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A unified classification system for eukaryotic transposable elements

Nature Reviews Genetics volume 8, pages 973–982 (2007)Cite this article

Abstract

Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.

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Figure 1: Proposed classification system for transposable elements (TEs).
Figure 2: Examples of transposable elements (TEs) that are classified as members of one family on the basis of their sequence homology.
Figure 3: Step by step transposable element (TE) classification.
Figure 4: Motifs and signals that are present in long terminal repeat (LTR) retrotransposons.

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Acknowledgements

The authors want to thank J. Estill (University of Georgia, Athens, USA) for very useful scientific discussions. We are particularly grateful to C. Feschotte (University of Texas, Austin, USA) and two other anonymous reviewers for their constructive comments and suggestions. J. W. Bizzaro and all the bioinformatics.org team are thanked for their hosting of WikiPoson and helping with its release. This work was supported by GDR 2157 of the Centre National de la Recherche Scientifique (CNRS; A.H.V., P.C & O.P.), by a University of Helsinki, Finland, Postdoctoral Fellowship (F.S.) and by the Institute of Plant Biology, Zurich, Switzerland (T.W.).

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Author notes

  1. Thomas Wicker, François Sabot and Aurélie Hua-Van: These authors contributed equally to this work.

Authors and Affiliations

  1. Thomas Wicker is at the Institute of Plant Biology, University Zurich, Zollikerstrasse 107, CH-8008 Zurich, Switzerland.,

    Thomas Wicker

  2. François Sabot and Alan H. Schulman are at MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. BOX 56, FIN-00014 Helsinki, Finland.,

    François Sabot & Alan H. Schulman

  3. Aurélie Hua-Van and Pierre Capy are at Laboratoire Evolution, Génomes et Spéciation, UPR 9034, CNRS 91198 Gif-sur Yvette Cedex, France and Université Paris-Sud 11, 91405 Orsay Cedex, France.,

    Aurélie Hua-Van & Pierre Capy

  4. Jeffrey L. Bennetzen is at the Department of Genetics, University of Georgia, Athens, Georgia, 30602-7223, USA.,

    Jeffrey L. Bennetzen

  5. Boulos Chalhoub is at Unité de Recherche en Génomique Végétale (URGV/URGI), Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux CP 5708, FR-91057 Evry Cedex, France.,

    Boulos Chalhoub

  6. Andrew Flavell is at the Plant Research Unit, University of Dundee at SCRI, DD2 5DA Invergowrie, Dundee, United Kingdom.,

    Andrew Flavell

  7. Philippe Leroy amd Etienne Paux are at INRA-Université Blaise-Pascal, UMR 1095, 234 avenue du Brézet, FR-63100 Clermont-Ferrand Cedex, France.,

    Philippe Leroy & Etienne Paux

  8. Michele Morgante is at Dipartimento di Scienze Agrarie ed Ambientali, Università di Udine, Via delle Scienze 208, I-33100 Udine, Italy.,

    Michele Morgante

  9. Olivier Panaud is at Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS-IRD-Université de Perpignan, 52 Avenue Paul Alduy, F-66860 Perpignan, France.,

    Olivier Panaud

  10. Phillip SanMiguel is at Purdue Genomics Core Facility, 170 South University Street, West Lafayette, IN, 47907-2072, USA.,

    Phillip SanMiguel

  11. Alan H. Schulman is also at Plant Genomics, Food and Biotechnology, MTT Agrifood Research Finland, Myllytie 10, FIN-31600 Jokioinen, Finland.,

    Alan H. Schulman

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  1. Thomas Wicker
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  2. François Sabot
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Correspondence to Alan H. Schulman.

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Wicker, T., Sabot, F., Hua-Van, A. et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8, 973–982 (2007). https://doi.org/10.1038/nrg2165

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