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TE-Tracker: systematic identification of transposition events through whole-genome resequencing

BACKGROUND: Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA seque...

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Autores principales: Gilly, Arthur, Etcheverry, Mathilde, Madoui, Mohammed-Amin, Guy, Julie, Quadrana, Leandro, Alberti, Adriana, Martin, Antoine, Heitkam, Tony, Engelen, Stefan, Labadie, Karine, Le Pen, Jeremie, Wincker, Patrick, Colot, Vincent, Aury, Jean-Marc
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279814/
https://www.ncbi.nlm.nih.gov/pubmed/25408240
http://dx.doi.org/10.1186/s12859-014-0377-z
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author Gilly, Arthur
Etcheverry, Mathilde
Madoui, Mohammed-Amin
Guy, Julie
Quadrana, Leandro
Alberti, Adriana
Martin, Antoine
Heitkam, Tony
Engelen, Stefan
Labadie, Karine
Le Pen, Jeremie
Wincker, Patrick
Colot, Vincent
Aury, Jean-Marc
author_facet Gilly, Arthur
Etcheverry, Mathilde
Madoui, Mohammed-Amin
Guy, Julie
Quadrana, Leandro
Alberti, Adriana
Martin, Antoine
Heitkam, Tony
Engelen, Stefan
Labadie, Karine
Le Pen, Jeremie
Wincker, Patrick
Colot, Vincent
Aury, Jean-Marc
author_sort Gilly, Arthur
collection PubMed
description BACKGROUND: Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now possible to resequence whole genomes in order to systematically characterize novel TE mobilization in a particular individual. However, this task is made difficult by the inherently repetitive nature of TE sequences, which in some eukaryotes compose over half of the genome sequence. Currently, only a few software tools dedicated to the detection of TE mobilization using next-generation-sequencing are described in the literature. They often target specific TEs for which annotation is available, and are only able to identify families of closely related TEs, rather than individual elements. RESULTS: We present TE-Tracker, a general and accurate computational method for the de-novo detection of germ line TE mobilization from re-sequenced genomes, as well as the identification of both their source and destination sequences. We compare our method with the two classes of existing software: specialized TE-detection tools and generic structural variant (SV) detection tools. We show that TE-Tracker, while working independently of any prior annotation, bridges the gap between these two approaches in terms of detection power. Indeed, its positive predictive value (PPV) is comparable to that of dedicated TE software while its sensitivity is typical of a generic SV detection tool. TE-Tracker demonstrates the benefit of adopting an annotation-independent, de novo approach for the detection of TE mobilization events. We use TE-Tracker to provide a comprehensive view of transposition events induced by loss of DNA methylation in Arabidopsis. TE-Tracker is freely available at http://www.genoscope.cns.fr/TE-Tracker. CONCLUSIONS: We show that TE-Tracker accurately detects both the source and destination of novel transposition events in re-sequenced genomes. Moreover, TE-Tracker is able to detect all potential donor sequences for a given insertion, and can identify the correct one among them. Furthermore, TE-Tracker produces significantly fewer false positives than common SV detection programs, thus greatly facilitating the detection and analysis of TE mobilization events. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0377-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-42798142015-01-22 TE-Tracker: systematic identification of transposition events through whole-genome resequencing Gilly, Arthur Etcheverry, Mathilde Madoui, Mohammed-Amin Guy, Julie Quadrana, Leandro Alberti, Adriana Martin, Antoine Heitkam, Tony Engelen, Stefan Labadie, Karine Le Pen, Jeremie Wincker, Patrick Colot, Vincent Aury, Jean-Marc BMC Bioinformatics Methodology Article BACKGROUND: Transposable elements (TEs) are DNA sequences that are able to move from their location in the genome by cutting or copying themselves to another locus. As such, they are increasingly recognized as impacting all aspects of genome function. With the dramatic reduction in cost of DNA sequencing, it is now possible to resequence whole genomes in order to systematically characterize novel TE mobilization in a particular individual. However, this task is made difficult by the inherently repetitive nature of TE sequences, which in some eukaryotes compose over half of the genome sequence. Currently, only a few software tools dedicated to the detection of TE mobilization using next-generation-sequencing are described in the literature. They often target specific TEs for which annotation is available, and are only able to identify families of closely related TEs, rather than individual elements. RESULTS: We present TE-Tracker, a general and accurate computational method for the de-novo detection of germ line TE mobilization from re-sequenced genomes, as well as the identification of both their source and destination sequences. We compare our method with the two classes of existing software: specialized TE-detection tools and generic structural variant (SV) detection tools. We show that TE-Tracker, while working independently of any prior annotation, bridges the gap between these two approaches in terms of detection power. Indeed, its positive predictive value (PPV) is comparable to that of dedicated TE software while its sensitivity is typical of a generic SV detection tool. TE-Tracker demonstrates the benefit of adopting an annotation-independent, de novo approach for the detection of TE mobilization events. We use TE-Tracker to provide a comprehensive view of transposition events induced by loss of DNA methylation in Arabidopsis. TE-Tracker is freely available at http://www.genoscope.cns.fr/TE-Tracker. CONCLUSIONS: We show that TE-Tracker accurately detects both the source and destination of novel transposition events in re-sequenced genomes. Moreover, TE-Tracker is able to detect all potential donor sequences for a given insertion, and can identify the correct one among them. Furthermore, TE-Tracker produces significantly fewer false positives than common SV detection programs, thus greatly facilitating the detection and analysis of TE mobilization events. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0377-z) contains supplementary material, which is available to authorized users. BioMed Central 2014-11-19 /pmc/articles/PMC4279814/ /pubmed/25408240 http://dx.doi.org/10.1186/s12859-014-0377-z Text en © Gilly et al.; licensee BioMed Central. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Gilly, Arthur
Etcheverry, Mathilde
Madoui, Mohammed-Amin
Guy, Julie
Quadrana, Leandro
Alberti, Adriana
Martin, Antoine
Heitkam, Tony
Engelen, Stefan
Labadie, Karine
Le Pen, Jeremie
Wincker, Patrick
Colot, Vincent
Aury, Jean-Marc
TE-Tracker: systematic identification of transposition events through whole-genome resequencing
title TE-Tracker: systematic identification of transposition events through whole-genome resequencing
title_full TE-Tracker: systematic identification of transposition events through whole-genome resequencing
title_fullStr TE-Tracker: systematic identification of transposition events through whole-genome resequencing
title_full_unstemmed TE-Tracker: systematic identification of transposition events through whole-genome resequencing
title_short TE-Tracker: systematic identification of transposition events through whole-genome resequencing
title_sort te-tracker: systematic identification of transposition events through whole-genome resequencing
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279814/
https://www.ncbi.nlm.nih.gov/pubmed/25408240
http://dx.doi.org/10.1186/s12859-014-0377-z
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