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Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications.

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.

SUBMITTER: Liu J

PROVIDER: S-EPMC6976628 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications.

Liu Jingwei J Hu Huihua H Panserat Stéphane S Marandel Lucie L

Scientific reports 20200122 1

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 ...[more]

PMID: 31969623

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Project description:Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation. We estimate a recent split between western and eastern gorillas of 150,000-180,000 years ago, with gene flow around 20,000 years ago, primarily between the Cross River and Grauer's gorilla subspecies. This gene flow event likely obscures evolutionary relationships within eastern gorillas: after excluding putatively introgressed genomic regions, we uncover a sister relationship between Virunga mountain gorillas and Grauer's gorillas to the exclusion of Bwindi mountain gorillas. This makes mountain gorillas paraphyletic. Eastern gorillas are less genetically diverse and more inbred than western gorillas, yet we detected lower genetic load in the eastern species. Analyses of indels fit remarkably well with differences in genetic diversity across gorilla taxa as recovered with nucleotide diversity measures. We also identified genes under selection and unique gene variants specific for each gorilla subspecies, encoding, among others, traits involved in immunity, diet, muscular development, hair morphology and behavior. The presence of this functional variation suggests that the subspecies may be locally adapted. In conclusion, using extensive genomic resources we provide a comprehensive overview of gorilla genomic diversity, including a so-far understudied Bwindi mountain gorilla population, identify putative genes involved in local adaptation, and detect population-specific gene flow across gorilla species.

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Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications.

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Evolutionary history of DNA methylation related genes in chordates: new insights from multiple whole genome duplications.

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