Combining mobilome-seq and de novo genome assemblies to reveal TE dynamics in plant populations

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Mirouze, Marie | Lanciano, Sophie | Llauro, Christel | Zhang, Panpan

Edité par CCSD -

International audience. Plant populations differ in their Transposable Element (TE) repertoire and in their capacities of controlling these TEs through epigenetic regulations. To better understand adaptive capacities of TEs in plants, a comprehensive analysis of both active TEs and TE insertion polymorphisms, implying high quality de novo genome assemblies, are needed. First, to have access to the repertoire of actively transposing TEs we developed the mobilome-seq. It consists in purifying extrachromosomal circular forms of active TEs and using high throughput sequencing both on the Illumina Miseq platform (short reads) and Oxford Nanopore Technology (ONT) MinION (single molecule sequencing, super high length reads). Using this approach we successfully detected active TEs in both Arabidopsis thaliana and Oryza sativa species. Second, to obtain high quality genome assemblies we developed a pipeline to assemble Arabidopsis thaliana genomes de novo using ONT-MinION data only. I will discuss the complementarity of both approaches and the promises they offer in our efforts to unravel the contribution of TEs to plant adaptation.

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