Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

Genome-wide DNA methylation profile changes associated with shell colouration in the Yesso scallop (Patinopecten yessoensis) as measured by whole-genome bisulfite sequencing

Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis...

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Bibliographic Details
Published in:BMC genomics 2021-10, Vol.22 (Suppl 3), p.1-740, Article 740
Main Authors: Yuan, Changzi, Mao, Junxia, Sun, Hongyan, Wang, Yiying, Guo, Ming, Wang, Xubo, Tian, Ying, Hao, Zhenlin, Ding, Jun, Chang, Yaqing
Format: Article
Language:eng
Subjects:
Biological activity
Biological research
Biology, Experimental
Biosynthesis
Bisulfite
Color
Color of animals
Deoxyribonucleic acid
DNA
DNA methylation
Epigenetic inheritance
Epigenetic regulation
Epigenetics
Eukaryotes
Gene expression
Gene sequencing
Genes
Genetic aspects
Genomes
Genomics
Mantle
Melanin
Methylation
Mollusca
Mollusks
Patinopecten yessoensis
Physiological aspects
Porphyrins
Preferences
Regulatory mechanisms (biology)
Scallops
Shell colouration
Shells
WGBS
Yesso scallop
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Summary:Mollusca, a phylum of highly rich species, possess vivid shell colours, but the underlying molecular mechanism remains to be elucidated. DNA methylation, one of the most common epigenetic modifications in eukaryotes, is believed to play a vital role in various biological processes. However, analysis of the effects of DNA methylation on shell colouration has rarely been performed in molluscs, limiting the current knowledge of the molecular mechanism of shell colour formation. In the present study, to reveal the role of epigenetic regulation in shell colouration, WGBS, the "gold standard" of DNA methylation analysis, was first performed on the mantle tissues of Yesso scallops (Patinopecten yessoensis) with different shell colours (brown and white), and DNA methylomes at single-base resolution were generated. About 3% of cytosines were methylated in the genome of the Yesso scallop. A slight increase in .sup.mCG percentage and methylation level was found in brown scallops. Sequence preference of nearby methylated cytosines differed between high and low methylation level sites and between the brown- and white-shelled scallops. DNA methylation levels varied among the different genomic regions; all the detected regions in the brown group exhibited higher methylation levels than the white group. A total of 41,175 DMRs (differentially methylated regions) were detected between brown and white scallops. GO functions and pathways associated with the biosynthesis of melanin and porphyrins were significantly enriched for DMRs, among which several key shell colour-related genes were identified. Further, different correlations between mRNA expression levels and DNA methylation status were found in these genes, suggesting that DNA methylation regulates shell colouration in the Yesso scallop. This study provides genome-wide DNA methylation landscapes of Yesso scallops with different shell colours, offering new insights into the epigenetic regulatory mechanism underlying shell colour.
ISSN:1471-2164
1471-2164