Chromosome Research

, Volume 16, Issue 7, pp 961–976

Survey of repetitive sequences in Silene latifolia with respect to their distribution on sex chromosomes

  • Tomas Cermak
  • Zdenek Kubat
  • Roman Hobza
  • Andrea Koblizkova
  • Alex Widmer
  • Jiri Macas
  • Boris Vyskot
  • Eduard Kejnovsky
Article

DOI: 10.1007/s10577-008-1254-2

Cite this article as:
Cermak, T., Kubat, Z., Hobza, R. et al. Chromosome Res (2008) 16: 961. doi:10.1007/s10577-008-1254-2

Abstract

We carried out a global survey of all major types of transposable elements in Silene latifolia, a model species with sex chromosomes that are in the early stages of their evolution. A shotgun genomic library was screened with genomic DNA to isolate and characterize the most abundant elements. We found that the most common types of elements were the subtelomeric tandem repeat X-43.1 and Gypsy retrotransposons, followed by Copia retrotransposons and LINE non-LTR elements. SINE elements and DNA transposons were less abundant. We also amplified transposable elements with degenerate primers and used them to screen the library. The localization of elements by FISH revealed that most of the Copia elements were accumulated on the Y chromosome. Surprisingly, one type of Gypsy element, which was similar to Ogre elements known from legumes, was almost absent on the Y chromosome but otherwise uniformly distributed on all chromosomes. Other types of elements were ubiquitous on all chromosomes. Moreover, we isolated and characterized two new tandem repeats. One of them, STAR-C, was localized at the centromeres of all chromosomes except the Y chromosome, where it was present on the p-arm. Its variant, STAR-Y, carrying a small deletion, was specifically localized on the q-arm of the Y chromosome. The second tandem repeat, TR1, co-localized with the 45S rDNA cluster in the subtelomeres of five pairs of autosomes. FISH analysis of other Silene species revealed that some elements (e.g., Ogre-like elements) are confined to the section Elisanthe while others (e.g. Copia or Athila-like elements) are present also in more distant species. Similarly, the centromeric satellite STAR-C was conserved in the genus Silene whereas the subtelomeric satellite X-43.1 was specific for Elisanthe section. Altogether, our data provide an overview of the repetitive sequences in Silene latifolia and revealed that genomic distribution and evolutionary dynamics differ among various repetitive elements. The unique pattern of repeat distribution is found on the Y chromosome, where some elements are accumulated while other elements are conspicuously absent, which probably reflects different forces shaping the Y chromosome.

Key words

satellitessex chromosomesSilene latifoliatransposable elements

Supplementary material

10577_2008_1254_MOESM1_ESM.doc (28 kb)
Table S1Clones used for FISH experiments. (DOC 27.5 kb)

Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Tomas Cermak
    • 1
  • Zdenek Kubat
    • 1
  • Roman Hobza
    • 1
  • Andrea Koblizkova
    • 2
  • Alex Widmer
    • 3
  • Jiri Macas
    • 2
  • Boris Vyskot
    • 1
  • Eduard Kejnovsky
    • 1
  1. 1.Laboratory of Plant Developmental GeneticsInstitute of Biophysics ASCRBrnoCzech Republic
  2. 2.Biology Centre ASCRInstitute of Plant Molecular BiologyCeske BudejoviceCzech Republic
  3. 3.ETH Zurich, Institute of Integrative Biology, Plant Ecological GeneticsZurichSwitzerland