The Brachypodium distachyon Pangenome Highlights Transposable Element Dynamics in the Species
2025
Confais, Johann | Saidi, Somia | Quesneville, Hadi | Unité de Recherche Génomique Info (URGI) ; Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) | IR BioInfOmics ; Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
International audience
Afficher plus [+] Moins [-]anglais. Individuals of the same species independently undergo transposable elements (TEs) insertions, causing inter-individual genetic variability. This variability 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 advent of long-read sequencing technologies makes now possible to approach this question better using several whole-genome de novo assembled of the same species to avoid the bias introduced by a single reference genome. We developed a new pipeline, called panREPET, to handle this data. It compares TE copies between each pair of individuals then identifies TE copies shared by a group of individuals. As we work on assembled genomes, we access to exact genomic contexts of TE copies and their exact sequences. We described the shared TEs insertions among 54 Brachypodium distachyon genomes. panREPET allows to improve TE families evolutionary history description and to date insertion events more precisely thanks to shared TE insertions. We dated two major TE bursts corresponding to major climate events: around 22 kya during the Last Glacial Maximum and 10 kya during the Holocene. We searched for factors affecting TE families evolutionary dynamics, we found that climate is a factor that may explain certain TE dynamics.
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