International Journal of Marine Science, 2025, Vol.15, No.5, 233-244 http://www.aquapublisher.com/index.php/ijms 234 2 Overall Characteristics of Oyster Genome 2.1 Progress in sequencing and assembly of oyster genomes With the development of high coverage long read and long sequencing and advanced assistive technologies, the quality of oyster genome assembly has been significantly improved. Using the third generation of PacBio sequencing (>200× depth) combined with Hi-C technology, researchers successfully constructed the chromosomal-level genome of Pacific oysters. Based on this chromosomal reference, researchers further resequencing 495 wild Pacific oyster individuals whole genome, constructed the first comprehensive oyster variation map, identified about 4.8 million high-quality SNPs, 600 000 small indexes, and 49 000 copy number variants (CNVs), revealing that there are variation differences in about 21% of genomic regions between individuals (Qi et al., 2021). In addition to Pacific oysters, genome sequencing of other oyster species has also made progress. For example, the genomes of American oysters and Portuguese oysters were assembled and announced successively, while oysters used nanopore sequencing to obtain a highly continuity genome of 613.9 Mb, of which 99.6% of the sequences were localized to 10 chromosomes (Li et al., 2023). 2.2 Genomic size, chromosomal structure and genetic diversity The genome size of most oyster species is about 0.5 Gb~0.7 Gb, and the number of chromosomes is generally 10 pairs. Although Pacific oysters and oysters belong to different lineages, their genome sizes are similar and the number of chromosomes is the same. Collinear analysis shows that the sequence consistency between the two is more than 95% (Qi et al., 2022). This shows that the oyster species are more conservative in the macroscopic structure of the genome. The oyster genome has a high degree of polymorphism and heterozygity. It is reported that there are more than 10 polymorphic loci per kilobase in the genome of Pacific oysters, with a much higher level of genetic diversity than most vertebrates. This is considered a genetic strategy for oysters to adapt to frequent environmental fluctuations: high variation provides rich material for natural selection. In addition to SNP, structural variations such as copy number variations further increase the breadth of genetic variation within the population. Studies have shown that there are a large number of gene duplication differences among individuals in eastern oysters (Crassostrea virginica), and some chromosomal regions are enriched with high-density duplication fragments (Modak et al., 2021). These structural variations allow populations to have greater genetic response space when facing different environments, which are believed to contribute to the evolutionary success of oysters. 2.3 Comparison with genomes of other bivalve species Compared with other bivalve shellfish, such as scallops and mussels, the oyster genome exhibits some unique features and similar patterns. On the one hand, multiple shellfish genomes are rich in repeat sequences and transposable elements, which may be an important basis for shellfish to adapt to complex environments (Takeuchi et al., 2016; McElroy et al., 2024). On the other hand, some of the gene families associated with environmental stress in the oyster genome have undergone significant expansion, which has also been reported in other bivalves, but the degree of oysters is particularly prominent. The HSP70 heat shock protein gene amplifies to dozens of copies in oysters, while the family is smaller in many mollusc species. For example, the solute carrier (SLC) gene family, research has found that it has expanded on a large scale in Oripe oysters and American oysters that adapt to low salinity estuaries (Figure 1), but it is not obvious in Pacific oysters living in open and open waters of high salinity. This phenomenon of gene amplification is considered a "convergent evolution" strategy carried out by different species for their respective habitats, suggesting that gene replication is crucial in shellfish stress adaptation. In addition, there are also differences in ploidy and genomic structures of different shellfish. Some clams are polyploid or highly heterogeneous heterogeneous genomes, while oysters are mainly diploid, with occasional reports of natural triploid individuals. 3 Types and Detection Technology of Genomic Structural Variants 3.1 The main types of structural mutations Genome structural variation generally refers to sequence changes of more than 50 bp relative to the reference
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