of individuals to their environment. A way to search for the potential role of TEs in host adaptation is through a pangenomic approach. The TE pangenome can be described by (i) TE insertions present in all individuals of the species (core-genome), (ii) insertions present only among a subset of individuals (dispensable-genome) or (iii) ecogenome when the individuals share the same environment, and finally (iv) individual-specific insertions. Current pangenome analysis methods are based on the alignment of reads from different genomes of the species to an assembled reference genome. But, the advent of the third-generation sequencing makes now possible to better approach this question using several assembled genomes of the same species to avoid the bias introduced by a single reference genome. I will present a new pipeline, called panREPET, which identify TE copies in a pangenome from several assembled genomes. There is therefore no dependency on a reference genome. This pipeline identifies copies shared by a group of individuals. This pipeline has been tested on 54 genomes of Brachypodium distachyon to describe its pangenomic compartments.
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titre
Insertion et exploitation de données hétérogènes dans un graphe de connaissance
auteur
Johann Confais, Nicolas Francillonne, Maela Semery, Iphigénie Gonnet
article
Journées du PEPI IBIS 2023, PEPI Ingénierie Bio Informatique et Statistique pour les données haut-débit (IBIS), Sep 2023, Paris, France
resume
Une base de données orientée graphe a été construite au sein de l’URGI sur 2 espèces modèles de plante : une monocotylédone (Brachypodium distachyon) et une dicotylédone (Arabidopsis thaliana). Elle intègre de nombreuses données hétérogènes: annotations de génome (annotations structurale et fonctionnelles de gènes, éléments transposables (ET), séquences non codantes conservées (CNS), site de fixation de facteur de transcription (TFBS), relations d’homologie et d’orthologie. De nombreuses études montrent que les éléments transposables (ET) sont cooptés dans des séquences cis-régulatrices. Les ET peuvent donc affecter la transcription des gènes adjacents en recrutant des facteurs de transcription supplémentaires par exemple. Certaines famille d’ET qui portent des TFBS sont notamment connus pour être activée en réponse à certains stress abiotique comme ONSEN/ATCOPIA78 qui est activée par un stress thermique chez Arabidopsis thaliana. La base graphe permet d’identifier quelles sont les familles d’ET spécifiquement liées à des TFBS. Une analyse approfondie sur ces familles d’ET et leurs relations avec les gènes et réseaux de gènes impliqués dans des traits d’adaptation permettra d’améliorer la prédiction de leur impact fonctionnel chez leur hôte. Ce travail s’intéresse aux questions d’exploitation et d’interrogation des relations existantes entre les données par le biais de l’outil base de données orientées graphe. Il permet de développer des questions complexes faisant interagir plusieurs sources de données.
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titre
Characterization of Transposable Elements in Pangenomes
auteur
Somia Saidi, Johann Confais, Hadi Quesneville
article
24th National Congress on Transposable Elements 2023 (CNET 2023), French research community working on transposable elements (CNET), Jul 2023, Perpignan, France
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titre
REPET novelties : a versatile and modular package
auteur
Johann Confais, Mariène Wan, Somia Saidi, Hadi H. Quesneville
article
CNET 2023 : 24th National Congress on Transposable Elements 2023, French research community working on transposable elements (CNET), Jul 2023, Perpignan, France
resume
The detection and annotation of transposable elements (TEs) are now considered mandatory to any genome sequencing project. To this aim, the REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyse TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement. Several implementations and algorithms to reduce the time required for analysing large genome have been tested. With our new speed improvements and tuned annotation strategies, REPET is now able to annotate and analyse easily large genomes up to 3 Gb. Now, we chain all required steps through a process called ”Repet-Factory”. This process uses parameters optimized for specificity and computing time. It is capable of successively annotate several genomes in batches with all the traceability required for reproducibility. We also simplified the distribution of REPET by developing a Docker image of REPET. And for an HPC usage, REPET is currently developped in SnakeMake with dependencies in Apptainer.
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titre
Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
auteur
Baptiste Imbert,, Jonathan Kreplak, Raphaël Flores, Grégoire Aubert, Judith Burstin, Nadim Tayeh
article
Forum des Jeunes Chercheurs UBFC 2023, Jun 2023, Besancon, France
resume
Legumes, and especially pulses, are an important source of protein for food and feed, and are appreciated for their positive impact on the “one health”. However, their unstable yields and their susceptibility to biotic and abiotic stresses highlight the need for varietal improvement in order to increase the cultivated areas and productivity. With the advent of sequencing technologies, a large pool of genetic and -omics resources, heterogeneous at the inter- and intra-species scale, is emerging. Thus, it is important to capitalize on these scattered heterogeneous data to develop translational research to boost breeding projects and crop diversification. To meet this need, we undertook the development of the Orthology-driven knowledge base framework for translational research (Ortho_KB). For a set of species of interest, it infers orthologous relationships between genes, proposes associated syntenic blocks between chromosomes and creates a graph database linking genetic and RNA-seq data. To explore the possibilities of this framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. This database includes four cultivated crops, namely Pisum sativum, Vicia faba, Lens culinaris and Vigna radiata, and the model legume Medicago truncatula. Available information on quantitative trait loci (QTL) for multiple traits are being integrated as well as expression data. The proposed database model was evaluated by studying the conservation of a flowering-promoting gene
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titre
Les outils de gestion de données de phénotypage soutenus par INRAE
auteur
Cyril Pommier
article
AG RARE, INRAE, May 2023, Toulouse, France
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https://hal.science/hal-04314299/file/2023-05-31-Introduction-pheno-pour-RG.pdf BibTex
titre
Practical training III : REPET pipeline
auteur
Johann Confais
article
11th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis, Laboratory of Molecular Cytogenetics of the Biology Centre CAS, May 2023, České Budějovice, Czech Republic
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titre
How to use REPET for de novo TE annotation
auteur
Johann Confais, Mariène Wan, Somia Saidi, Hadi Quesneville
article
11th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis, Laboratory of Molecular Cytogenetics of the Biology Centre CAS, May 2023, České Budějovice, Czech Republic
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Other publications

titre
Ontology mapping for wheat trait information management
auteur
Claire Nédellec, Sophie Aubin, Clara Sauvion, Sonia Bravo, Jacques Le Gouis, Thierry C. Marcel, Cyril Pommier, Robert Bossy, Michael Alaux
article
Séminaire résidentiel INRAE Semantic Linked Data, 2023
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Poster communications

titre
REPET evolutions: faster and easier
auteur
Johann Confais, Mariène Wan, Hadi Quesneville
article
Annual Meeting of the Society for Molecular Biology and Evolution (SMBE), Jul 2023, Ferrara, Italy.
