Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy

Abstract

Polyploidy has been recognized as a widespread and common phenomenon among flowering plants. DNA-5′-CCGG site cytosine methylation (C-methylation) is one of the major and immediate epigenetic responses of the plant genome. Elucidating the ways in which altered C-methylation patterns, either at the whole genomic level or at specific sites can affect genome stability in polyploidy will require substantial additional investigation. Methylation sensitive amplification polymorphism profiling was used to evaluate variation in C-methylation among a set of 20 Chrysanthemum species and their close relatives of varying ploidy levels from diploid to decaploid. The range in relative C-methylation level was within 10%, and there was no significant difference neither between different ploidy levels nor between different species in the same ploidy level (U-values < 1.96). The transcript abundances of MET1 and DDM1 genes, which both involved in the regulation of C-methylation at CpG sites, were enhanced with increased ploidy level, but only MET1 was positively correlated with the nuclear DNA content. Considering the key role and efficiency of MET1 in maintaining CpG methylation, the limited variation observed with respect to C-methylation may reflect a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation.

Genomic and transcriptomic alterations following intergeneric hybridization and polyploidization in the Chrysanthemum nankingense×Tanacetum vulgare hybrid and allopolyploid (Asteraceae)

“…The Asteraceae genus Chrysanthemum includes ploidy states ranging from diploid to decaploid 27 . Although numerous studies have provided valuable information about the rapid genomic and transcriptomic changes in many other plants, little is known about these changes in Asteraceae 28 .…”

An eruption of LTR retrotransposons in the autopolyploid genomes of Chrysanthemum nankingense (Asteraceae)

“…Cytosine methylation machinery responses might act as a "genome defence" system in Chrysanthemum spp. during allopolyploid formation, potentially re ecting a balance between the increased activity of MET1 in the higher ploidy genomes and the larger number of CpG dinucleotide sites available for methylation [10,33]. These ndings suggest the need to expand the current evolutionary framework to encompass the genetic/epigenetic dimension when seeking to understand allopolyploidization.…”

“…Polyploidization is a prominent driver of evolution among angiosperms [1], affecting not only the current distribution and success but also the evolution of these species. Coincidentally, polyploidization generally occurs with greater frequency among Asteraceae species than among other angiosperm families, and this increased frequency also provides an ideal opportunity for investigations of the rapid adaptations associated with polyploidization [31][32][33]. The Asteraceae genus Chrysanthemum harbours several polyploidization species.…”

“…Considerable variations at the ploidy level have been observed in this genus (from 2n = 2x = 18, to 2n = 36, 54, 72, up to 90) [33][34][35]. In previous studies, we investigated the genomic, transcriptomic and epigenomic alterations in allopolyploids of this genus [33,[36][37][38]. Genome-wide transcriptomic alterations were detected in a set of synthetic allohexaploids.…”

An Eruption of LTR Retrotransposons in the Autopolyploid Genomes of Chrysanthemum nankingense (Asteraceae)

“…Polyploidization is a prominent driver of evolution among angiosperms [ 1 ], affecting not only the current distribution and success but also the evolution of these species. Coincidentally, polyploidization occurs with greater frequency among Asteraceae species than among other angiosperm families, and this increased frequency also provides an ideal opportunity for investigations of the rapid adaptations associated with polyploidization [ 33 , 34 , 35 ]. The Asteraceae genus Chrysanthemum harbours several polyploid species.…”