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Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome

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Abstract

Miniature inverted-repeat transposable elements (MITEs) are short, non autonomous DNA elements that are widespread and abundant in plant genomes. The high sequence and size conservation observed in many MITE families suggest that they have spread recently throughout their respective host genomes. Here we present a maize genome wide analysis of three Tourist-like MITE families, mPIF, and two previously uncharacterized families, ZmV1 and Zead8. We undertook a bioinformatic analysis of MITE insertion sites, developed methyl-sensitive transposon display (M-STD) assays to estimate the associated level of CpG methylation at MITE flanking regions, and conducted a population genetics approach to investigate MITE patterns of expansion. Our results reveal that the three MITE families insert into genomic regions that present specific molecular features: they are preferentially AT rich, present low level of cytosine methylation as compared to the LTR retrotransposon Grande, and target site duplications are flanked by large and conserved palindromic sequences. Moreover, the analysis of MITE distances from predicted genes shows that 73% of 263 copies are inserted at less than 5 kb from the nearest predicted gene, and copies from Zead8 family are significantly more abundant upstream of genes. By employing a population genetic approach we identified contrasting patterns of expansion among the three MITE families. All elements seem to have inserted roughly 1 million years ago but ZmV1 and Zead8 families present evidences for activity of several master copies within the last 0.4 Mya.

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Acknowledgments

We thank Catherine Damerval, Domenica Manicacci and Clementine Vitte for critical reading of the manuscript and Julie Dawson for review of the text. Corinne Mhiri provided with technical advices and support. This work was funded by the Agence Nationale de la Recherche (ANR-05-JCJC-0067-01 to M.I.T.).

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Authors and Affiliations

  1. CNRS, UMR 0320/UMR 8120, Génétique Végétale, F-91190, Gif-sur-Yvette, France

    Tatiana Zerjal & Maud I. Tenaillon

  2. INRA, UMR 0320/UMR 8120, Génétique Végétale, F-91190, Gif-sur-Yvette, France

    Johann Joets

  3. AgroParisTech, UMR 0320/UMR 8120, Génétique Végétale, F-91190, Gif-sur-Yvette, France

    Karine Alix

  4. INRA, Laboratoire De Biologie Cellulaire, Institut Jean-Pierre Bourgin, 78026, Versailles cedex, France

    Marie-Angèle Grandbastien

  5. UMR de Génétique Végétale, INRA/Univ Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, F-91190, Gif-sur-Yvette, France

    Tatiana Zerjal

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  1. Tatiana Zerjal
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Zerjal, T., Joets, J., Alix, K. et al. Contrasting evolutionary patterns and target specificities among three Tourist-like MITE families in the maize genome. Plant Mol Biol 71, 99–114 (2009). https://doi.org/10.1007/s11103-009-9511-0

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