A transposon story : from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore.

Transposable elements (TEs) are the main components of genomes. Due to their repetitive nature, they are very difficult to study from DNA sequence data based on short read technologies. Here we provide an efficient pipeline to accurately recover TE insertion sites and sequences from long reads obtained using Oxford Nanopore Technology (ONT) sequencing. Focusing on wild-type strains of Drosophila melanogaster and Drosophila simulans, we were able to precisely describe the landscapes of the most recent TE insertions (TEIs). This allowed us to propose that both species are more similar than previously thought regarding this subset of TE sequences. The chromosome assemblies obtained following this pipeline also allowed to recover piRNA cluster sequences, which was so far impossible using short read data. In addition, we applied our pipeline on a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We were able to faithfully rely on single reads to identify new insertions displaying intact Target Site Duplications (TSDs). Moreover, the thorough analysis of TEIs of wild-type strains as well as of the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.