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Publications

URGI members are underlined in authors list. In the talks sections, names in bold are the speakers.

There are different types of publications, Papers with reading comittee (ACL), Papers in books (ACT), Invited talks (INV), Talks (COM), Posters (COM), Specialised Media and Press (SMP) and Thesis.

Other
COM (communication)
 07 Jul 2023 [hal-04156193] REPET novelties : a versatile and modular package
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.
et al.
In ProdINRA
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COM (communication)
 05 Jul 2023 [hal-04152917] Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes
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.
et al.
In ProdINRA
...
COM (communication)
 20 Jun 2023 [hal-04102220] A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat
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.
et al.
In ProdINRA
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COM (communication)
 16 Jun 2023 [hal-04130857] Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
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
et al.
In ProdINRA
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COM (communication)
 05 Jun 2023 [hal-04117938] Practical training III : REPET pipeline
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et al.
In ProdINRA
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COM (communication)
 05 Jun 2023 [hal-04117937] How to use REPET for de novo TE annotation
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et al.
In ProdINRA
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Update: 19 Nov 2010
Creation date: 01 Dec 2009