resume
The detection and annotation of transposable elements (TEs) are now considered mandatory to any genome sequencing project. To this aim, the REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyse TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement. Several implementations and algorithms to reduce the time required for analysing large genome have been tested. With our new speed improvements and tuned annotation strategies, REPET is now able to annotate and analyse easily large genomes up to 3 Gb. Now, we chain all required steps through a process called "Repet-Factory". This process uses parameters optimized for specificity and computing time. It is capable of successively annotate several genomes in batches with all the traceability required for reproducibility. We also simplified the distribution of REPET by developing a Docker image of REPET
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titre
Characterization of Transposable Elements in Pangenomes
auteur
Somia Saidi, Johann Confais, Hadi Quesneville
article
JOBIM 2023, Jun 2023, Tours, France
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titre
Learning path development for plant data management
auteur
Vanita Haurheeram, Célia Michotey, Cyril Pommier, Anne-Françoise Adam-Blondon, Elixir Training Platform
article
ELIXIR All Hands 2023, Jun 2023, Dublin, Ireland. f1000research.com, https://doi.org/10.7490/f1000research.1119444.1, 2023, ⟨10.7490/f1000research.1119444.1⟩
resume
The ELIXIR CONVERGE project goal is to connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services. In the context of the WP5 of this project, we have been working on the development of a learning path for plant phenotyping and plant genomic data management targeting researchers and data managers specialized in plant research. A learning path is a collection of courses that need to be followed in a specific order to acquire knowledge and skills on a precise domain. This work has been achieved during the 2022 ELIXIR BioHackathon, in which the Elixir training platform was testing a template that can be used to develop new learning paths. The first version delivered during the BioHackathon has then been refined later on by members of the ELIXIR plant science community. Existing training material found in TeSS (Training eSupport System) or gathered by the ELIXIR plant community was then mapped on the learning path in order to identify gaps to be addressed. Finally, the FAIRness of each training material of this collection was assessed following criterias derived from "Ten simple rules for making training materials FAIR" by Garcia L, Batut B, Burke ML, Kuzak M, Psomopoulos F, et al (2020) https://doi.org/10.1371/journal.pcbi.1007854.
DOI
DOI : 10.7490/f1000research.1119444.1
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Software

titre
CAULIFINDER
auteur
Florian Maumus, Véronique Jamilloux, Héléna Vassilieff, Sana Haddad
article
2023, ⟨swh:1:dir:847d2324e957f8b013b184bc7e6f12ece8528c04;origin=https://hal.archives-ouvertes.fr/hal-03906699;visit=swh:1:snp:e421e307ac9e1511e9e38b6f711c136c654d4b7b;anchor=swh:1:rel:b66fda6313cdad30b851aba54df98fa7e88721e3;path=/⟩
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.
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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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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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titre
Recent Acquisition of Functional m6A RNA Demethylase Domain in Orchid Ty3/Gypsy Elements
auteur
Luis Alvarado-Marchena, Mireya Martínez-Pérez, Frederic Aparicio, Vicente Pallas, Florian Maumus
article
Frontiers in Plant Science, 2022, 13, ⟨10.3389/fpls.2022.939843⟩
resume
Long terminal repeats (LTR) retrotransposons are transposable elements (TEs) representing major components of most plant genomes. The fixation of additional conserved protein domains in their genomes is considered a rare event in the course of their evolution. Such changes can bring novel functions and increase their fitness by playing a role in the regulation of their replicative cycle or by affecting their integration landscape so that the detection of new domains can in turn reveal important aspects of host-TE interactions. We have mined angiosperm genomes for the presence of additional domains in LTR retrotransposons. We report a lineage of large (25 kbp) Gypsy-type elements in the genomes of Phalaenopsis orchids that contain an additional open reading frame containing a 2-ODD domain with close similarity to those responsible for m6A RNA demethylase activity in AlkB proteins. By performing in vitro assays, we demonstrate the RNA binding capability and the demethylase activity of the Gypsy-encoded AlkB protein, suggesting it could be functional against cognate TE mRNA or any cellular RNA in planta . In line with recent literature, we propose that the fixation of an RNA demethylase in this lineage of LTR retrotransposons may reflect an important role for epitranscriptomic control in host surveillance against TEs.
