(Epi)genetic diversity in the native European flat oyster

Motivation

My PhD project focusses on the (epi)genetic diversity of European flat oyster (Ostrea edulis) populations. The flat oyster was once very abundant in the North
Sea, but disease outbreaks, habitat degradation, and overfishing have decimated
populations to the extent of local functional extinction. The shellfish reefs
created by the oyster provide foraging and reproduction grounds to other marine
species and are of major importance to the overall biodiversity of the North
Sea. Restoration projects aim to restore populations by translocating oysters
from non-native regions or by introducing cultured native oysters produced in
hatcheries. The effects of such translocations on the genetic diversity of wild
native oysters remains elusive. It is imperative to maintain genetic diversity
for sustainable restoration of flat oyster populations. Therefore, genetic
characterization of wild oyster populations is required along with genetic
monitoring of oysters introduced through restoration initiatives.

The preservation of genetic diversity can be challenging in a species displaying sweepstakes reproductive success whereby the number parent contributing to the breeding population can fluctuate large per reproductive cohort. Additionally, flat oysters are sequential hermaphrodites that reverse sex throughout their lifetime. Sex identification is challenging as oysters display no sexual dimorphism and have no identified sex chromosomes. Skewed sex-ratios can hamper the transfer of genetic diversity and so monitoring of sex ratios is crucial for restoration projects. However, sex-identification solely relies on histological analysis of gonadal tissue and requires sacrificing of oysters. Consequently, sex ratios in both wild and cultured populations are often unknown. Recently, the association between sex reversal and epigenetics has been observed in multiple marine invertebrates. In oysters, DNA methylation, the most familiar epigenetic mechanism, is involved with sex reversal and sex determination through influencing gene expression in response to changing environmental conditions. Unraveling the link between epigenetic mechanisms and sex reversal is pivotal to better understand the reproductive strategy of the species and can help improve culturing practices for restoration. Therefore, this part of my research focusses on characterizing sex-specific differences in DNA methylation patterns that can be utilized for non-lethal methods of sex-identification.

Interestingly, we found that hermaphrodite oysters display the most distinct DNA methylation profile in gill tissue. Our findings showed that sex-specific DNA methylation in gill tissue is mostly associated with energy homeostasis and metabolic processes, implying a remodeling of the energy balance during sex reversal. Find the full publication here if you want to read more: https://pubmed.ncbi.nlm.nih.gov/40481401/. The sex-specific DNA methylation patterns found in gill tissue pave the way for non-lethal sex identification using epigenetic biomarkers, which will be the next step of my research.

Aim

The aim of my project is to characterize genetic diversity across flat oyster
populations in the Netherlands and analyze genetic connectivity between wild
populations and introduced oysters for restoration purposes.

Methodology

• SNP characterization
• Structural variant detection
• Nanopore sequencing
• DNA methylation