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International,  COM (communication) 14 Nov 2023   [hal-04283863] Characterization of Transposable Elements in Pangenomes

Transposable elements (TEs) are mobile DNA elements that can invade genomes by transposition. Despite their reputation as parasitic sequences, they can enrich the genomes with functional novelties that foster genome evolution. The impact of 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. 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 assembled genomes of the same species to avoid the bias introduced by a single reference genome. I will present a new pipeline, called panREPET, which identify TE copies in a pangenome from several assembled genomes. There is therefore no dependency on a reference genome. This pipeline identifies copies shared by a group of individuals. This pipeline has been tested on 54 genomes of Brachypodium distachyon to describe its pangenomic compartments.


Creation date: 30 Nov 2023