Thèse Caractérisation Pan-Génomique des Dynamiques d'Élément Transposables chez des Populations d'Arabidopsis Autogames et Hétérogames H/F - Doctorat.Gouv.Fr

Établissement : École normale supérieure - PSL (ENS-PSL) École doctorale : Sciences du Vivant Laboratoire de recherche : Institut de Biologie de l'École Normale Supérieure Direction de la thèse : Pierre BADUEL ORCID 0000000293382962 Début de la thèse : 2026-11-01 Date limite de candidature : 2026-08-31T23:59:59 Le projet MATTEL vise à explorer comment les modes de reproduction des plantes (auto-fécondation vs auto-incompatibilité) façonnent l'architecture de leur génome, en se concentrant sur une composante essentielle mais souvent masquée de la diversité génétique : les éléments transposables (ET). Ces séquences d'ADN, par leur capacité à se déplacer et à se multiplier au travers du génome, représentent une source majeure de mutations à large effet, parfois adaptatives mais le plus souvent délétères. Longtemps difficiles à analyser car très répétitifs, ces éléments seront ici cartographiés grâce à des technologies de séquençage en lectures longues. En comparant trois espèces apparentées du genre Arabidopsis, dont le mode de reproduction varie entre espèces mais aussi au sein de deux d'entre elles, nous déterminerons si l'autofécondation favorise l'accumulation des ET ou facilite au contraire leur élimination. Grâce à une approche interdisciplinaire rassemblant des expertises en analyse génomique et pan-génomique des ET, en évolution des modes de reproduction, et en génétique des populations, le projet vise à résoudre une question fondamentale en génomique : comment les stratégies de reproduction influencent la diversité génétique et ainsi l'évolution des espèces. Transposable elements (TEs) are sequences that can move and replicate around the genome. Although they have long been viewed as mere genomic parasites, with the advent of genomics TEs are now recognized as key players in genome regulation and evolution. Indeed, much of the variation in genome size among eukaryotes results from differences in the amount of TE sequences they harbor (1,2) and multiple lines of evidence indicate that TE sequences have often been co-opted/exapted in animals and plants to create new genes, coordinate the expression of many genes and rewire gene regulatory networks (3). Nonetheless, TEs remain endogenous mutagens with potentially devastating consequences, notably through disruption of genes or alterations in gene expression (3). Yet, despite their importance in understanding genomes, the determinants of TE mobilization dynamics remain largely unknown.
This knowledge gap results in large part from the difficulties posed by the study of repeat elements and structural variants in genome sequences obtained using short-reads technologies. However, with the development of long-read sequencing technologies such as Oxford Nanopore Technology (ONT) or PACBIO HiFi, the situation is changing radically and it is now possible to identify unambiguously any types of structural variants, including TE presence/absence polymorphisms (4). We are thus for the first time in a position to provide, in an efficient and cost-effective manner, comprehensive answers to the nature, the dynamics, and the impact of TE mobilization within and across species.Theoretical considerations predict a major impact of the mating system on the dynamics of TEs (5). Specifically, outcrossing is expected to be associated with an epidemic-like spread of active TEs, as these can shuffle among strains more readily than in selfing species (Hypothesis I). However, due to the smaller effective population size of selfing species, the efficacy of selection against weakly deleterious mutations is expected to be weaker in these species, enabling active TEs to accumulate more readily in them than in outcrossing species (Hypothesis II)(6). Yet, selfing lineages are also predicted to be able to purge more efficiently accumulating (recessive) deleterious mutations (Hypothesis III) (7). Thus, the impact of mating systems on TE dynamics is still unclear.The Arabidopsis genus represents a prime system to study the impact of selfing on the TE landscapes, as contrasted mating types have been described between the predominantly outcrossing Arabidopsis lyrata, and A. halleri and the self-compatible A. thaliana (8) as well as within A. lyrata (9). Moreover, these species have relatively small genomes (120Mbp to 250Mbp) that can be readily assembled de novo using long-read sequencing technologies. Their small genome size is associated with a reduced TE content (15-30%), yet that contains a large repertoire of active TE families encompassing a broad diversity of TEs of all classes and superfamilies (10). Analysis of A. lyrata and A. halleri genomes by the CASTRIC team revealed that these two mostly outcrossing Brassicaceae have an abundant population of recently inserted TEs (11), which are almost entirely absent from A. thaliana. In contrast, the population of ancient TEs is almost identical among the three species. These findings suggest an important role of the mating system in the accumulation of TEs, since selfing originated in A. thaliana only recently (8). Nonetheless, work from the host team has shown that despite the low abundance of recent TEs in A. thaliana, over half of the TE families annotated in the reference genome sequence are still active at the species level (10). Moreover, pan-genome graph analysis of recently mobile TEs in 90 long-read genomes by the host team revealed a previously-undescribed diversity of TEs at the species-level (Petit et al. in prep) suggesting the TE landscape is more variable among accessions in A. thaliana compared to its outcrossing relatives. Yet, the causes of the differences observed between A. thaliana and its two relatives A. lyrata and A. halleri in terms of TE composition remain unclear.Here, building on the expertise of the two partner teams and their collaborators and a large dataset of long-read genomes of A. thaliana, A. lyrata, and A. halleri, including for North-American A. lyrata and Japanese A. halleri strains (12) from natural populations with contrasted mating modes, we will assess the impact of selfing on TE landscapes at intra and inter-species evolutionary scales. Pan-genomic characterization of transposable elements dynamics in selfing and outcrossing Arabidopsis populations Following the reconstruction of the population history and loss of self-incompatibility in North-American A. lyrata and Japanese A. halleri, performed by collaborators, the PhD student will be responsible for the pan-genome graph analyses of recently mobile TEs using the long-read A. lyrata and A. halleri genomes. The PhD student will then proceed to analyze TE insertion polymorphisms throughout populations and estimate the effects of the shifts to selfing within and between selfing on TE landscapes.

Master 2 en bioinformatique, maitrise de l'environnement linux d'un cluster HPC et de l'analyse des données de séquençage en courtes et longues lectures, de l'assemblage des génomes, et de l'analyse des éléments transposables. Compétences en analyse de graphes de pan-génomes souhaitées. Notions en génétique des populations. Intérêt pour l'évolution et l'adaptation des plantes.