Skip to Main content Skip to Navigation
Journal articles

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

Abstract : 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 of Drosophila 2 melanogaster and Drosophila 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 so far impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable 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.
Complete list of metadata

Cited literature [74 references]  Display  Hide  Download

https://hal.archives-ouvertes.fr/hal-02905128
Contributor : Francois Sabot <>
Submitted on : Thursday, July 23, 2020 - 10:38:03 AM
Last modification on : Saturday, September 18, 2021 - 3:37:25 AM
Long-term archiving on: : Tuesday, December 1, 2020 - 5:23:06 AM

File

cells-864342-revised.pdf
Files produced by the author(s)

Identifiers

Citation

Mohamed Mourdas, Nguyet Dang, Yuki Ogyama, Nelly Burlet, Bruno Mugat, et al.. A transposon story : from TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford Nanopore. Cells, MDPI, In press, ⟨10.3390/cells9081776⟩. ⟨hal-02905128⟩

Share

Metrics

Record views

463

Files downloads

393