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15 Jul 2024 [hal-04646807] URGI Plant Bioinformatics Facility (PlantBioinfoPF) data management plan

The Plant Bioinformatics Facility (PlantBioinfoPF - doi:10.15454/1.5572414581735654E12) supports research activities in plant genetics and genomics. It is hosted by URGI, an INRAE research unit. The services offered by the platform cover database design, software engineering, software hosting, data integration and training. The platform's activities benefit from URGI's research activities (data integration, annotation of repeats, study of genome structure and evolution). PlantBioinfoPF belongs to IFB (Institut Français de Bioinformatique), the French node of the Elixir European network of bioinformatics platforms. It has been certified by INRAE's ISC (Infrastructure Scientifique Collective) committee and by the GIS IBISA (Groupement d'Intérêt Scientifique - Infrastructures en Biologie Sante et Agronomie) as a national strategic platform. The platform also belongs to the INRAE Research Infrastructure BioinfOmics and is part of the Saclay Plant Science Network and the Biosphera Graduate School. It is ISO9001 v. 2015 certified. PlantBioinfoPF's data management plan describes the lifecycle of the data managed by the platform via 3 management modes: 1) "Information Systems" details the management of data in our Information systems (GnpIS warehouse and p PlantBioinfoPF's data management plan describes the various stages in the lifecycle of the data managed by the platform via 3 management modes: 1) "Information systems" details the management of data in our Information systems (GnpIS warehouse and data federation portals), 2) "Software" details the management of the source code of the software we develop and 3) "Genome analysis" details the management of data as part of our genome analyses.

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COM (communication)
06 May 2024 [hal-04570060] RepetDB: A TE database

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 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 (‘googlelike 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.

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In ProdINRA

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COM (communication)
06 May 2024 [hal-04570060] RepetDB: A TE database

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 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 (‘googlelike 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.

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In ProdINRA

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COM (communication)
22 Mar 2024 [hal-04516410] panREPET: A Pipeline to characterize Transposable Elements in Pangenomes on de novo assembled genomes

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, the advent of the third-generation sequencing makes now possible to better approach this question using several 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 allows to improve the description of the evolutionary history of TE families and to date insertion events more precisely. We have also searched for factors affecting the evolutionary dynamics of TE families: we found that climate is a factor that may explain certain TE dynamics.

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COM (communication)
11 Mar 2024 [hal-04498577] Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing

Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions. Here, we use the Zymoseptoria tritici-wheat model to elucidate the genetic architecture of quantitative pathogenicity and mechanisms mediating host adaptation. With a multi-host genome-wide association study, we identify 19 high-confidence candidate genes associated with quantitative pathogenicity. Analysis of genetic diversity reveals that sequence polymorphism is the main evolutionary process mediating differences in quantitative pathogenicity, a process that is likely facilitated by genetic recombination and transposable element dynamics. Finally, we use functional approaches to confirm the role of an effector-like gene and a methyltransferase in phenotypic variation. This study highlights the complex genetic architecture of quantitative pathogenicity, extensive diversifying selection and plausible mechanisms facilitating pathogen adaptation.

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COM (communication)
05 Mar 2024 [hal-04490876] Comment les nouveaux OGM relancent la question de la brevetabilité du vivant

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