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Article

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore

1
Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France
2
IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France
3
Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France
4
Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
5
MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, 34094 Montpellier, France
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Cells 2020, 9(8), 1776; https://doi.org/10.3390/cells9081776
Received: 27 June 2020 / Revised: 17 July 2020 / Accepted: 23 July 2020 / Published: 25 July 2020
(This article belongs to the Special Issue Evolution of Epigenetic Mechanisms and Signatures)
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 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 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. View Full-Text
Keywords: transposable elements; ONT; Drosophila melanogaster; Drosophila simulans; piRNA transposable elements; ONT; Drosophila melanogaster; Drosophila simulans; piRNA
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MDPI and ACS Style

Mohamed, M.; Dang, N.T.-M.; Ogyama, Y.; Burlet, N.; Mugat, B.; Boulesteix, M.; Mérel, V.; Veber, P.; Salces-Ortiz, J.; Severac, D.; Pélisson, A.; Vieira, C.; Sabot, F.; Fablet, M.; Chambeyron, S. A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Cells 2020, 9, 1776. https://doi.org/10.3390/cells9081776

AMA Style

Mohamed M, Dang NT-M, Ogyama Y, Burlet N, Mugat B, Boulesteix M, Mérel V, Veber P, Salces-Ortiz J, Severac D, Pélisson A, Vieira C, Sabot F, Fablet M, Chambeyron S. A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Cells. 2020; 9(8):1776. https://doi.org/10.3390/cells9081776

Chicago/Turabian Style

Mohamed, Mourdas, Nguyet T.-M. Dang, Yuki Ogyama, Nelly Burlet, Bruno Mugat, Matthieu Boulesteix, Vincent Mérel, Philippe Veber, Judit Salces-Ortiz, Dany Severac, Alain Pélisson, Cristina Vieira, François Sabot, Marie Fablet, and Séverine Chambeyron. 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, no. 8: 1776. https://doi.org/10.3390/cells9081776

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