Abstract 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 distachyo n 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.