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Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives

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Abstract

Genome-wide analyses of repetitive DNA suggest a significant impact particularly of transposable elements on genome size and evolution of virtually all eukaryotic organisms. In this study, we analyzed the abundance and diversity of the hAT transposon superfamily of the sugar beet (B. vulgaris) genome, using molecular, bioinformatic and cytogenetic approaches. We identified 81 transposase-coding sequences, three of which are part of structurally intact but nonfunctional hAT transposons (BvhAT), in a B. vulgaris BAC library as well as in whole genome sequencing-derived data sets. Additionally, 116 complete and 497 truncated non-autonomous BvhAT derivatives lacking the transposase gene were in silico-detected. The 116 complete derivatives were subdivided into four BvhATpin groups each characterized by a distinct terminal inverted repeat motif. Both BvhAT and BvhATpin transposons are specific for species of the genus Beta and closely related species, showing a localization on B. vulgaris chromosomes predominantely in euchromatic regions. The lack of any BvhAT transposase function together with the high degree of degeneration observed for the BvhAT and the BvhATpin genomic fraction contrasts with the abundance and activity of autonomous and non-autonomous hAT transposons revealed in other plant species. This indicates a possible genus-specific structural and functional repression of the hAT transposon superfamily during Beta diversification and evolution.

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Acknowledgments

We thank Ines Walter for excellent technical assistance. This work has been funded by the “Verbundprojekt GABI BeetSeq: Erstellung einer Referenzsequenz für das Genom der Zuckerrübe (Beta vulgaris)”, FKZ 0315069A and 0315069B (to H.H. and B.W.).

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Authors and Affiliations

  1. Center for Biotechnology, University of Bielefeld, 33594, Bielefeld, Germany

    Daniela Holtgräwe & Bernd Weisshaar

  2. Centre for Genomic Regulation (CRG) and UPF, 08003, Barcelona, Spain

    André E. Minoche, Juliane C. Dohm & Heinz Himmelbauer

  3. Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195, Berlin, Germany

    André E. Minoche, Juliane C. Dohm & Heinz Himmelbauer

  4. Institute of Botany, Dresden University of Technology, 01062, Dresden, Germany

    Gerhard Menzel, Carmen Krebs, Mercedes Diez & Thomas Schmidt

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  1. Gerhard Menzel
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  2. Carmen Krebs
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  3. Mercedes Diez
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  4. Daniela Holtgräwe
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  8. Heinz Himmelbauer
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  9. Thomas Schmidt
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Correspondence to Thomas Schmidt.

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Menzel, G., Krebs, C., Diez, M. et al. Survey of sugar beet (Beta vulgaris L.) hAT transposons and MITE-like hATpin derivatives. Plant Mol Biol 78, 393–405 (2012). https://doi.org/10.1007/s11103-011-9872-z

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  • DOI: https://doi.org/10.1007/s11103-011-9872-z

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