RepetDB: a unified resource for transposable element references View Full Text


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Article Info

DATE

2019-12

AUTHORS

Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michael Alaux, Françoise Alfama-Depauw, Véronique Jamilloux, Florian Maumus, Thomas Letellier, Isabelle Luyten, Cyril Pommier, Anne-Françoise Adam-Blondon, Hadi Quesneville

ABSTRACT

Background: Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation are considered essential in any genome sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements in high-throughput sequencing technologies. A fully automated de novo annotation process for TEs is therefore required to cope with the deluge of sequence data.However, all automated procedures are error-prone, and an automated procedure for TE identification and classification would be no exception. It is therefore crucial to provide not only the TE reference sequences, but also evidence justifying their classification, at the scale of the whole genome. A few TE databases already exist, but none provides evidence to justify TE classification. Moreover, biological information about the sequences remains globally poor. Results: We present here the RepetDB database developed in the framework of GnpIS, a genetic and genomic information system. RepetDB is designed to store and retrieve detected, classified and annotated TEs in a standardized manner. RepetDB is an implementation with extensions of InterMine, an open-source data warehouse framework used here to store, search, browse, analyze and compare all the data recorded for each TE reference sequence. InterMine can display diverse information for each sequence and allows simple to very complex queries. Finally, TE data are displayed via a worldwide data discovery portal. RepetDB is accessible at urgi.versailles.inra.fr/repetdb. Conclusions: RepetDB is designed to be a TE knowledge base populated with full de novo TE annotations of complete (or near-complete) genome sequences. Indeed, the description and classification of TEs facilitates the exploration of specific TE families, superfamilies or orders across a large range of species. It also makes possible cross-species searches and comparisons of TE family content between genomes. More... »

PAGES

6

References to SciGraph publications

  • 2011-12. A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome in FUNCTIONAL & INTEGRATIVE GENOMICS
  • 2015-12. Repbase Update, a database of repetitive elements in eukaryotic genomes in MOBILE DNA
  • 2007-12. A unified classification system for eukaryotic transposable elements in NATURE REVIEWS GENETICS
  • 2016-06. Coming of age: ten years of next-generation sequencing technologies in NATURE REVIEWS GENETICS
  • 2007-04. Transposable elements and the epigenetic regulation of the genome in NATURE REVIEWS GENETICS
  • 2004. Genome Plasticity in GENOMICS, PROTEOMICS, AND CLINICAL BACTERIOLOGY
  • 2013-01. How important are transposons for plant evolution? in NATURE REVIEWS GENETICS
  • 2009. Analysis of Transposable Element Sequences Using CENSOR and RepeatMasker in BIOINFORMATICS FOR DNA SEQUENCE ANALYSIS
  • 2015-12. Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes in BMC GENOMICS
  • 2016-03-15. The FAIR Guiding Principles for scientific data management and stewardship in SCIENTIFIC DATA
  • 2003-08. Detection of New Transposable Element Families in Drosophila melanogaster and Anopheles gambiae Genomes in JOURNAL OF MOLECULAR EVOLUTION
  • 2017-12. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters in BMC GENOMICS
  • 2016-12. JBrowse: a dynamic web platform for genome visualization and analysis in GENOME BIOLOGY
  • 2013-09. The wheat powdery mildew genome shows the unique evolution of an obligate biotroph in NATURE GENETICS
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    DIMENSIONS

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    PUBMED

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