Horizon / Plein textes La base de ressources documentaires de l'IRD

IRD

Publications des scientifiques de l'IRD

Debladis E., Llauro C., Carpentier M. C., Mirouze Marie, Panaud O. (2017). Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology. BMC Genomics, 18, art. 537 [8 p.]. ISSN 1471-2164

Fichier PDF disponible http://horizon.documentation.ird.fr/exl-doc/pleins_textes/divers17-08/010070371.pdf

Lien direct chez l'éditeur doi:10.1186/s12864-017-3753-zg

En Libre Accès sur HAL http://hal.ird.fr/ird-01626046

Titre
Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology
Année de publication2017
Type de documentArticle référencé dans le Web of Science WOS:000405889200005
AuteursDebladis E., Llauro C., Carpentier M. C., Mirouze Marie, Panaud O.
SourceBMC Genomics, 2017, 18, p. art. 537 [8 p.]. p. art. 537 [8 p.] ISSN 1471-2164
RésuméBackground: Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because 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. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV). However, these have relied on Illumina platform that generates short reads (up to 350 nucleotides). This limitation in size of sequence reads can cause high false discovery rate (FDR) and therefore limit the power of detection of TEASVs, especially in the case of large, complex genomes. The newest sequencing technologies, such as Oxford Nanopore Technologies (ONT) can generate kilobases-long reads thus representing a promising tool for TEASV detection in plant and animals. Results: We present the results of a pilot experiment for TEASV detection on the model plant species Arabidopsis thaliana using ONT sequencing and show that it can be used efficiently to detect TE movements. We generated a similar to 0.8X genome coverage of a met1-derived epigenetic recombinant inbred line (epiRIL) using a MinIon device with R7 chemistry. We were able to detect nine new copies of the LTR-retrotransposon Evade (EVD). We also evidenced the activity of the DNA transposon CACTA, CAC1. Conclusions: Even at a low sequence coverage (0.8X), ONT sequencing allowed us to reliably detect several TE insertions in Arabidopsis thaliana genome. The long read length allowed a precise and un-ambiguous mapping of the structural variations caused by the activity of TEs. This suggests that the trade-off between read length and genome coverage for TEASV detection may be in favor of the former. Should 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.
Plan de classementSciences du monde végétal [076]
LocalisationFonds IRD [F B010070371]
Identifiant IRDfdi:010070371
Lien permanenthttp://www.documentation.ird.fr/hor/fdi:010070371

Export des données

Disponibilité des documents

Télechargment fichier PDF téléchargeable

Lien sur le Web lien chez l'éditeur

Accès réservé en accès réservé

HAL en libre accès sur HAL


Accès aux documents originaux :

Le FDI est labellisé CollEx

Accès direct

Bureau du chercheur

Site de la documentation

Espace intranet IST (accès réservé)

Suivi des publications IRD (accès réservé)

Mentions légales

Services Horizon

Poser une question

Consulter l'aide en ligne

Déposer une publication (accès réservé)

S'abonner au flux RSS

Voir les tableaux chronologiques et thématiques

Centres de documentation

Bondy

Montpellier (centre IRD)

Montpellier (MSE)

Nouméa

Papeete

Niamey

Ouagadougou

Tunis

La Paz

Quito