Data from: Ocean acidification induces subtle shifts in gene expression and DNA methylation in mantle tissue of the Eastern oyster (Crassostrea virginica)

Early evidence suggests that DNA methylation can mediate phenotypic
responses of marine calcifying species to ocean acidification (OA). Few
studies, however, have explicitly studied DNA methylation in calcifying
tissues through time. Here, we examined the phenotypic and molecular
responses in the extrapallial fluid and mantle (fluid and tissue at the
calcification site) in adult eastern oyster (Crassostrea virginica)
exposed to experimental OA over 80 days. Oysters were reared under three
experimental pCO2 treatments (‘control’, 580 μatm; ‘moderate OA’, 1000
μatm; ‘high OA’, 2800 μatm) and sampled at 6 time points (24 hours - 80
days). We found that high OA initially induced an increase in the pH of
the extrapallial fluid (pHEPF) relative to the external seawater that
peaked at day 9, but then diminished over time. Calcification rates were
significantly lower in the high OA treatment compared to the other
treatments. To explore how oysters regulate their extrapallial fluid, gene
expression and DNA methylation were examined in the mantle-edge tissue of
oysters from days 9 and 80 in the control and high OA treatments. Mantle
tissue mounted a significant global molecular response (both in the
transcriptome and methylome) to OA that shifted through time. Although we
did not find individual genes that were significantly differentially
expressed under OA, the pHEPF was significantly correlated with the
eigengene expression of several co-expressed gene clusters. A small number
of OA-induced differentially methylated loci were discovered, which
corresponded with a weak association between OA-induced changes in
genome-wide gene body DNA methylation and gene expression. Gene body
methylation, however, was not significantly correlated with the eigengene
expression of pHEPF-correlated gene clusters. These results suggest that
OA induces a subtle response in a large number of genes in C. virginica,
but also indicate that plasticity at the molecular level may be limited.
Our study highlights the need to reassess our understanding of
tissue-specific molecular responses in marine calcifiers, as well as the
role of DNA methylation and gene expression in mediating physiological and
biomineralization responses to OA.