bioRxiv preprint : https://doi.org/10.1101/2024.06.17.598857

The Brachypodium distachyon pangenome highlights Transposable Element dynamics in the species

The role of transposable elements (TEs) in host adaptation can be explored with a pangenomic
approach. Individuals of the same species undergo independent TE insertions, causing genetic
variability upon which natural selection acts. This can lead to improved adaptation of individuals
to their environment. The advent of third-generation sequencing has enabled use of multiple
whole-genome de novo assemblies for a given species, avoiding bias introduced by a single
reference genome. We developed a new pipeline, panREPET, for such data. It compares TE copies
between each pair of individuals then identifies copies shared by a group of individuals. This gives
the exact sequence and genomic context of each TE copy. We describe here TE insertions shared
among 54 Brachypodium distachyon genomes. We were able to date two major TE bursts
corresponding to major climate events: 22 kya during the Last Glacial Maximum and 10 kya
during the Holocene.

panTEannot source code is available at https://forgemia.inra.fr/urgi-anagen/panTEannot
panrREPET source code is available at https://forgemia.inra.fr/urgi-anagen/panREPET