International Journal of Marine Science, 2025, Vol.15, No.1, 1-14 http://www.aquapublisher.com/index.php/ijms 12 7 Conclusion This study used the whole genome data of abalone to deeply analyze the evolutionary relationship and adaptation mechanism between different species. We constructed a phylogenetic tree containing multiple representative species, clarified the taxonomic structure of the genus Abalone, and proposed some taxonomic revision suggestions. Molecular clock analysis showed that the differentiation of abalone in the geological history was highly correlated with plate movement and climate change events. Through comparative genome and selection analysis, we identified several key genes related to environmental adaptation, including heat shock proteins for temperature tolerance, antifreeze proteins, transport proteins for regulating salinity, and receptors and signaling molecules with special changes in immune pathways. We also observed that the shell matrix proteins that control shell structure have independent expansions in different abalone lineages, indicating that their shell formation mechanisms are diverse. In addition, structural variations and hotspots in the genomes of different species indicate that the adaptive evolution of abalone occurs not only at the gene level, but also in large fragments of genome structure. The results of this study provide strong support for the protection and breeding of abalone resources. In terms of protection, we revealed the genetic structure of different species and populations, which is helpful to define more scientific protection units and formulate reasonable germplasm exchange strategies to maintain genetic diversity and adaptation potential. In terms of breeding, the functional genes such as heat resistance and disease resistance we identified provide targets for molecular marker-assisted breeding, which can improve breeding efficiency and accuracy. We also found some gene regions related to hybrid vigor, which can be used to optimize parental combinations and cultivate strains with better comprehensive traits. Combining whole genome selection and genome monitoring methods is expected to promote abalone from traditional empirical breeding to precision breeding, and timely evaluate the genetic health of the population, prevent inbreeding and germplasm degradation, so as to achieve a win-win situation of industry quality improvement and sustainable resources. Although this study has made initial progress, there are still many directions worth exploring in abalone genomics. The specific functions of positively selected genes and expansion families need to be verified by transcriptome analysis, gene knockout and other means; more resequencing data of wild and farmed populations will also help reveal the impact of human activities on the genome; the introduction of long-read sequencing and Hi-C technology will improve the quality of genome assembly and discover more key variants. In addition, this study found that abalone lacks the MAVSgene, and the alternative path of this immune mechanism deserves attention. In the future, functional research should be strengthened to explore the unique immune strategy of abalone. At the same time, cross-species comparisons and genomic breeding practices should also be promoted simultaneously, such as constructing selection indices and conducting gene editing experiments. As research deepens, we are expected to have a more comprehensive understanding of the evolution and adaptation process of abalone, promote its efficient breeding and resource protection, and contribute to the development of marine ecology and industry. Acknowledgments We are grateful to Dr. W. Jin for his assistance with the serious reading and helpful discussions during the course of this work. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest.p References Agius J., Ackerly D., Beddoe T., and Helbig K.J., 2024, Analysis of the presence of anti-viral innate immune pathways in Australian abalone (H. laevigata), Comparative Immunology Reports, 6: 200145. https://doi.org/10.1016/j.cirep.2024.200145 Barkan R., Cooke I.R., Watson S.A., Lau S.C.Y., and Strugnell J., 2024, Chromosome-scale genome assembly of the tropical abalone (Haliotis asinina), Scientific Data, 11(1): 999. https://doi.org/10.1038/s41597-024-03840-w
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