DOI
DOI : 10.3389/fpls.2022.939843
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https://hal.inrae.fr/hal-03717458/file/fpls-13-939843.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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titre
Health Education in Primary Schools: A Difficult Task
auteur
Philippe Masson, Michael Racodon, Alessandro Porrovecchio, Guillaume Duchateau
article
Central European Journal of Educational Research, 2022, 4 (1), pp.1-10. ⟨10.37441/cejer/2022/4/1/10735⟩
resume
This study was conducted in a medium-sized French city, in a neighbourhood falling into poverty, with children aged from 9 to 10 years old. Its aim is to build an adapted strategy to improve children’s healthy habits. Our study was based on a mixed methods interdisciplinary approach using interviews, questionnaires, sleep diaries and accelerometers. The unemployment rate of the target population is above 40%, and the families have four children on average. The children of the sample (N=29) practice less physical activity than recommended by the institutions in charge of health matters. The parents correctly manage the sleep cycles of their children, and stand firm when they have to go to school the next day. When the next day is a non-school day, children play more video games in the evening, both on their own and with their families. Healthy habits can be improved through cooperation with the various members of the educational community (parents, teachers and structures in charge of the children). Since it is difficult to manage health education solely during PE classes, this process must be continued both inside and outside school by the community, even more so the family.
DOI
DOI : 10.37441/cejer/2022/4/1/10735
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titre
ELIXIR biovalidator for semantic validation of life science metadata
auteur
Isuru Liyanage, Tony Burdett, Bert Droesbeke, Karoly Erdos, Rolando Fernandez, Alasdair Gray, Muhammad Haseeb, Simon Jupp, Flavia Penim, Cyril Pommier, Philippe Rocca-Serra, Mélanie Courtot, Frederik Coppens
article
Bioinformatics, 2022, 38 (11), pp.3141-3142. ⟨10.1093/bioinformatics/btac195⟩
resume
Abstract Summary To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents. Availability and implementation Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate. Supplementary information Supplementary data are available at Bioinformatics online.
DOI
DOI : 10.1093/bioinformatics/btac195
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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, Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Fedor Čiampor, Claudio Ciofi, Angelica Crottini, José Godoy, Jacob Hoglund, Joanna Malukiewicz, Alice Mouton, Rebekah Oomen, Sadye Paez, Per Palsbøll, Christophe Pampoulie, María José Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Goujie Zhang, Camila Mazzoni, Erich Jarvis, Miklós Bálint, 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, 37 (3), pp.197-202. ⟨10.1016/j.tree.2021.11.008⟩
DOI
DOI : 10.1016/j.tree.2021.11.008
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titre
Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
auteur
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, Paul Kersey, Stephan Weise, Richard Finkers, Baron Koylass, Timothee Cezard, Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
article
F1000Research, 2022, 11, pp.231. ⟨10.12688/f1000research.109080.1⟩
resume
In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of (meta-) data in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. VCF files are an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant call data (for example, the HapMap format and the gVCF format), but none currently have the reach of VCF. In VCF, only the sites of variation are described, whereas in gVCF, all positions are listed, and confidence values are also provided. For the sake of simplicity, we will only discuss VCF and our recommendations for its use. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse (if any) descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from the plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.
DOI
DOI : 10.12688/f1000research.109080.1
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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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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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https://hal.science/hal-03807727/file/2022_Rech_Nature%20Communications.pdf BibTex
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://univ-lemans.hal.science/hal-03658789/file/Zidi_2022.pdf BibTex

Conference papers

titre
Characterization of Transposable Elements in Pangenomes
auteur
Somia Saidi, Johann Confais, Hadi Quesneville
article
GDR CNRS 3546 Mobil-ET Annual Meeting, Mobil-ET GDR CNRS 3546, Dec 2022, Paris, France
resume
The impact of TEs in a genome is explored by searching for insertions events. Individuals (or accessions) of the same species independently undergo TE insertions causing inter-individual genetic variability. This variability between individuals is the basis of the natural selection that leads to an increased adaptation of individuals to their environment. A way to search for the potential role of TEs in host adaptation is through a pangenomic approach. The TE pangenome is described by (i) TE insertions present in all individuals of the species (core-genome), (ii) insertions present only among a subset of individuals (dispensable-genome) or (iii) ecogenome when the individuals share the same environment, and finally (iv) insertions specific to an individual. Current pangenome analysis methods are based on the alignment of reads from different accessions of the species to an assembled reference genome. But, the advent of the third-generation sequencing makes now possible to approach this question on several assembled genomes of the same species. I will present a new pipeline which identify the TEs in pangenome compartments from several assembled genomes. There is therefore no dependency on a reference genome. This new pipeline identifies copies shared by a group of individuals. This pipeline has been tested on Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon pangenomes and compared with results from Minigraph, a pan-genome graph method to identify sequence variations.
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titre
Transposable elements, from their annotation to their integration into knowledge graphs
auteur
Johann Confais, Mariène Wan, Somia Saidi, Nicolas Francillonne, Hadi Quesneville
article
Journée thématique - Annotation, Intelligence Artificielle et Text-mining, PEPI IBIS, Nov 2022, Jouy-en-Josas, France
resume
Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. Individuals of the same species independently undergo TE insertions causing inter-individual genetic variability. This variability between individuals is the basis of the natural selection that leads to an increased adaptation of individuals to their environment. A way to search for the potential role of TEs in host adaptation is through a pangenomic approach. The REPET package integrates bioinformatics pipelines dedicated to detect and annotate TEs in genomes. Then the PanREPET pipeline allows to describe (i) TE insertions present in all individuals of the species (core-genome), (ii) insertions present only among a subset of individuals (dispensable-genome) or (iii) ecogenome when the individuals share the same environment, and finally (iv) insertions specific to an individual. To identify TE candidate putatively involved in local adaptation, environmental knowledge and genome annotations have been integrated in a semantic knowledge graph.
