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A unified classification system for eukaryotic transposable elements

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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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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