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.