Epigenomic and transcriptomic regulation of environmental responses in the Pacific oyster, Crassostrea gigas

Thesis (Ph.D.)--University of Washington, 2014Intertidal invertebrates such as bivalve molluscs live in constantly changing and frequently stressful environments and must be equipped to both detect and quickly respond to environmental changes. Our understanding of the molecular and cellular response systems in these organisms are an important part of species conservation and well as our ability to predict their response and limits to environmental stress. This dissertation explores environmental responses in oysters using transcriptomic and epigenomic approaches. The first chapter examines the transcriptomic responses of oysters from two locations with varying anthropogenic input using ultra short high-throughput sequencing reads. The work presented in Chapter 2 provides the first evidence that DNA methylation is present in the genome of a bivalve mollusc and suggests a regulatory role in these species. Chapter 3 provides the first whole methylome analysis of a locotrophozoan and identifies relationships between DNA methylation and gene expression. Finally, Chapter 4 presents a review of the current DNA methylation data available for bivalves and proposes new hypotheses for how DNA methylation may be regulating the genome in oysters. By combining transcriptional and epigenetic datasets, this work provides the most complete picture of epigenomic regulation for any molluscan species and paves the way into future investigations of the role of epigenetics in environmental regulation and local adaptation and evolution in marine invertebrates