Mohamed M., Dang Nguyet Thi-Minh, Ogyama Y., Burlet N., Mugat B., Boulesteix M., Merel V., Veber P., Salces-Ortiz J., Severac D., Pelisson A., Vieira C., Sabot François, Fablet M., Chambeyron S. (2020). A transposon story : from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore. Cells, 9 (8), 1776 [23p.].
Titre du document
A transposon story : from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore
Année de publication
2020
Auteurs
Mohamed M., Dang Nguyet Thi-Minh, Ogyama Y., Burlet N., Mugat B., Boulesteix M., Merel V., Veber P., Salces-Ortiz J., Severac D., Pelisson A., Vieira C., Sabot François, Fablet M., Chambeyron S.
Source
Cells, 2020,
9 (8), 1776 [23p.]
Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains ofDrosophila melanogasterandDrosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from aD. melanogasterunstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020]
;
Sciences du monde animal [080]
Localisation
Fonds IRD [F B010079692]
Identifiant IRD
fdi:010079692
