International Journal of Marine Science, 2025, Vol.15, No.1, 35-44 http://www.aquapublisher.com/index.php/ijms 43 epigenomic data on the basis of genome comparison to analyze the evolution of gene expression regulation. For example, the comparison of tissue-specific expression profiles of different shrimps can reveal how gene regulatory networks evolve new functions; the contribution of microRNAs and long non-coding RNAs unique to crustaceans to adaptability is also worth studying. In addition, for previously discovered important repeat sequence expansions (such as SSRs and transposons), population genomics and molecular experiments should be combined to verify their specific mechanisms of action in adaptation. For example, transgenic lines containing different SSR lengths can be constructed to test their effects on gene expression and phenotype. In short, expanding from focusing on "genes" to focusing on "genomic elements" will make the conclusions of comparative genomics more comprehensive. 8.3 Establishing pan-genomes and population comparisons Traditional comparative genomes mostly use a single reference genome to represent species, but a single genome is difficult to cover all genetic diversity within a species. To solve this problem, a "pan-genome" can be constructed for important shrimp species in the future, that is, a collection of genomic variations that integrate multiple individuals. The pan-genome can more comprehensively display the gene pool of species and help discover genes or structural variations that are missing in the reference genome. For example, pan-genome research on LitoPenaeus vannamei has been put on the agenda in order to discover variations related to traits such as stress resistance and growth (Chen et al., 2023). When comparing different species, population-level genome comparisons can also be used, that is, comparing the variation spectrum within each species and then comparing it with other species. This method can distinguish between conserved functional elements and rapidly evolving fragments, and more keenly capture adaptive evolutionary signals. For example, by comparing the population selection sweep areas of closely related shrimps, genes that adapt to different environments can be located and changes left over from common ancestors can be distinguished from changes that have evolved independently. With the increase in sequencing throughput, population-scale comparative genomics will become possible. Acknowledgments We are grateful to Miss Xu for critically reading the manuscript and providing valuable feedback that improved the clarity of the text. 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. References Chak S.T., Harris S.E., Hultgren K.M., Jeffery N.W., and Rubenstein D.R., 2021, Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements, Proceedings of the National Academy of Sciences, 118(24): e2025051118. https://doi.org/10.1073/pnas.2025051118 Chen S., Xu W., Lu S., Hu W., Wang D., Hu X., Zhou Q., Liu Q., Zhao Z., Qin Q., Wang S., Liu Y., and Cui Z., 2023, Development strategy for aquatic breeding biotechnology, Strategic Study of Chinese Academy of Engineering, 25(4): 214-226. https://doi.org/10.15302/J-SSCAE-2023.07.023 Choi H., Yu O.H., and Eyun S.I., 2025, Evolutionary insights into adaptation of hemocyanins from deep-sea hydrothermal vent shrimps, Marine Pollution Bulletin, 215: 117872. https://doi.org/10.1016/j.marpolbul.2025.117872 Fu S., Zhuo H., and Liu J., 2024, Molecular breeding of LitoPenaeus vannamei: a review, Journal of Fishery Sciences of China, 31(3): 368-379. Guryanova S.V., Balandin S.V., Belogurova-Ovchinnikova O.Y., and Ovchinnikova T.V., 2023, Marine invertebrate antimicrobial peptides and their potential as novel peptide antibiotics, Marine Drugs, 21(10): 503. https://doi.org/10.3390/md21100503 Gutekunst J., Andriantsoa R., Falckenhayn C., Hanna K., Stein W., Rasamy J., and Lyko F., 2018, Clonal genome evolution and rapid invasive spread of the marbled crayfish, Nature ecology and Evolution, 2(3): 567-573. https://doi.org/10.1038/s41559-018-0467-9 Kawato S., Nishitsuji K., Arimoto A., Hisata K., Kawamitsu M., Nozaki R., Kondo H., Shinzato C., Ohira T., Satoh N., Shoguchi E., and Hirono I., 2021, Genome and transcriptome assemblies of the kuruma shrimp Marsupenaeus japonicus, G3, 11(11): jkab268. https://doi.org/10.1093/g3journal/jkab268 Li M.M., 2024, Comparative genomics of fish: insights into evolutionary processes, International Journal of Molecular Zoology, 14(4): 222-232. https://doi.org/10.5376/ijmz.2024.14.0020
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