@article{fdi:010079692,
  title = {{A} transposon story : from {TE} content to {TE} dynamic invasion of {D}rosophila genomes using the single-molecule sequencing technology from {O}xford {N}anopore},
  author = {{M}ohamed, {M}. and {D}ang, {N}guyet {T}hi-{M}inh and {O}gyama, {Y}. and {B}urlet, {N}. and {M}ugat, {B}. and {B}oulesteix, {M}. and {M}erel, {V}. and {V}eber, {P}. and {S}alces-{O}rtiz, {J}. and {S}everac, {D}. and {P}elisson, {A}. and {V}ieira, {C}. and {S}abot, {F}ran{\c{c}}ois and {F}ablet, {M}. and {C}hambeyron, {S}.},
  editor = {},
  language = {{ENG}},
  abstract = {{T}ransposable elements ({TE}s) are the main components of genomes. {H}owever, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. {H}ere, we describe an efficient pipeline to accurately recover {TE} insertion ({TEI}) sites and sequences from long reads obtained by {O}xford {N}anopore {T}echnology ({ONT}) sequencing. {W}ith this pipeline, we could precisely describe the landscapes of the most recent {TEI}s in wild-type strains of{D}rosophila melanogasterand{D}rosophila simulans. {T}heir comparison suggests that this subset of {TE} sequences is more similar than previously thought in these two species. {T}he chromosome assemblies obtained using this pipeline also allowed recovering pi{RNA} cluster sequences, which was impossible using short-read sequencing. {F}inally, we used our pipeline to analyze {ONT} sequencing data from a{D}. melanogasterunstable line in which {LTR} transposition was derepressed for 73 successive generations. {W}e could rely on single reads to identify new insertions with intact target site duplications. {M}oreover, the detailed analysis of {TEI}s in the wild-type strains and the unstable line did not support the trap model claiming that pi{RNA} clusters are hotspots of {TE} insertions.},
  keywords = {transposable elements ; {ONT} ; {D}rosophila melanogaster ; {D}rosophila simulans ; pi{RNA}},
  booktitle = {},
  journal = {{C}ells},
  volume = {9},
  numero = {8},
  pages = {1776 [23]},
  year = {2020},
  DOI = {10.3390/cells9081776},
  URL = {https://www.documentation.ird.fr/hor/fdi:010079692},
}