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Transposable elements (TEs) are mobile DNA elements that can invade the genomes by transposition. Despite their reputation as parasitic sequences, these elements can enrich the genomes with functional novelties that foster genome evolution. Indeed, TEs can impact genes through insertional mutagenesis, supplies of new transcription factor binding sites (TFBS), or by epigenetic regulation. 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 di↵erent 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 pangenome compartments from several assembled genomes. There is therefore no dependency on a reference genome. This new pipeline uses a bidirectional best hits strategy to detect the copies located at the same position and shared by one or more accessions. The pipeline have been tested with Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon pangenomes.
Creation date: 30 Nov 2022
eZ PublishPublication supervisor: A-F. Adam-Blondon
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