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titre
Identification of CTG.CAG contraction factors in Myotonic Dystrophy type 1
auteur
Laure de Pontual, Guillaume Diop, Sonia Lameiras, Tina Alaeitabar, Sylvain Baulande, François-Xavier Lejeune, Geneviève Gourdon, Vincent Dion, Stéphanie Tomé
article
19ème Journées de la Société Française de Myologie (JSFM), Nov 2022, Toulouse, France
resume
Objectifs Myotonic dystrophy type 1 (DM1) is a neuromuscular disease caused by an unstable CTG repeat expansion in the DMPK gene. Larger expansions are associated with more severe symptoms and a decreasing age of onset. We hypothesize that the development of innovative therapeutic strategies, aimed at decreasing the CTG repeat length, and thus to stop or reverse the progression of the disease, may improve the quality of life of patients. The specific objective of our work is to uncover bioactive molecules able to induce repeat contractions in trinucleotide repeat (TNR) models and to decipher the mechanisms promoting these contractions using efficient tools. Contenu We performed a large-scale screen for pharmacologically relevant chemical modulators of instability using the Prestwick Library taking advantage of a chromosomal GFP reporter that can accurately measure CTG repeat changes in a HEK293 cell population. The effect of selected molecules directly on the dynamics of CTG repeat instability is studied in HEK293 cells as well as DM1 fibroblasts using targeted long-read sequencing. During the chemical screen, we identified candidate molecules notably involved in epigenetic regulation pathways, that may modulate the size of CTG repeats. Some of these molecules induced stabilization or even contractions of CTG repeats in the HEK cell model and in DM1 fibroblasts. The direct perspective of our work is to identify new small molecules and new druggable targets promoting CAG.CTG repeat contractions, thus offering new therapeutic perspectives for DM1 and TNR diseases.
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titre
Demo session : REPET
auteur
Johann Confais
article
6th Uppsala Transposon Symposium, Oct 2022, Uppsala, Sweden
resume
https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/tutorial-with-Docker-image-of-REPET
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titre
RepetDB: a unified resource for transposable element references
auteur
Mariène Wan, Nicolas Francillonne, Raphaël Flores, Françoise Alfama, Johann Confais, Joëlle Amselem, Nathalie Choisne
article
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, SFBI; IFB; GDR BIM, Jul 2022, Rennes, France
resume
Transposable elements (TEs) are major players in the structure and evolution of eukaryote genomes. Thanks to their ability to move around and replicate within genomes, they are probably the most important contributors to genome plasticity. The insertion of TEs close to genes can affect gene structure, expression and function, contributing to the genetic diversity underlying species adaptation. Many studies have shown that TEs are generally silenced through epigenetic defense mechanisms, and that these elements play an important role in epigenetic genome regulation. Their detection and annotation are considered essential and must be undertaken in the frame of any genome sequencing project. Here, we will present the new version of RepetDB [1] (Amselem et al., Mobile DNA, 2019), (https://urgi.versailles.inrae.fr/repetdb) our TE database developed to store and retrieve detected, classified and annotated TEs in a standardized manner. This RepetDB v2 new version was updated with 31 more species of plants and fungi and provides TE consensi with evidences able to justify their classification. RepetDB v2 is a customized implementation of InterMine [2,3], 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 provides powerful capabilities to query and visualize all biological information on TE. It allows to make simple search on the database using the QuickSearch (‘google like search’) or make more complex queries using the Querybuilder to display various desired information. RepetDB v2 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. References 1. Amselem, J., Cornut, G., Choisne, N., Alaux, M., Alfama-Depauw, F., Jamilloux, V., Maumus, F., Letellier, T., Luyten, I., Pommier, C., Adam-Blondon, A. F., & Quesneville, H. (2019). RepetDB: a unified resource for transposable element references. Mobile DNA, 10, 6. https://doi.org/10.1186/s13100-019-0150-y 2. InterMine: extensive web services for modern biology. Kalderimis A, Lyne R, Butano D, Contrino S, Lyne M, Heimbach J, Hu F, Smith R, Stˇepán R, Sullivan J, Micklem G. Nucleic Acids Res. 2014 Jul; 42 (Web Server issue): W468-72 3. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Smith RN, Aleksic J, Butano D, Carr A, Contrino S, Hu F, Lyne M, Lyne R, Kalderimis A, Rutherford K, Stepan R, Sullivan J, Wakeling M, Watkins X, Micklem G. Bioinformatics (2012) 28 (23): 3163-3165.
