Differential DNA methylation across environments has no effect on gene expression in the eastern oyster

Abstract

It has been hypothesized that environmentally induced changes to gene body methylation could facilitate adaptive transgenerational responses to changing environments. We compared patterns of global gene expression (Tag‐seq) and gene body methylation (reduced representation bisulfite sequencing) in 80 eastern oysters Crassostrea virginica from six full‐sib families, common gardened for 14 months at two sites in the northern Gulf of Mexico that differed in mean salinity. At the time of sampling, oysters from the two sites differed in mass by 60% and in parasite loads by nearly two orders of magnitude. They also differentially expressed 35% of measured transcripts. However, we observed differential methylation at only 1.4% of potentially methylated loci in comparisons between individuals from these different environments, and little correspondence between differential methylation and differential gene expression. Instead, methylation patterns were largely driven by genetic differences among families, with a PERMANOVA analysis indicating nearly a two orders of magnitude greater number of genes differentially methylated between families than between environments. An analysis of CpG observed/expected values (CpG O/E) across the C. virginica genome showed a distinct bimodal distribution, with genes from the first cluster showing the lower CpG O/E values, greater methylation and higher and more stable gene expression, while genes from the second cluster showed lower methylation, and lower and more variable gene expression. Taken together, the differential methylation results suggest that only a small portion of the C. virginica genome is affected by environmentally induced changes in methylation. At this point, there is little evidence to suggest that environmentally induced methylation states would play a leading role in regulating gene expression responses to new environments.

Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification

“…The concentration of DML in genes is consistent with the literature examining molluscan methylome responses to ocean acidification [4, 6–8], disease [12], pesticide exposure [13], salinity (Johnson et al 2021), and heat stress [10], as well as environmental responses in corals [9, 14], urchins [11], and pteropods [5]. This differs from the vertebrate model of methylation, in which CpG islands are found in promoter regions upstream of transcription start sites [1].…”

“…salinity (Johnson et al 2021), and heat stress [10], as well as environmental responses in corals [9,14], urchins [11], and pteropods [5]. This differs from the vertebrate model of methylation, in Low pH influence on oyster methylome which CpG islands are found in promoter regions upstream of transcription start sites [1].…”

“…Methylation regulation of gene expression could then influence plasticity in response to environmental stressors [1]. Ocean acidification [4][5][6][7][8][9], heat stress [10], upwelling conditions [11], disease [12], salinity (Johnson et al 2021), pesticide exposure [13], and temperature and salinity [9,14] have all elicited changes in marine invertebrate methylomes, demonstrating a potential for methylation to regulate organismal responses to environmental conditions.…”

Lack of genotype‐by‐environment interaction suggests limited potential for evolutionary changes in plasticity in the eastern oyster,Crassostrea virginica

“…We generated the nucleotide diversity (Pi) for the coding + intron, upstream and downstream region using reduced representation bisulphite sequencing data for the same 80 oysters (K. M. Johnson et al, 2020). SNPs were called using the program bs‐snper while requiring a minimum heterozygous SNP frequency of 0.1; a minimum homozygous SNP frequency of 0.85; ‐‐minimum base quality of 15; a minimum depth of covered reads of 10; a maximum depth of covered reads of 1,000; a minimum mutation reads of 2; a minimum mutation rate of 0.02; and a Minimum read mapping value of 20 (Gao et al, 2015).…”

Understanding climate change response in the age of genomics

“…However, as attractive as this hypothesis may be, environmentally induced epigenetic modifications are not always responsible for phenotypic changes and careful genomic analysis is required to establish an association between such epigenetic changes and physiological responses and their adaptive function. In this Special Feature, Johnson et al (2021) use a combination of common garden experiments, Tag‐seq and reduced representation bisulfite sequencing to show that differential DNA methylation has no effect on gene expression across environments in the eastern oyster Crassostrea virginica . The authors compared patterns of gene body methylation and global gene expression for oysters in common gardens at two sites that differed in mean salinity.…”