Publications

COM (communication)
09 Aug 2024 [hal-04669685] Complete genome of the Medicago anthracnose fungus, Colletotrichum destructivum , reveals a mini-chromosome-like region within a core chromosome

Abstract Colletotrichum destructivum ( Cd ) is a phytopathogenic fungus causing significant economic losses on forage legume crops ( Medicago and Trifolium species) worldwide. To gain insights into the genetic basis of fungal virulence and host specificity, we sequenced the genome of an isolate from M. sativa using long-read (PacBio) technology. The resulting genome assembly has a total length of 51.7 Mb and comprises 10 core chromosomes and two accessory chromosomes, all of which were sequenced from telomere to telomere. A total of 15,631 gene models were predicted, including genes encoding potentially pathogenicity-related proteins such as candidate secreted effectors (484), secondary metabolism key enzymes (110) and carbohydrate-active enzymes (619). Synteny analysis revealed extensive structural rearrangements in the genome of Cd relative to the closely-related Brassicaceae pathogen, C. higginsianum . In addition, a 1.2 Mb species-specific region was detected within the largest core chromosome of Cd that has all the characteristics of fungal accessory chromosomes (transposon-rich, gene-poor, distinct codon usage), providing evidence for exchange between these two genomic compartments. This region was also unique in having undergone extensive intra-chromosomal segmental duplications. Our findings provide insights into the evolution of accessory regions and possible mechanisms for generating genetic diversity in this asexual fungal pathogen. Impact statement Colletotrichum is a large genus of fungal phytopathogens that cause major economic losses on a wide range of crop plants throughout the world. These pathogens vary widely in their host specificity and may have either broad or narrow host ranges. Here, we report the first complete genome of the alfalfa ( Medicago sativa ) pathogen, Colletotrichum destructivum , which will facilitate the genomic analysis of host adaptation and comparison with other members of the Destructivum species complex. We identified a species-specific 1.2 Mb region within chromosome 1 displaying all the hallmarks of fungal accessory chromosomes, which may have arisen through the integration of a mini-chromosome into a core chromosome and could be linked to the pathogenicity of this fungus. We show this region is also a focus for segmental duplications, which may contribute to generating genetic diversity for adaptive evolution. Finally, we report infection by this fungus of the model legume, Medicago truncatula , providing a novel pathosystem for studying fungal-plant interactions. Data summary All RNA-seq data were submitted to the NCBI GEO portal under the GEO accession GSE246592. C. destructivum genome assembly and annotation are available under the NCBI BioProject PRJNA1029933 with sequence accessions CP137305 - CP137317 . Supplementary data (genomic and annotation files, genome browser) are available from the INRAE BIOGER Bioinformatics platform ( https://bioinfo.bioger.inrae.fr/ ). Transposable Elements consensus sequences are also available from the French national data repository, research.data.gouv.fr with doi 10.57745/TOO1JS.

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COM (communication)
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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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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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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