title: TE-Tracker: systematic identification of transposition events through whole-genome resequencing.
abstract: 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.
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. ag15@sanger.ac.uk.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. ag15@sanger.ac.uk.|Universite d'Evry, UMR 8030, CP5706, Evry, France. ag15@sanger.ac.uk.|Current address: The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. ag15@sanger.ac.uk.
authors.forename: Arthur
authors.initials: A
authors.lastname: Gilly
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, F-75230, Paris, Cedex 05, France. etcheverry.mathilde@biologie.ens.fr.|Centre National de la Recherche Scientifique (CNRS), UMR 8197, F-75230, Paris, Cedex 05, France. etcheverry.mathilde@biologie.ens.fr.|Institut national de la santé et de la recherche médicale (INSERM), U1024, F-75230, Paris, Cedex 05, France. etcheverry.mathilde@biologie.ens.fr.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Etcheverry
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. amadoui@genoscope.cns.fr.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. amadoui@genoscope.cns.fr.|Universite d'Evry, UMR 8030, CP5706, Evry, France. amadoui@genoscope.cns.fr.
authors.forename: Mohammed-Amin
authors.initials: MA
authors.lastname: Madoui
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. jguy@genoscope.cns.fr.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. jguy@genoscope.cns.fr.|Universite d'Evry, UMR 8030, CP5706, Evry, France. jguy@genoscope.cns.fr.
authors.forename: Julie
authors.initials: J
authors.lastname: Guy
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, F-75230, Paris, Cedex 05, France. quadrana@biologie.ens.fr.|Centre National de la Recherche Scientifique (CNRS), UMR 8197, F-75230, Paris, Cedex 05, France. quadrana@biologie.ens.fr.|Institut national de la santé et de la recherche médicale (INSERM), U1024, F-75230, Paris, Cedex 05, France. quadrana@biologie.ens.fr.
authors.forename: Leandro
authors.initials: L
authors.lastname: Quadrana
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. aalberti@genoscope.cns.fr.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. aalberti@genoscope.cns.fr.|Universite d'Evry, UMR 8030, CP5706, Evry, France. aalberti@genoscope.cns.fr.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, F-75230, Paris, Cedex 05, France. Antoine.martin@supagro.inra.fr.|Centre National de la Recherche Scientifique (CNRS), UMR 8197, F-75230, Paris, Cedex 05, France. Antoine.martin@supagro.inra.fr.|Institut national de la santé et de la recherche médicale (INSERM), U1024, F-75230, Paris, Cedex 05, France. Antoine.martin@supagro.inra.fr.|Current address: Technische Universität Dresden, Institute of Bota, ny, Plant Cell and Molecular Biology, D-01062, Dresden, Germany. Antoine.martin@supagro.inra.fr.
authors.forename: Antoine
authors.initials: A
authors.lastname: Martin
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, F-75230, Paris, Cedex 05, France. tony.heitkam@tu-dresden.de.|Centre National de la Recherche Scientifique (CNRS), UMR 8197, F-75230, Paris, Cedex 05, France. tony.heitkam@tu-dresden.de.|Institut national de la santé et de la recherche médicale (INSERM), U1024, F-75230, Paris, Cedex 05, France. tony.heitkam@tu-dresden.de.|Current address: Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes 'Claude Grignon', UMR CNRS/INRA/SupAgro/UM2, Place Viala, 34060, Montpellier, Cedex, France. tony.heitkam@tu-dresden.de.
authors.forename: Tony
authors.initials: T
authors.lastname: Heitkam
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. sengelen@genoscope.cns.fr.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. sengelen@genoscope.cns.fr.|Universite d'Evry, UMR 8030, CP5706, Evry, France. sengelen@genoscope.cns.fr.
authors.forename: Stefan
authors.initials: S
authors.lastname: Engelen
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. klabadie@genoscope.cns.fr.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. klabadie@genoscope.cns.fr.|Universite d'Evry, UMR 8030, CP5706, Evry, France. klabadie@genoscope.cns.fr.
authors.forename: Karine
authors.initials: K
authors.lastname: Labadie
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, F-75230, Paris, Cedex 05, France. jl572@cam.ac.uk.|Centre National de la Recherche Scientifique (CNRS), UMR 8197, F-75230, Paris, Cedex 05, France. jl572@cam.ac.uk.|Institut national de la santé et de la recherche médicale (INSERM), U1024, F-75230, Paris, Cedex 05, France. jl572@cam.ac.uk.|Current address: Gurdon Institute and Department of Biochemistry, University of Cambridge, The Henry Wellcome Building of Cancer and Developmental Biology, Tennis Court Rd, Cambridge, CB2 1QN, UK. jl572@cam.ac.uk.
authors.forename: Jeremie
authors.initials: J
authors.lastname: Le Pen
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. pwincker@genoscope.cns.fr.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. pwincker@genoscope.cns.fr.|Universite d'Evry, UMR 8030, CP5706, Evry, France. pwincker@genoscope.cns.fr.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: Institut de Biologie de l'Ecole Normale Supérieure, F-75230, Paris, Cedex 05, France. colot@biologie.ens.fr.|Centre National de la Recherche Scientifique (CNRS), UMR 8197, F-75230, Paris, Cedex 05, France. colot@biologie.ens.fr.|Institut national de la santé et de la recherche médicale (INSERM), U1024, F-75230, Paris, Cedex 05, France. colot@biologie.ens.fr.
authors.forename: Vincent
authors.initials: V
authors.lastname: Colot
authors.affiliation: Commissariat a l'Energie Atomique (CEA), Institut de Genomique (IG), Genoscope, 2 rue Gaston Crémieux, BP5706, 91057, Evry, France. jmaury@genoscope.cns.fr.|Centre National de Recherche Scientifique (CNRS), UMR 8030, CP5706, Evry, France. jmaury@genoscope.cns.fr.|Universite d'Evry, UMR 8030, CP5706, Evry, France. jmaury@genoscope.cns.fr.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics*; D017343:Genes, Plant / Q000235:genetics*; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012984:Software
chemical_list: D004251:DNA Transposable Elements