International Journal of Marine Science, 2025, Vol.15, No.1, 1-14 http://www.aquapublisher.com/index.php/ijms 7 (CYP450 family) has many members in the abalone genome, which may be related to its broad-spectrum diet and detoxification needs. Another example is that abalone also has extra copies of enzyme genes involved in amino acid degradation and urea cycle, which is speculated to be related to its high-protein seaweed diet. It is particularly noteworthy that abalone's neuroendocrine and growth hormone regulatory genes also have an expansion trend. For example, more than 40 neuropeptide precursors were identified in the green abalone genome, which is more than other mollusks. These neuropeptides may have redundant and diverse functions in regulating gonad development and growth metabolism. For another example, abalone also has a relatively rich insulin-related peptide and receptor genes, which contribute to its growth rate and regulation of glucose and lipid metabolism. The expansion of the shell structure and metabolism-related gene family reflects the functional enhancement of abalone to adapt to its ecological niche: the hard shell requires a complex matrix protein network to support it, and rapid growth and movement require an efficient metabolic regulation system. These genomic characteristics are consistent with the evolutionary lifestyle of abalone occupying the coastal reef ecological niche and eating nutrient-rich macroalgae. 4.3 Adaptive structural variants and genomic islands of divergence The genetic changes of abalone do not only occur in a single gene. On a larger scale, their genomes have also undergone some adjustments, such as rearrangements and structural changes. These changes appear in some particularly obvious areas, namely "hot spots". When comparing the genomes of different abalone species, this study found that some chromosome segments changed particularly quickly, and some regions were highly diverse. For example, in the comparison between the wrinkled abalone and the nine-hole abalone, several large regions showed structural changes, some of which were reversed in gene order (called inversion) and some of which were moved in position (called translocation). These large genomic changes may be one of the reasons for the separation of the two species. Because these changes make it difficult for genes in related regions to recombine, that is, they cannot be freely combined as before, so that the differences between the two species are fixed more quickly. This study also used the method of population resequencing to analyze the genomic differences of wrinkled abalone in different regions of China. The results showed that some regions on the chromosome had particularly high F_st values (this is an indicator of the difference between two populations). These "differentiation islands" often contain genes related to environmental adaptation (Huang et al., 2021). For example, on chromosome 7, there is a region that is very different between northern and southern abalone. There are some genes related to immune response and stress response. This result shows that these regions may be subject to selection pressures from different environments, such as different water temperatures and water quality, and are the key to the adaptation of the group to the environment. Similar situations also occur in the comparison between green abalone and black abalone. In the gene region that controls shell color and shape, the allele frequencies of the two species are different. This difference may be due to natural selection. Further analysis found that changes in some traits are related to changes in genome structure. For example, studies have shown that the green abalone genome lacks a gene that can regulate pigment deposition that black abalone has, which may explain the difference in their shell color (Botwright et al., 2019). There are some particularly variable regions in the abalone genome, such as microsatellites and VNTR (variable tandem repeats). These regions vary in length in different species, and many of them appear in the place where genes are regulated, which may affect gene expression, that is, whether the genes are turned on or off, thereby affecting the adaptability of abalone. The evolution of the abalone genome is not just a matter of slowly changing genes one by one, but also a large segment of changes together. These changes may have played a big role in the process of species formation and adaptation. For example, some areas may prevent different species of abalone from interbreeding (creating reproductive isolation), or they may help them adapt to new environments more quickly. 5 Case Studies: Phylogenomics and Adaptation in Representative Species 5.1 Haliotis discus hannai: high-latitude adaptation and immune responses Japanese abalone (Haliotis discus hannai) is native to the cold temperate waters of the North Pacific, including northern China, the Korean Peninsula and the coast of Japan. It is currently the abalone species with the highest
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