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titre
REPET evolutions: faster and easier
auteur
Johann Confais, Mariène Wan, Hadi Quesneville
article
23rd National Congress on Transposable Elements (CNET 2022), French research community working on transposable elements (CNET), Jul 2022, Gif-Sur-Yvette, France
resume
Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. Their detection and annotation are considered essential and must be undertaken in any genome sequencing project. The REPET package [1, 2] integrates bioinformatics pipelines dedicated to detect, annotate and analyze TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them [3] according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement for speed by parallelizing several key bottleneck steps. In addition, several strategies which reduce the time required for analyzing large genome have been tested. With the speed improvement and adapted strategies, REPET is now able to annotate and analyze genomes such as the maize with more than 85% of TEs on a 2.3 Gb genome [4] on current computer cluster. With this tool, the PlantBioinfoPF platform ensures a TE annotation service. Indeed, we are now able to propose an automatic TE annotation of good quality through a process called ”Repet-Factory”. This process uses the REPET software suite with parameters optimized for TE detection specificity and computing time. This process is capable of successively annotate several genomes in batches with the required traceability and reproducibility of the analyzes. Moreover, a Virtual Research Environment (VRE) for TE annotation and its analysis has been developed on Virtual Machines (VM). An ansible script instantiate VMs with all packages and tools required for a complete genome annotation with the REPET package. This script allows this VRE to be easily re-instantiated in other infrastructures which greatly simplify the REPET package installation with all its required dependencies. We also simplified the distribution of REPET to increase its availability and portability to users, by developing a Docker image of REPET (https://hub.docker.com/r/urgi/docker vre aio). The REPET tool is a cornerstone of the platform. In addition to its use in the genome TE annotation service and its availability for download, it is also the basis of the RepetDB [5] database (https://urgi.versailles.inrae.fr/repetdb) hosted by the platform which provides libraries of reference TE sequences for more than 50 species
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titre
Characterization of Transposable Elements in Pangenomes
auteur
Somia Saidi, Johann Confais, Hadi Quesneville
article
23rd National Congress on Transposable Elements (CNET 2022), French research community working on transposable elements (CNET), Jul 2022, Gif-Sur-Yvette, France
resume
Transposable elements (TEs) are mobile DNA elements that can invade the genomes by transposition. Despite their reputation as parasitic sequences, these elements can enrich the genomes with functional novelties that foster genome evolution. Indeed, TEs can impact genes through insertional mutagenesis, supplies of new transcription factor binding sites (TFBS), or by epigenetic regulation. The impact of TEs in a genome is explored by searching for insertions events. Individuals (or accessions) of the same species independently undergo TE insertions causing inter-individual genetic variability. This variability between individuals is the basis of the natural selection that leads to an increased adaptation of individuals to their environment. A way to search for the potential role of TEs in host adaptation is through a pangenomic approach. The TE pangenome is described by (i) TE insertions present in all individuals of the species (core-genome), (ii) insertions present only among a subset of individuals (dispensable-genome) or (iii) ecogenome when the individuals share the same environment, and finally (iv) insertions specific to an individual. Current pangenome analysis methods are based on the alignment of reads from di↵erent accessions of the species to an assembled reference genome. But, the advent of the third-generation sequencing makes now possible to approach this question on several assembled genomes of the same species. I will present a new pipeline which identify the TEs pangenome compartments from several assembled genomes. There is therefore no dependency on a reference genome. This new pipeline uses a bidirectional best hits strategy to detect the copies located at the same position and shared by one or more accessions. The pipeline have been tested with Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon pangenomes.
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titre
Identification of CTG.CAG contraction factors in Myotonic Dystrophy type 1
auteur
Laure de Pontual, Antoine Mangin, Sonia Lameiras, Bin Yang, Tina Alaeitabar, François-Xavier Lejeune, Sylvain Baulande, Geneviève Gourdon, Vincent Dion, Stéphanie Tomé
article
FASEB, The dynamic DNA structures in biology conference, Jun 2022, Nova Scotia, Canada
resume
Background: Myotonic dystrophy type 1 (DM1) is a neuromuscular disease caused by an abnormal CTG repeat expansion in the 3’UTR region of the DMPK gene. In patients, the CTG repeat size ranges from 50 to thousands of CTG and usually increases over generations and time in the tissues. Larger expansions are associated with more severe symptoms and a decreasing age of onset. We hypothesize that the development of innovative therapeutic strategies, aimed at decreasing the CTG repeat length, and thus to stop or reverse the progression of the disease, may improve the quality of life of DM1 patients. Although many studies have provided insight into the mechanisms underlying the formation of expansions, how the contractions occur remains elusive. Aims: The specific objective of our work is to uncover bioactive molecules able to induce repeat contractions in trinucleotide repeat (TNR) models and to decipher the mechanisms promoting these contractions using efficient tools. Methods: We performed a large-scale screen for pharmacologically relevant chemical modulators of instability using the Prestwick Library (>1200 FDA-approved drugs) taking advantage of a chromosomal GFP reporter that can accurately measure both expansions and contractions in the same HEK293 cell population1. The effect of selected molecules directly on the dynamics of CTG.CAG repeat instability is studied in HEK293 cells as well as DM1 fibroblasts using targeted long-read sequencing developed by Pacific Biosciences2. Results: During the chemical screen, we identified several candidate molecules notably involved in epigenetic regulation pathways, that may change the size of CTG repeats. Some of these molecules induced stabilization or even contractions of CTG repeats in the HEK cell model and in DM1 fibroblasts. Conclusions: The next step is to better understand the mechanisms by which these molecules act on CTG repeat instability. The direct perspective of our work is to identify new small molecules and new druggable targets promoting CAG.CTG repeat contractions, thus offering new therapeutic perspectives for DM1 but also for other TNR diseases. 1Santillan et al. (2014). PloS One 9, e113952. 2Mangin et al. (2021). Int J Mol Sci 22, 2616.
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titre
Plant science data management and integration: the heterogeneity and dispersion challenge
auteur
Cyril Pommier
article
Applied Bioinformatics in Life Sciences (4th edition), Mar 2022, Louvain, Belgium
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Poster communications

titre
REPET evolutions: faster and easier
auteur
Johann Confais, Mariène Wan, Hadi Quesneville
article
6th Uppsala Transposon Symposium, Oct 2022, Uppsala, Sweden.
resume
The detection and annotation of transposable elements (TEs) are now considered mandatory to any genome sequencing project. To this aim, the REPET package integrates bioinformatics pipelines dedicated to detect, annotate and analyse TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement. Several implementations and algorithms to reduce the time required for analysing large genome have been tested. With our new speed improvements and tuned annotation strategies, REPET is now able to annotate and analyse easily large genomes up to 3 Gb. Now, we chain all required steps through a process called "Repet-Factory". This process uses parameters optimized for specificity and computing time. It is capable of successively annotate several genomes in batches with all the traceability required for reproducibility. We also simplified the distribution of REPET by developing a Docker image of REPET (https://hub.docker.com/r/urgi/docker_vre_aio).
