Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome

Authors

  • Zdenek Kubat,

    Corresponding author
    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
    2. Laboratory of Genome Dynamics, CEITEC – Central European Institute of Technology, Masaryk University, Brno, Czech Republic
    • Author for correspondence:

      Zdenek Kubat

      Tel: +420 541 517 203

      Email: kubat@ibp.cz

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  • Jitka Zluvova,

    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
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  • Ivan Vogel,

    1. Laboratory of Genome Dynamics, CEITEC – Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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  • Viera Kovacova,

    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
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  • Tomas Cermak,

    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
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  • Radim Cegan,

    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
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  • Roman Hobza,

    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
    2. Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
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  • Boris Vyskot,

    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
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  • Eduard Kejnovsky

    1. Department of Plant Developmental Genetics, Institute of Biophysics ASCR, Brno, Czech Republic
    2. Laboratory of Genome Dynamics, CEITEC – Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Summary

  • Some transposable elements (TEs) show extraordinary variance in abundance along sex chromosomes but the mechanisms responsible for this variance are unknown. Here, we studied Ogre long terminal repeat (LTR) retrotransposons in Silene latifolia, a dioecious plant with evolutionarily young heteromorphic sex chromosomes. Ogre elements are ubiquitous in the S. latifolia genome but surprisingly absent on the Y chromosome.
  • Bacterial artificial chromosome (BAC) library analysis and fluorescence in situ hybridization (FISH) were used to determine Ogre structure and chromosomal localization. Next generation sequencing (NGS) data were analysed to assess the transcription level and abundance of small RNAs. Methylation of Ogres was determined by bisulphite sequencing. Phylogenetic analysis was used to determine mobilization time and selection forces acting on Ogre elements.
  • We characterized three Ogre families ubiquitous in the S. latifolia genome. One family is nearly absent on the Y chromosome despite all the families having similar structures and spreading mechanisms. We showed that Ogre retrotransposons evolved before sex chromosomes appeared but were mobilized after formation of the Y chromosome. Our data suggest that the absence of one Ogre family on the Y chromosome may be caused by 24-nucleotide (24-nt) small RNA-mediated silencing leading to female-specific spreading.
  • Our findings highlight epigenetic silencing mechanisms as potentially crucial factors in sex-specific spreading of some TEs, but other possible mechanisms are also discussed.

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