@article{fdi:010070371,
  title = {{D}etection of active transposable elements in {A}rabidopsis thaliana using {O}xford {N}anopore {S}equencing technology},
  author = {{D}ebladis, {E}. and {L}lauro, {C}. and {C}arpentier, {M}. {C}. and {M}irouze, {M}arie and {P}anaud, {O}.},
  editor = {},
  language = {{ENG}},
  abstract = {{B}ackground: {T}ransposables elements ({TE}s) contribute to both structural and functional dynamics of most eukaryotic genomes. {B}ecause of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today's genomics. {T}he recent development of {NGS} (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of {T}ransposable {E}lements-associated {S}tructural {V}ariants ({TEASV}). {H}owever, these have relied on {I}llumina platform that generates short reads (up to 350 nucleotides). {T}his limitation in size of sequence reads can cause high false discovery rate ({FDR}) and therefore limit the power of detection of {TEASV}s, especially in the case of large, complex genomes. {T}he newest sequencing technologies, such as {O}xford {N}anopore {T}echnologies ({ONT}) can generate kilobases-long reads thus representing a promising tool for {TEASV} detection in plant and animals. {R}esults: {W}e present the results of a pilot experiment for {TEASV} detection on the model plant species {A}rabidopsis thaliana using {ONT} sequencing and show that it can be used efficiently to detect {TE} movements. {W}e generated a similar to 0.8{X} genome coverage of a met1-derived epigenetic recombinant inbred line (epi{RIL}) using a {M}in{I}on device with {R}7 chemistry. {W}e were able to detect nine new copies of the {LTR}-retrotransposon {E}vade ({EVD}). {W}e also evidenced the activity of the {DNA} transposon {CACTA}, {CAC}1. {C}onclusions: {E}ven at a low sequence coverage (0.8{X}), {ONT} sequencing allowed us to reliably detect several {TE} insertions in {A}rabidopsis thaliana genome. {T}he long read length allowed a precise and un-ambiguous mapping of the structural variations caused by the activity of {TE}s. {T}his suggests that the trade-off between read length and genome coverage for {TEASV} detection may be in favor of the former. {S}hould the technology be further improved both in terms of lower error rate and operation costs, it could be efficiently used in diversity studies at population level.},
  keywords = {{T}ransposable elements ; {A}rabidopsis ; {O}xford {N}anopore {T}echnology ; {S}equencing},
  booktitle = {},
  journal = {{BMC} {G}enomics},
  volume = {18},
  numero = {},
  pages = {art. 537 [8 p.]},
  ISSN = {1471-2164},
  year = {2017},
  DOI = {10.1186/s12864-017-3753-zg},
  URL = {https://www.documentation.ird.fr/hor/fdi:010070371},
}