This repository contains scripts and output examining the influence of ocean acidification on Pacific oyster (Crassostrea gigas) DNA methylation in two populations.
Changes in DNA Methylation in Diploid & Triploid Crassostrea gigas Exposed to Different pH Levels (ID: Haws)
The experiment was run by Dr. Maria Haws' Lab at the University of Hawaiʻi Hilo. Adult diploid (n = 24), adult triploid (n = 24), diploid spat (n = 24), and triploid spat (n = 14) Crassostrea gigas were exposed to low pH (pH = 7.75) [adult diploid (n = 12), adult triploid (n = 12), diploid spat (n = 12), and triploid spat (n = 8)] or high pH (pH = 8.2) [adult diploid (n=12), adult triploid (n = 12), diploid spat (n = 12), and triploid spat (n = 6)] for six weeks. After treatment period (20200815), ctenida, gonad, and mantle were collected from each adult and stored in RNA/DNA Shield (ZymoResearch). Spat were not dissected and were preserved whole in RNA/DNA Shield (ZymoResearch). Samples were received by us (Roberts Lab) on 20208020 and stored @ -80oC.
For this analysis, Sam White extracted DNA from ctenidia tissue and sent for whole genome bisulfite sequencing (ZymoResearch). Initial FastQC assessment of raw sequencing data can be found here.
Yaamini Venkataraman exposed adult C. gigas from Willapa Bay to either low and ambient pH conditions for seven weeks (February 4, 2017 to April 8, 2017). Oysters were separated into six tanks: Tanks 1-3 experienced low pH conditions, and Tanks 4-6 experienced ambient pH conditions. Water samples from each experimental tank and the two header tanks were collected twice a week and poisoned with mercuric chloride for chemistry analysis. Before and after pH exposure, ctenida, mantle and adductor tissues were sampled from twenty individuals and flash frozen. Additional ctenida tissue was placed in ethanol for downstream DNA analyses, and gonad tissue was used for histological analyses to evaluate maturation. Live weight, empty shell weight and shell lengths were also recorded.
This trial will elucidate how a single stressor affects methylation in gonad tissues. Based on the observed negative maternal carryover effect, DNA was extracted from female gonad tissue preserved in histology samples. The DNA was then sent for whole genome bisulfite sequencing (ZymoResearch).