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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)
 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.
et al.
In ProdINRA
...
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.
et al.
In ProdINRA
...
COM (communication)
 05 Mar 2024 [hal-04490876] Comment les nouveaux OGM relancent la question de la brevetabilité du vivant
[...]
et al.
In ProdINRA
...
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
...
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
[...]
et al.
In ProdINRA
...
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Update: 19 Nov 2010
Creation date: 01 Dec 2009