Résumé
Transposable elements (TEs) represent a main source of genomic diversity and an evolutionary force in both plants and animals. Host genomes have developed epigenetic mechanisms to control and prevent their proliferation. However, under specific stress conditions or at precise developmental stages, some TEs can be remobilized and proliferate in plant genomes. In plants, only a few active TEs have been identified so far and the mobile part of the genome or mobilome, comprising these elements, is unknown. To establish an unbiased repertoire of mobile TEs after stress or during development, we have developed a strategy of high throughput sequencing that detects TEs extrachromosomal forms. Our method successfully identified known and novel active TEs in Arabidopsis and rice samples with destabilised epigenomes. I will present the identification of a new active retrotransposon in rice, which is both controlled by epigenetic and genetic mechanisms. The activity of this retrotransposon in different rice species suggests that it could play a role in plant development. Finally, I will show that this method can be applied to various organisms and represents a novel approach to understand and evaluate the extent and impact of real time TE mobility on eukaryotic genomes.This work is funded by an ANR JCJC (Extrachrom, 2014-2017).