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Open Access Research article

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

Tina Sehrish1, V Vaughan Symonds1, Douglas E Soltis23, Pamela S Soltis3 and Jennifer A Tate1*

Author Affiliations

1 Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

2 Department of Biology, University of Florida, Gainesville, Florida, USA

3 Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA

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BMC Genomics 2014, 15:701  doi:10.1186/1471-2164-15-701

Published: 22 August 2014

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.

Keywords:
Allopolyploidy; DNA methylation; Gene silencing; Tragopogon; Whole-genome duplication