International Journal of Marine Science, 2025, Vol.15, No.4, 179-185 http://www.aquapublisher.com/index.php/ijms 182 4.3 Epigenetics and environmental response Genetics isn’t the whole picture. Epigenetic changes-especially DNA methylation—are now seen as another layer of adaptation. For example, intertidal oysters tend to show lower methylation levels and more flexibility in methylation patterns when exposed to heat stress. In contrast, subtidal species have higher, more stable methylation profiles. These methylation changes affect the expression of genes involved in cell death, development, and ion balance. In other words, it’s not just about what genes oysters have-but also how they’re regulated. This may give oysters the ability to respond quickly to environmental changes (Wang et al., 2020). 5 Functional Insights from Transcriptome Analyses 5.1 Expression in intertidal and subtidal species Not only does the environment affect the characteristics of oysters, but their gene expression also shows how they adapt step by step. The activity of some genes in different salinities is often related to the growth rate or survival rate of oysters (Wang et al., 2020; Zhang et al., 2022). However, this relationship is not absolute. Different species have different responses, and the interaction between genes and environment cannot always be accurately predicted (Liu and Huang, 2024). 5.2 Response to pollution and pathogens When oysters encounter pollution or infection, some specific genes are activated. For example, the GPCR gene family will produce different responses when facing heavy metals or pathogens (Zhang et al., 2016; Fu et al., 2022). These genes can help oysters reduce stress and are important for them to survive in harsh or polluted waters. But adaptation isn’t just controlled by one or two genes. Many of these responses involve multiple genes working together, and the effect can depend on the environment. This is known as polygenic adaptation, and it shows how complex oyster responses to stress can be (Bernatchez et al., 2018; Fu et al., 2022). 6 Evolution of Oyster Immune Systems 6.1 Innate immune gene expansions In the intertidal zones where pathogens are abundant and environmental conditions fluctuate frequently, oysters have gradually evolved a complex innate immune system. Studies have shown that several immune-related gene families have expanded in oyster genomes, particularly Toll-like receptors (TLRs), inhibitor of apoptosis proteins (IAPs), and caspases. These key genes exhibit both increased copy numbers and enhanced expression across multiple oyster species (PZhang et al., 2016; Owell et al., 2018). Such expansions help oysters recognize a wide range of pathogens and improve their ability to regulate cellular stress responses. 6.2 Pathogen recognition systems The Toll-like receptor (TLR) family has expanded considerably in oysters. This helps explain their ability to sense a wide range of pathogens in environments where microbial diversity is high (Zhang et al., 2016; Powell et al., 2018). But again, not all TLRs act the same, and some are more responsive than others depending on the challenge. Lectins and antimicrobial peptides are another major line of defense. These molecules identify and neutralize pathogens directly. Oysters show a great deal of variation in these genes, which is thought to support their survival across different microbial landscapes (Zhang et al., 2016; Powell et al., 2018). 7 Case Study: Genetic Comparison of Pacific and Hong Kong Oysters 7.1 Genetic differences and salinity adaptation There are obvious genetic differences between Pacific oysters (Crassostrea gigas) and Hong Kong oysters (Crassostrea hongkongensis). Pacific oysters are more adapted to living in seawater with higher salinity, while Hong Kong oysters are more adapted to environments with lower salinity (Zhang et al., 2022). This difference is not only reflected in their distribution areas, but also in their growth rates and survival rates, and each performs better in the environment they are adapted to. When faced with salinity changes, the genes activated by the two oysters are also different. They respond to stress through different gene regulation methods. This difference is closely related to the environment in which they live for a long time, indicating that they gradually adapt to their respective living conditions through genetic changes.
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