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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)
26 Jan 2024 [hal-04419364] Evolutionary Dynamics of Transposable Elements in Brachypodium distachyon Based on a Pangenomic Approach
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.
et al.
In ProdINRA
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COM (communication)
14 Nov 2023 [hal-04283863] Characterization of Transposable Elements in Pangenomes
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.
et al.
In ProdINRA
...
COM (communication)
10 Nov 2023 [hal-04072018] Sidestepping Darwin: horizontal gene transfer from plants to insects
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et al.
In ProdINRA
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COM (communication)
02 Nov 2023 [hal-04267953] SNP discovery by exome capture and resequencing in a pea genetic resource collection
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
et al.
In ProdINRA
...
COM (communication)
11 Oct 2023 [hal-04237621] Linking heterogeneous data from model plant species in a graph database
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.
et al.
In ProdINRA
...
COM (communication)
15 Sep 2023 [hal-04208925] Insertion et exploitation de données hétérogènes dans un graphe de connaissance
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.
et al.
In ProdINRA
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Update: 19 Nov 2010
Creation date: 01 Dec 2009