A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a...

The role of transposable elements (TEs) in host adaptation has gained interest in recent years. Individuals of the same species undergo independent TE insertions, providing genetic variability within populations, upon which natural selection can act to foster adaptation to environmental conditions.

As de novo assembled genomes are becoming increasingly affordable, helping to overcome the bias introduced by relying on a single reference genome, there is a growing need for suitable pangenomic tools to explore the genomic diversity within a species. We developed a new pipeline called panREPET that identifies TE insertions shared by groups of individuals. Unlike other pangenomic tools, panREPET operates independently of a reference genome and provides the precise sequence and genomic coordinates of each TE copy for each genome.

We showcase the potential of this tool by identifying TE insertions shared among 42 Brachypodium distachyon genomes and by comparing our results with those of existing tools to demonstrate its advantages. Using panREPET, 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, showing a potential link between environmental stress and TE activity.