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International,  COM (communication) 30 Nov 2022   [hal-03876510] Transposable elements, from their annotation to their integration into knowledge graphs

Transposable elements (TEs) are major players of structure and evolution of eukaryote genomes. Thanks to their ability to move around and to replicate within genomes, they are probably the most important contributors to genome plasticity. 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 REPET package integrates bioinformatics pipelines dedicated to detect and annotate TEs in genomes. Then the PanREPET pipeline allows to describe (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. To identify TE candidate putatively involved in local adaptation, environmental knowledge and genome annotations have been integrated in a semantic knowledge graph.

Update: 13 Dec 2022
Creation date: 30 Nov 2022