Abstract
DNA methylation is an important epigenetic mechanism involved in many biological processes, i.e. gametogenesis and embryonic development. However, increased copy numbers of DNA methylation related genes (dnmt, tet and tdg) have been found during chordate evolution due to successive whole genome duplication (WGD) events. Their evolutionary history and phylogenetic relationships remain unclear. The present study is the first to clarify the evolutionary history of DNA methylation genes in chordates. In particular, our results highlight the fixation of several dnmt3-related genes following successive WGD throughout evolution. The rainbow trout genome offered a unique opportunity to study the early evolutionary fates of duplicated genes due to a recent round of WGD at the radiation of salmonids. Differences highlighted in transcriptional patterns of these genes during gametogenesis and ontogenesis in trout indicated that they might be subjected to sub- or neo-functionalisation after WDG. The fixation of multiple dnmt3 genes in genomes after WGD could contribute to the diversification and plastic adaptation of the teleost.
Highlights
DNA methylation is an important epigenetic mechanism involving the covalent binding of a methyl group to the 5th carbon position of cytosine in CpG dinucleotides in vertebrates[1]
To explore if whole genome duplication (WGD) events lead to sub- or neo-functionalisation of DNA methylation genes, estimations of the expression patterns of DNA methylation genes were done during gametogenesis and early development in trout
We annotated them as dnmt1a and dnmt1b according to ZFIN Nomenclature
Summary
DNA methylation is an important epigenetic mechanism involving the covalent binding of a methyl group to the 5th carbon position of cytosine in CpG dinucleotides in vertebrates[1] This mechanism is generally considered as a repressive epigenetic mark that inhibits gene expression[2]. Following WGD or SSD events, duplicated genes can either be lost or retained with three distinct outcomes: conservation of the ancestral gene functions, sub-functionalisation, or neo-functionalisation[31] Through these processes, the fixation of extra copies of DNA methylation genes in teleost genomes may contribute to the diversification and plastic adaptation of teleosts. The present study aimed to refine the current knowledge concerning the evolutionary history of dnmt genes in vertebrates, and to update the existing story with all DNA methylation genes (dnmt, tet and tdg) for extended taxa within the chordate phylum. To explore if WGD events lead to sub- or neo-functionalisation of DNA methylation genes, estimations of the expression patterns of DNA methylation genes were done during gametogenesis and early development in trout
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