Date of Award

Fall 2025

Project Type

Dissertation

Program or Major

Biological Sciences

Degree Name

Doctor of Philosophy

First Advisor

Bonnie L. Brown

Second Advisor

Elizabeth Harvey

Third Advisor

W. Kelley Thomas

Abstract

Eastern oysters, Crassostrea virginica, are foundational estuarine species that contribute to a variety of ecosystem services including water filtration, nutrient cycling, habitat creation, and shoreline protection. However, populations have declined due to disease, overharvesting, habitat loss, and climate change, especially in northern systems such as New Hampshire’s Great Bay Estuary (GBE), located in the Gulf of Maine, one of the world’s fastest warming waters. This dissertation uses genomic and transcriptomic approaches to understand the drivers of population structure, decline, and resilience in GBE oyster populations, aiming to aid restoration and aquaculture. Chapter 1 used low-coverage whole-genome sequencing to understand population structure, differentiation, and effective population size in cultivated, wild, and restored oyster populations. Results showed that heritage (rather than location) explains population clustering, with low differentiation and small effective breeding sizes across sites. Future restoration efforts should aim to maintain and expand genomic diversity to ensure population success. Chapter 2 demonstrated a method for extracting ultra-long DNA from oysters using Oxford Nanopore ultra-long DNA sequencing to generate a supplemental reference genome. This improved coverage of difficult genomic regions and supports future studies of structural variation. Chapter 3 investigated differential gene expression in oysters from varied heritage and environmental conditions and showed molecular responses to stressors like salinity and temperature. Results identified candidate pathways associated with temporal tolerance and local adaptation, offering targets for enhanced selective breeding for aquaculture. Chapter 4 explored epigenetic regulation using Oxford Nanopore native RNA sequencing to identify and study non-coding RNAs (ncRNAs) potentially involved in environmental response. These findings in Chapter 4 highlight the role of inherited and plastic mechanisms in oyster resilience. Together, these studies illuminate specific genomic and epigenomic mechanisms shaping the resilience and adaptability of C. virginica populations in Great Bay Estuary (GBE). Genomically, low-coverage whole-genome sequencing revealed that heritage, rather than geographic location, drives population structure, with low differentiation and small effective breeding sizes across sites. This highlights the need to preserve and expand genomic diversity in restoration efforts. Advances in ultra-long DNA sequencing produced a supplemental reference genome that improves resolution of complex genomic regions, laying the groundwork for detecting structural variants relevant to adaptation. At the functional level, differential gene expression analyses identified key molecular pathways responding to stressors such as salinity and temperature, pointing to candidate genes and processes for selective breeding aimed at enhancing aquaculture resilience. Epigenomically, native RNA sequencing uncovered long non-coding RNAs (lncRNAs) potentially involved in regulating stress responses and local adaptation, suggesting a layer of both inherited and plastic regulatory control that may buffer oysters against environmental variability. Collectively, these genomic and epigenomic insights provide actionable guidance for tailoring restoration strategies to local genetic contexts, informing selective breeding programs for robust aquaculture stocks, and supporting management decisions to protect and restore ecosystem function in rapidly changing estuarine environments.

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