Mobilome sequencing: a new technique to identify active retrotransposons and analyse their epigenetic impacts on tropical crop phenotypes

Transposable elements (TEs) are now recognised as major drivers of plant genome evolution, both through their mutagenic properties and though the epigenetic regulation that they can drive. TEs can be mobilized when plants have to face environmental challenges and this might have phenotypic, genetic, and epigenetic consequences. However, the repertoire of mobile TEs in stressed crops is not known. It is indeed technically challenging to identify mobile TEs that can be mobilized in a subset of the plant cells. To tackle this problem we have developed a new technique to identify the diversity of mobile elements, constituting the mobile part of the genome or “mobilome” in plants. This technique is based on the targeted high-throuput sequencing of the extrachromosomal part of the genome, notably constituted by active TEs. Using this technique we have successfully identified previously known mobile TEs in the model plant Arabidopsis and in rice. Furthermore we have identified an interesting novel TE that is active in specific developmental stages in rice.