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titre
Research Data Management Toolkit (RDMkit): guidelines for plant phenotyping data management and sharing
auteur
Erwan Le Floch, Anne-Françoise Adam-Blondon, Isabelle Alic, Bert Droesbeke, Stijn Dhondt, Daniel Faria, Sebastian Beier, Pascal Neveu, Nicolas Francillonne, Célia Michotey, Cyril Pommier.
article
7th International Plant Phenotyping Symposium, Sep 2022, Wageningen, Netherlands. , 2022, ⟨10.5281/zenodo.7148792⟩
resume
Efficient sharing of plant phenotyping data is a challenge that has been addressed during the last two decades by European infrastructures (ELIXIR, EMPHASIS) and international communities (CGIAR), that allowed to coordinate the effort of major institutes developing activities in the domain. They produced consistent and interoperable sets of resources to support plant phenotyping data management: - data standards: Minimum Information About Plant Phenotyping Experiment (MIAPPE) and the Breeding API (BrAPI) - databases: PIPPA, PHIS, GnpIS, e!DAL-PGP among others - exchange file formats: MIAPPE Template, ISA-Tab These systems and standards have been designed to be as close as possible to researchers and experimenters needs. As a consequence, important efforts have been made to ease their adoption through documentations and trainings. However all these resources remain dispersed, and it can be complicated for new users to know where to get the right information. To address this issue, ELIXIR has developed in the frame of the ELIXIR-CONVERGE project a central portal of guidelines and resources supporting FAIR data management in Life Sciences: the Research Data Management toolkit (RDMkit). RDMkit is a one stop portal that gives a general overview and understanding of the complementarity of the solutions, and links back to the extended documentation and training materials maintained for each of them. To develop and sustain this portal, ELIXIR has engaged with various communities, infrastructures and projects, among which the ELIXIR plant science community and the AGENT project. In the RDMkit, the plant community has built a set of pages and in particular is building plant phenotyping guidelines. The present poster gives an overview of the RDMkit logic and of the solutions presented in the plant sciences pages, including the procedures and contact to submit enrichment and additional solutions.
DOI
DOI : 10.5281/zenodo.7148792
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https://hal.inrae.fr/hal-03800325/file/2022-09-RDMkit-IPPS-poster-final.pdf BibTex
titre
REPET evolutions: faster and easier
auteur
Mariène WAN, Johann Confais, Hadi Quesneville
article
Jobim 2022, Jul 2022, Rennes, France.
resume
Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. Their detection and annotation are considered essential and must be undertaken in any genome sequencing project. The REPET package [1, 2] integrates bioinformatics pipelines dedicated to detect, annotate and analyze TEs in genomic sequences. The two main pipelines are (i) TEdenovo, that search for interspersed repeats, build consensus sequences and classify them [3] according to TE features and (ii) TEannot, which mines a genome with a library of TE sequences, for instance the one produced by the TEdenovo pipeline, to provide TE annotations. The REPET package is in continuous improvement for speed by parallelizing several key bottleneck steps. In addition, several strategies which reduce the time required for analyzing large genome have been tested. With the speed improvement and adapted strategies, REPET is now able to annotate and analyze genomes such as the maize with more than 85% of TEs on a 2.3 Gb genome [4] on current computer cluster. With this tool, the PlantBioinfoPF platform ensures a TE annotation service. Indeed, we are now able to propose an automatic TE annotation of good quality through a process called "Repet-Factory". This process uses the REPET software suite with parameters optimized for TE detection specificity and computing time. This process is capable of successively annotate several genomes in batches with the required traceability and reproducibility of the analyzes. Moreover, a Virtual Research Environment (VRE) for TE annotation and its analysis has been developed on Virtual Machines (VM). An ansible script instantiate VMs with all packages and tools required for a complete genome annotation with the REPET package. This script allows this VRE to be easily re-instantiated in other infrastructures which greatly simplify the REPET package installation with all its required dependencies. We also simplified the distribution of REPET to increase its availability and portability to users, by developing a Docker image of REPET (https://hub.docker.com/r/urgi/docker_vre_aio). The REPET tool is a cornerstone of the platform. In addition to its use in the genome TE annotation service and its availability for download, it is also the basis of the RepetDB [5] database (https://urgi.versailles.inrae.fr/repetdb) hosted by the platform which provides libraries of reference TE sequences for more than 50 species. References 1. Flutre T, Duprat E, Feuillet C, Quesneville H (2011) Considering Transposable Element Diversification in De Novo Annotation Approaches. PLoS ONE 6(1): e16526. https://doi.org/10.1371/journal.pone.0016526 2. Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, et al. (2005) Combined Evidence Annotation of Transposable Elements in Genome Sequences. PLoS Comput Biol 1(2): e22. https://doi.org/10.1371/journal.pcbi.0010022 3. Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, et al. (2014) PASTEC: An Automatic Transposable Element Classification Tool. PLoS ONE 9(5): e91929. https://doi.org/10.1371/journal.pone.0091929 4. V. Jamilloux, J. Daron, F. Choulet and H. Quesneville, "De Novo Annotation of Transposable Elements: Tackling the Fat Genome Issue," in Proceedings of the IEEE, vol. 105, no. 3, pp. 474-481, March 2017, doi: 10.1109/JPROC.2016.2590833. 5. Amselem, J., Cornut, G., Choisne, N., Alaux, M., Alfama-Depauw, F., Jamilloux, V., Maumus, F., Letellier, T., Luyten, I., Pommier, C., Adam-Blondon, A. F., & Quesneville, H. (2019). RepetDB: a unified resource for transposable element references. Mobile DNA, 10, 6. https://doi.org/10.1186/s13100-019-0150-y
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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
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⟩
resume
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
titre
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, 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, Véronique Jorge
article
Global Ecology and Biogeography, 2021, 30 (3), pp.590-597. ⟨10.1111/geb.13239⟩
resume
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⟩
resume
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
titre
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⟩
resume
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
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.1-24. ⟨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.
