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International,  COM (communication) 27 Dec 2022   [hal-03890780] Characterization of Transposable Elements in Pangenomes

The impact of TEs in a genome is explored by searching for insertions events. Individuals (or accessions) 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 is 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) insertions specific to an individual. Current pangenome analysis methods are based on the alignment of reads from different accessions of the species to an assembled reference genome. But, the advent of the third-generation sequencing makes now possible to approach this question on several assembled genomes of the same species. I will present a new pipeline which identify the TEs in pangenome compartments from several assembled genomes. There is therefore no dependency on a reference genome. This new pipeline identifies copies shared by a group of individuals. This pipeline has been tested on Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon pangenomes and compared with results from Minigraph, a pan-genome graph method to identify sequence variations.

Update: 02 Jan 2023
Creation date: 31 Dec 2022