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Transposable Element Annotation in Completely Sequenced Eukaryote Genomes

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Plant Transposable Elements

Part of the book series: Topics in Current Genetics ((TCG,volume 24))

Abstract

With the development of new sequencing techniques, the number of sequenced plant genomes is increasing. However, accurate annotation of these sequences remains a major challenge, in particular with regard to transposable elements (TEs). The aim of this chapter is to provide a roadmap for researchers involved in genome projects to address this issue. We list several widely used tools for each step of the TE annotation process, from the identification of TE families to the annotation of TE copies. We assess the complementarities of these tools and suggest that combined approaches, using both de novo and knowledge-based TE detection methods, are likely to produce reasonably comprehensive and sensitive results. Nevertheless, existing approaches still need to be supplemented by expert manual curation. Hence, we describe good practice required for manual curation of TE consensus sequences.

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Acknowledgments

This work was supported in part by grants from the Agence Nationale de la Recherche (Holocentrism project, to HQ [grant number ANR-07-BLAN-0057]) and the Centre National de la Recherche Scientifique—Groupement de Recherche “Elements Transposables.” TF was supported by a PhD studentship from the Institut National de la Recherche Agronomique. EP was supported by a postdoctoral fellowship from the Agence Nationale de la Recherche.

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  1. INRA, UR 1164, URGI, Unité de Recherche en Génomique-Info, 78026, Versailles cedex, France

    Timothée Flutre, Emmanuelle Permal & Hadi Quesneville

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  1. Timothée Flutre
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  2. Emmanuelle Permal
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  3. Hadi Quesneville
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Correspondence to Hadi Quesneville .

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  1. , Institut Jean-Pierre Bourgin (IJPB), INRA Versailles, UMR 1318, Versailles Cedex, 78026, France

    Marie-Angèle Grandbastien

  2. , Centre de Recerca en Agrigenomica (CRAG), CSIC-RTA-UAB, Barcelona, 08193, Spain

    Josep M. Casacuberta

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Flutre, T., Permal, E., Quesneville, H. (2012). Transposable Element Annotation in Completely Sequenced Eukaryote Genomes. In: Grandbastien, MA., Casacuberta, J. (eds) Plant Transposable Elements. Topics in Current Genetics, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31842-9_2

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