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So Many Repeats and So Little Time: How to Classify Transposable Elements

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Plant Transposable Elements

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

Abstract

Transposable elements (TEs) are present in all genomes. Often there are hundreds to thousands of different TE families contributing the majority of the genomic DNA. Although probably only a very small portion of TEs actually contributes to the function and thereby to the survival of an organism, they still have to be analysed, annotated and classified. To filter out the scarce meaningful signals from the deluge of data produced by modern sequencing technologies, researchers need to be able to efficiently and reliably characterise TE sequences. This process requires three things: First, clear guidelines how to classify and characterise TEs. Second, high-quality databases that contain well-characterised reference sequences, and third, computational tools for efficient TE searches and annotations. This article is intended as a summary of recent developments in TE classification as well as a “little helper” for researchers burdened with the epic task of TE annotation in genomic sequences.

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  1. Institute of Plant Biology, University of Zurich, Ollikerstrasse 107, CH-8008, Zurich, Switzerland

    Thomas Wicker

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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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Wicker, T. (2012). So Many Repeats and So Little Time: How to Classify Transposable Elements. 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_1

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