Abstract
BackgroundHybridization 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.ResultsComparative 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.ConclusionsThese results indicate that Tragopogon miscellus allopolyploids employ diverse mechanisms, including DNA methylation, to respond to the potential shock of genome merger and doubling.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-701) contains supplementary material, which is available to authorized users.
Highlights
Hybridization coupled with whole-genome duplication leads to a variety of genetic and epigenetic modifications in the resultant merged genomes
CG methylation regulates duplicate gene expression Genomic and bisulfite-converted sequences were acquired for four loci [TDF-44 [43], S2, S3, and S18 [42]] from allopolyploid Tragopogon miscellus and the diploid parents T. dubius and T. pratensis (Table 1)
A fifth locus (S8, putative acetyl transferase) identified as silenced in Buggs et al [42] was not amenable for study because no single nucleotide polymorphisms (SNPs) between the diploids were maintained following bisulfite conversion to distinguish the parental copies in the allopolyploid (Figure 1a)
Summary
Hybridization coupled with whole-genome duplication (allopolyploidy) leads to a variety of genetic and epigenetic modifications in the resultant merged genomes. We investigated DNA methylation as a potential mechanism for gene silencing in Tragopogon miscellus (Asteraceae), a recent and recurrently formed allopolyploid. This species, which exhibits extensive gene loss, was formed from the diploids T. dubius and T. pratensis. Genetic modifications can include gene loss, genome down-sizing, variable mutation rates of the duplicated genes (homeologs), chromosomal rearrangements and regulatory incompatibilities resulting from post-transcriptional modifications in the merged genomes [16,17,18,19,20,21,22,23,24].
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