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The diversification and activity of hAT transposons in Musa genomes

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Abstract

Sequencing of plant genomes often identified the hAT superfamily as the largest group of DNA transposons. Nevertheless, detailed information on the diversity, abundance and chromosomal localization of plant hAT families are rare. By in silico analyses of the reference genome assembly and bacterial artificial chromosome (BAC) sequences, respectively, we performed the classification and molecular characterization of hAT transposon families in Musa acuminata. Musa hAT transposons are organized in three families designated MuhAT I, MuhAT II and MuhAT III. In total, 70 complete autonomous elements of the MuhAT I and MuhAT II families were detected, while no autonomous MuhAT III transposons were found. Based on the terminal inverted repeat (TIR)-specific sequence information of the autonomous transposons, 1722 MuhAT I- and MuhAT II-specific miniature inverted-repeat transposable elements (MuhMITEs) were identified. Autonomous MuhAT I and MuhAT II elements are only moderately abundant in the sections of the genus Musa, while the corresponding MITEs exhibit an amplification in Musa genomes. By fluorescent in situ hybridization (FISH), autonomous MuhAT transposons as well as MuhMITEs were localized in subtelomeric, most likely gene-rich regions of M. acuminata chromosomes. A comparison of homoeologous regions of M. acuminata and Musa balbisiana BACs revealed the species-specific mobility of MuhMITEs. In particular, the activity of MuhMITEs II showing transduplications of genomic sequences might indicate the presence of active MuhAT transposons, thus suggesting a potential role of MuhMITEs as modulators of genome evolution of Musa.

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Acknowledgments

We are indebted to Nadin Fliegner and Ines Walter for the excellent technical assistance. We thank the DAAD-British Council ARC Academic Research Collaboration project for support of the collaboration. We thank the Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement (CIRAD), Montpellier (France), and the Musa Genome Resource Centre (MGRC) at the Institute of Experimental Botany (IEB), Olomouc (Czech Republic) for the production, storage and distribution of Musa DNA samples used here. We thank the TU Dresden Center for Information Services and High Performance Computing (ZIH) for the computer time allocations.

Conflict of interest

The authors Gerhard Menzel, Tony Heitkam, Kathrin M. Seibt, Faisal Nouroz, Manuela Müller-Stoermer, John S. Heslop-Harrison and Thomas Schmidt declare that they have no conflict of interest.

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Authors and Affiliations

  1. Institute of Botany, Technische Universität Dresden, 01062, Dresden, Germany

    Gerhard Menzel, Tony Heitkam, Kathrin M. Seibt, Manuela Müller-Stoermer & Thomas Schmidt

  2. Department of Biology, University of Leicester, Leicester, LE1 7RH, UK

    Faisal Nouroz & John S. Heslop-Harrison

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  1. Gerhard Menzel
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  2. Tony Heitkam
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Correspondence to Thomas Schmidt.

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Menzel, G., Heitkam, T., Seibt, K.M. et al. The diversification and activity of hAT transposons in Musa genomes. Chromosome Res 22, 559–571 (2014). https://doi.org/10.1007/s10577-014-9445-5

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