International Journal of Marine Science, 2025, Vol.15, No.5, 233-244 http://www.aquapublisher.com/index.php/ijms 237 SV is distributed in almost all 10 chromosomes, but there are differences in the frequency of SV on different chromosomes. Among them, individual chromosomes carry significantly more repeated amplification regions than average, presenting SV "hot spot" regions. At the same time, SVs vary greatly between individuals, with some regions having repeated or deletion variations in different individuals, while others remain stable in most individuals (Quan et al., 2021). The population variation map of Pacific oysters also provides similar information: about 21% of genomic regions have CNV differences between individuals, indicating that the sequence copy number of these regions is frequently changed (Jiao et al., 2021). Typically, these highly variable regions tend to be rich in repeat sequences or multigene families. 4.2 Structural variations associated with repeat sequences and transposons There is a lot of evidence that repeat sequences and transposable moving elements in the genome are often one of the sources of structural variation. The oyster genome contains a high proportion of scattered repeats and various types of transposons. The replication and insertion of these elements within the genome will directly form new structural mutations. For example, the insertion of retrotransposons can be considered as a special insertion-like SV; non-allergic recombination of multiple homologous transposons can lead to the deletion or repetition of large fragments (Wang et al., 2019). The study found that the SINE-like transposon activity in the oyster genome contributes a large number of structural polymorphic sites. For oysters, stresses such as high salt and heavy metals may induce some transposon activation, resulting in genomic rearrangements and enhance the phenotypic plasticity of oysters to adversity. Although more experimental evidence is needed to support this aspect, similar speculations have been made in the resilient adaptation of other shellfish such as mussels. Repeat sequences are also prone to induce non-allelic homologous recombination (NAHR), resulting in duplication or deletion of large fragments (Tunjić-Cvitanić et al., 2024). There are many tandem repeat gene clusters and intraspheric repeats in the oyster genome, and these regions often experience NAHR and form CNV. For example, oyster immune-related genes are often distributed in clusters, and if unequal exchange occurs, it is possible to amplify the number of genes in that cluster in one individual, while some genes are missing in the other (Modak et al., 2021). Therefore, at the population level, such regions exhibit rich structural variation. 4.3 Population differences in structural variation Oyster populations live in different geographical and ecological environments, and their genomic structural variation spectrum may also vary. Population genetics studies have confirmed that there is differentiation in allelic frequencies of oyster populations from different origins, including conventional mutations and structural variations. Research on eastern oysters shows that structural variation forms an important part of population genetic variation. They found that in different geographical groups of oysters in the eastern region, the distribution frequency of repeated segments is different. Some repeated segments are found in almost every group, but rarely in another group. This means that these SVs may be affected by habitat environmental selection pressures. In addition, there are also SV differences between different breeding lines. Artificial targeted breeding may inadvertently fix some structural variations that are beneficial to the target traits, while losing some variations in natural populations. The study found that the genetic diversity of artificially bred Oyster population is lower than that of wild populations, which may include loss of some structural variation, suggesting that attention should be paid to the problem of decreased genetic diversity caused by long-term breeding (Biet et al., 2023). 5 The Relationship Between Structural Variation and Environmental Adaptability 5.1 The effect of structural variation on gene expression and regulation Genome structural mutations can affect gene expression levels and regulatory methods through various mechanisms, thus physiologically affecting the organism's ability to respond to the environment. First, structural variation changes the dosage and structure of the gene. Gene deletion will directly lead to a lack of relevant gene products, reducing biological tolerance in harmful environments. Modak et al. (2021) pointed out that a considerable proportion of repeat region fragments in the eastern oyster genome are located in the gene or contain exons, which means that a large number of SVs directly affect the structure and copy number of the gene (Modak et al., 2021).
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