DOI
DOI : 10.1371/journal.pone.0257996
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https://hal.science/hal-03807721/file/2021_Ben%20Amara_Plos%20One.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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Conference papers

titre
Mise en relation de données hétérogènes chez l’espèce modèle Arabidopsis thaliana dans une base de données graphe
auteur
Johann Confais, Nicolas Francillonne, Yanis Toumert
article
Work4Graph Integration, Dec 2021, Paris, France
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titre
FAIR characterization data of genetic resources: making it real?
auteur
Anne-Françoise Adam-Blondon
article
INTEGRAPE 2021 - Achievements, industry needs and next steps, Anne-Françoise Adam-Blondon; Mario Pezzotti, Jun 2021, Virtuel, France
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https://hal.inrae.fr/hal-03316847/file/Integrape_3rdAG_RG_FAIR_data_010721_vf.pdf BibTex

Report chapter

titre
ELIXIR-CONVERGE: Connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services (871075)
auteur
Laura Portell Silva, Salvador Capella-Guttierez, Pinar Alper, Teresa d'Altri, Adam Hospital, Espen Aberg, Daniel Faria, Anne-Françoise Adam-Blondon
article
2021
resume
The goal of ELIXIR Converge WP5 is to assess the capacity of ELIXIR and its national nodes to assist users’ projects in implementing Data Management Plans (DMPs) in their projects at a EU scale. To do that, six demonstrator use-cases were created and they are described in the previous deliverable (D5.1 - 10.5281/zenodo.4674490 ). This deliverable includes a description of the main resources that can be used to assess researchers in the process of creating DMPs for at least two use-cases including a gap analysis. The DMPs are related to the demonstrator use-case #1 (Plant sciences) and #3 (Marine metagenomics). Moreover, specific aspects for use-cases #4 (Human data) and #6 (Biomolecular simulation) are also added. The main activities described in this deliverable are related to the ELIXIR Research Data Management Kit (RDMkit : https://rdmkit.elixir-europe.org/) and the Data StewardshipWizard (DSW : https://ds-wizard.org/) in connection with ELIXIR Converge WP3 activities. For all use-cases except use-case 5 (Toxicology data), a ‘Your domain’ page in the RDMkit has been assembled with the information necessary to consider when managing research data in their corresponding domains. Also, a ‘Tool assembly’ page in the RDMkit for the plant sciences, marine metagenomics and human data use-cases have been added. Finally, the DSW has been used to perform the initial description of the first DMPs including a gap analysis. Since ELIXIR Converge started, the work of WP5 has been centered in understanding the needs of the demonstrator use-cases to develop, if necessary, customized DMPs for each of them considering the domains they are part of. Also, once this characterization was done, several resources have been created to help users in the development of their DMPs. Indeed, these demonstrators are expected to serve as examples for researchers developing their own DMPs. The domain and tool assemblies pages added in the RDMkit are ready to use internally in ELIXIR after the beta-release in February, 2021. They provide a valuable resource for researchers and data stewards in the life sciences to help them in their data management processes. The Knowledge Models (KMs), the central component of the DSW, are under periodic revision to incorporate outcomes from ELIXIR Converge including specific aspects identified by the use-cases in order to complete their content and release an official version of them. The final objective is to provide refined DMP versions for the remaining 4 use-cases. This will allow us to cover a broad range of data-driven demonstrators, with its associated challenges, and assess how the general process scales up when applied to other communities served by ELIXIR. All these efforts will contribute to harden the work developed in other ELIXIR Converge WPs like the RDMkit and the DSW (WP3), the dedicated training materials and capacity building actions (WP2) as well as to provide reference information to the data management experts network (WP1) and external members to the project, e.g. Industry, in WP4.
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https://hal.inrae.fr/hal-03310250/file/ELIXIR-CONVERGE%20D5.2%20Report%20on%20the%20first%20two%20DMP%20processes.pdf BibTex

Other publications

titre
Toward a critical assessment of virus detection in plants
auteur
Hadi Quesneville
article
2021, pp.100007. ⟨10.24072/pci.genomics.100007⟩
resume
The advent of High Throughput Sequencing (HTS) since the last decade has revealed previously unsuspected diversity of viruses as well as their (sometimes) unexpected presence in some healthy individuals. These results demonstrate that genomics offers a powerful tool for studying viruses at the individual level, allowing an in-depth inventory of those that are infecting an organism. Such approaches make it possible to study viromeswith an unprecedented level of detail, both qualitative and quantitative, which opens new venues for analyses of viruses of humans, animals and plants. Consequently, the diagnostic field is using more and more HTS, fueling the need for efficient and reliable bioinformatics tools
DOI
DOI : 10.24072/pci.genomics.100007
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https://hal.science/hal-03189070/file/DOC.pdf BibTex
titre
ELIXIR Plant sciences 2020-2023 Roadmap
auteur
Cyril Pommier, Kristina Gruden, Astrid Junker, Frederik Coppens, Richard Finkers, Keywan Hassani-Pak, Daniel Faria, John M Hancock, Sebastian Beier, Bruno Costa, Célia Miguel, Inês Chaves, Robert P Davey, Bruno Contreras-Moreira
article
2021, ⟨10.7490/f1000research.1118482.1⟩
resume
The Plant Sciences Community is an interdisciplinary group of researchers with diverse backgrounds from computer science to different fields of plant biology. We answer the needs of both bioinformaticians and plant biologists. The Community objective is to develop an infrastructure supporting the integration and linking of phenotypic, genotypic, *omics (e.g. expression, metabolomic, ...) and bibliographic data. The underlying scientific use cases encompass genetics and genomics approaches in plant sciences with an extension of the scope towards system biology. The community aims at promoting tools, databases, standards and best practices for plant research. The present document describe the Plant Community activites in the frame of the ELIXIR Scientific Programme 2019-2023 (https://doi.org/10.7490/f1000research.1117352.1).
