International Journal of Marine Science, 2025, Vol.15, No.5, 233-244 http://www.aquapublisher.com/index.php/ijms 236 conduct long-read-length SV detection on two oyster reference genomes, identifying about 190 000 to 220 000 SVs, covering 31%~35% of the genome, far exceeding the detection capabilities of previous short-read-length methods (Yildiz et al., 2022). 3.3 Prospects of multiomics method combined with SV research Although a single genomic assay can locate SV, it is difficult to directly explain its functional consequences. By introducing data such as transcriptome, epigenetic group, proteome, etc., the mechanism by which SV affects biological traits can be revealed from a functional level. This idea has begun to emerge in the study of oyster adaptability (Jiao et al., 2021). Some studies have integrated genomic variation, acetylation modification and phenotypic data of oysters, and found that under the action of environmental selection, oyster populations have genetic differentiated on a subtle geographical scale, and high phenotypic plasticity is consistent with the adaptation direction. They also found that some genes associated with energy metabolism and antioxidant exhibited co-differentiation of genomic structural variation and gene expression during adaptation, suggesting that SV may participate in adaptive evolution through regulatory metabolic pathways (Figure 2) (Bai et al., 2023; Lu et al., 2024). Some studies compared the genomic differences between the intertidal and subtidal oysters and found that there was no significant difference in structural variation between the two, but there was heritable differentiation in the genomic methylation pattern, indicating the role of epigenetics in environmental "memory". Figure 2 Rapid reconstruction of the Crassostrea nippona shell. Abbreviations as in figure 2, and DEGs, differentially expressed genes; ME, mantle edge; MC, mantle center; NS, Non-significant expression; SLs, shell layers (Adopted from Bai et al., 2023) Image caption: (A) Differential gene expression and number of DEGs encoding SMPs in mantle tissues of non-drilled C. nippona and (B) drilled oysters. (C) Schematic illustration of shell-drilling experiment and observation of shell regeneration process of C. nippona. Scale bar, 5 mm. (D) Ultrastructure of cross section of the whole repaired shell (Adopted from Bai et al., 2023) 4 Structural Variant Distribution and Characteristics in Oyster Genome 4.1 SV distribution patterns in different chromosomal regions Genome structural variations are not randomly distributed in the oyster genome. Studies have shown that some chromosomes or regions are enriched with high density of variation, while others are relatively conservative. In the study of the eastern oyster genome, Modak et al. used high-quality reference sequence alignment to find that
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