Gene silencing via DNA methylation in naturally occurring Tragopogon miscellus (Asteraceae) allopolyploids

BMC Genomics. 2014 Aug 22;15(1):701. doi: 10.1186/1471-2164-15-701.

Abstract

Background: Hybridization coupled with whole-genome duplication (allopolyploidy) leads to a variety of genetic and epigenetic modifications in the resultant merged genomes. In particular, gene loss and gene silencing are commonly observed post-polyploidization. Here, we investigated DNA methylation as a potential mechanism for gene silencing in Tragopogon miscellus (Asteraceae), a recent and recurrently formed allopolyploid. This species, which also exhibits extensive gene loss, was formed from the diploids T. dubius and T. pratensis.

Results: Comparative bisulfite sequencing revealed CG methylation of parental homeologs for three loci (S2, S18 and TDF-44) that were previously identified as silenced in T. miscellus individuals relative to the diploid progenitors. One other locus (S3) examined did not show methylation, indicating that other transcriptional and post-transcriptional mechanisms are likely responsible for silencing that homeologous locus.

Conclusions: These results indicate that Tragopogon miscellus allopolyploids employ diverse mechanisms, including DNA methylation, to respond to the potential shock of genome merger and doubling.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA Methylation / genetics*
  • Gene Silencing*
  • Genetic Loci / genetics
  • Polyploidy*
  • Sequence Analysis, DNA
  • Sulfites / pharmacology
  • Tragopogon / genetics*

Substances

  • Sulfites
  • hydrogen sulfite