DOI
DOI : 10.7490/f1000research.1118482.1
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Poster communications

titre
Transposable Element annotation in allotetraploid Nicotiana tabacum and its extant diploid progenitor genomes
auteur
C Mhiri, V Jamilloux, N Choisne, M.-A Grandbastien
article
POLYDIV Polyploidy & Biodiversity, Oct 2021, Rennes, France.
resume
Allopolyploidy is known to have a significant impact on plant evolution, frequently causing epigenetic, structural and functional genomic modifications. Due to their transpositional activity and repetitive nature, transposable elements (TEs) may play a key role in these genomic alterations. We focused our investigations on one of the most recent Nicotiana allopolyploids (formed ca 0.5 MYA), i.e. N. tabacum (tobacco), which arose from hybridization between progenitors of the extant diploid species N. sylvestris and N. tomentosiformis, and which contains well characterized active TEs. We conducted TE annotations by using pipelines of the REPET suite on publicly available genomes. REPET analysis reveals that TEs represent over 65% of the three Nicotiana genomes, with a major contribution of retrotransposons (over 40%). Around 1900 to 2230 TE consensus sequences were generated for each genome, and clustered by the MCL algorithm. We analyzed the distribution and genome coverage of different active endogenous retrotransposon families - including Tnt1- across tobacco and its parental genomes. Preliminary results show that the distribution of clusters matching these families over the 3 Nicotiana species fits well with what is known about these retrotransposon biology, abundance and diversity. As shown for Tnt1, complete copies display a higher copy number and genome coverage than incomplete ones, underlying the persistent activity of this retrotransposon in these Nicotiana species. Such analysis could be adapted to infer the dynamics of other not fully characterized Nicotiana retrotransposon families.
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titre
TE Hub: a community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation
auteur
Tyler A. Elliott, Tony Heitkam, Robert Hubley, Hadi Quesneville, Alexander Suh, Travis J. Wheeler, . The Te Hub Consortium
article
The Mobile DNA Conference: Evolution, Diversity, and Impact, Jun 2021, Virtuel, France. 2021
resume
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, create, and integrate resources and methods.
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03357402/file/Wheeler_FASEB_2021_TEHub_final.pdf BibTex

Reports

titre
ELIXIR-CONVERGE: Connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services (871075)
auteur
Anne-Françoise Adam-Blondon, Pinar Alper, Salvador Capella-Guttierez, Daniel Faria, Laura Portell Silva, Adam Hospital, Nils-Peder Willassen
article
[Research Report] INRAE. 2021
resume
Task 5.1 aims to analyse the different demonstrators in light of the process necessary to implement their DMPs and to propose a categorization based on users’ needs. This effort will provide input to WP1 with respect to needs in terms of experts and resources across ELIXIR Nodes (Task 1.3, Business plans). It is expected that some of them will be generic whereas others will be very specific to projects, which is an important factor for establishing a strategy towards the sustainability of such a service in all its diversity. D5.1 therefore describes the needs in terms of DMP of the demonstrator use-cases and proposes a project categorization from the point of view of : - Area of expertise - The resources they use / toolkit - Training needs The first challenge was to develop a method to describe the needs of the users and their current practices in terms of data management as a prerequisite to the development of an adequate toolkit. The method adopted with the guidance of WP2 and WP3 relied on the description of users stories, and scenarios for different types of personas. In addition, a table was also developed to collect knowledge on the current practices and existing resources in terms of data management with guidance from WP1 and WP3. The six demonstrator use-cases are divided into two waves to facilitate having a broad diversity of data types, potential users and variable expertise and, at the same time, have first mature demonstrator use-cases that can start providing input to other WPs in the projects. The Plant and the Marine Metagenomics demonstrator use-cases were used as testers for the method developed as they are the two selected ones for the first wave. Federated access to human genomics data belongs to the second wave of demonstrator use-cases. However, considering its broad reach, it has been partially developed for this deliverable. User stories and scenarios with personas were developed by WP5 partners on the Plant, Marine metagenomics and Federated access to human genomics data: GDPR use-cases. The table on existing tools and resources was also filled in by WP5 partners and target interviews of researchers for some of the demonstrator use-cases. Additional input was sought from the ELIXIR communities for the demonstrator use-cases mentioned before. This method implemented to describe the demonstrator use-cases in detail has been efficient to isolate the specific context of each case, and to identify specific tools/resources in relation with the use-cases that can be used for data management. The main aspect used to classify a new use-case is the type of biological material linked to the data that links to many specific requirements, e.g. legal and scientific metadata. The second is the relation of the personas with the data, e.g. consumers/producers, and the type of data, including workflows, models, and the various types of experimental data. The landscape analysis of the resources already available in relation with the demonstrator use-cases and the different stages of a data management plan, showed that the guidelines developed by WP1 are very useful to clarify the scope of these stages before filling such a survey. The personas/users related to the use-cases are very diverse but always include the researchers in various positions, e.g. data consumer, data producer, data owner, PI writing a proposal, and the data curators. This will be further developed in collaboration with WP2. Finally, the work achieved to deliver D5.1 facilitated the development of pages dedicated to the “domains” in the RDMKit website (https://rdmkit.elixir-europe.org/) for demonstrator use-case 1, 3, 4 and 6. In these pages, specific challenges linked with the demonstrator use-cases are highlighted, and dedicated resources to solve them are listed. These tools have also been flagged in bio.tools with the domain name.
DOI
DOI : 10.5281/zenodo.4674491
Accès au texte intégral et bibtex
https://hal.inrae.fr/hal-03310082/file/ELIXIR-CONVERGE%20D5.1%20Categorisation%20of%20the%20pilot%20projects.pdf BibTex