International Journal of Marine Science, 2025, Vol.15, No.4, 179-185 http://www.aquapublisher.com/index.php/ijms 180 oyster combines multiple sequencing methods to improve the accuracy of gene identification (Gundappa et al., 2022; Adkins and Mrowicki, 2023). The genome of the Hong Kong oyster helps study some ancient gene families, such as the homeobox gene (Li et al., 2020). 2.2 Common sequencing methods and existing problems There is no single method that fits all oyster species. Researchers usually combine several sequencing technologies-such as long-read platforms like PacBio and Oxford Nanopore, short-read Illumina sequencing, and Hi-C mapping to assemble the genome (Qi et al., 2021; Gundappa et al., 2022). However, assembling the oyster genome is not easy. Many oysters have a large number of repeated fragments in their DNA, sometimes even accounting for more than half, and the differences between genes are also large. In addition, some structural changes, such as gene duplication, will make the assembly process more complicated (Qi et al., 2021; Li et al., 2024b). To solve these problems, researchers will also introduce transcriptome information and genetic maps to help improve the accuracy of gene annotation (Gundappa et al., 2022). Despite these difficulties, the recently completed oyster genome has a high level of completeness, and the identification of some important genes has become clearer. These data have begun to play a role in oyster biological research, adaptation analysis and breeding practices (Qi et al., 2021; Gundappa et al., 2022). 3 Genomic Architecture and Species Variation 3.1 Genome size and repetitive elements Oyster genomes vary greatly in size, and many contain a large number of repetitive sequences. For example, the genome of the Pacific oyster (Crassostrea gigas) has many transposable elements. These “jumping genes” may increase genetic diversity and help improve adaptability (Zhang et al., 2012). Another case is the Sydney rock oyster (Saccostrea glomerata), whose genome is about 784 Mb and also rich in repetitive sequences (Powell et al., 2018). These repetitive features aren’t random noise. In marine bivalves generally, they seem to have a function: helping the organisms adapt quickly to environmental changes. That said, not every species shows the same pattern in the same way, and the relationship between genome architecture and adaptability is still being investigated (Zhang et al., 2012; Powell et al., 2018). 3.2 Species-specific genes and structural features Gene families that help oysters deal with stress and pathogens have expanded in some species more than others. In both C. gigas andS. glomerata, for example, researchers have found more copies of genes like heat shock proteins and apoptosis inhibitors-proteins that help deal with stress, salinity swings, or infections (Zhang et al., 2012; Zhang et al., 2016; Powell et al., 2018). In Crassostrea ariakensis, certain genes-especially those from solute carrier families that help cells manage salt and temperature stress-show clear signs of being favored by natural selection (Zhang et al., 2022). It’s not just the genes themselves that matter. The regions that control when and how these genes are activated also differ, which can influence how oysters respond to their environment. 4 Genomic Features of Adaptation to Marine Environments 4.1 Genes related to temperature and salt tolerance To survive in complex and changing marine environments, oysters have evolved several key gene families related to temperature and salinity tolerance. These include solute carrier genes, heat stress response genes, and various regulatory elements. In multiple oyster species, these genes exhibit signs of adaptive evolution, indicating their critical role in responding to environmental stress (She et al., 2018). For example, in the estuarine oyster, several solute carrier genes under positive selection-such as Slc23a2 and Mct12-have been identified. These genes are primarily located on chromosome 9 and form distinct gene clusters. As shown in the CIRCOS plot below, these clusters are highlighted in purple-red arcs, indicating a concentrated distribution. This pattern suggests that these regions may be under directional selection, playing a specialized role in salinity adaptation (Figure 1) (Li et al., 2021).
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