International Journal of Marine Science, 2025, Vol.15, No.3, 154-166 http://www.aquapublisher.com/index.php/ijms 163 gender differentiation. In recent years, research on Japanese marsh shrimp has identified a batch of key genes related to gender differentiation, providing clues to explore the evolutionary mechanism of its gender decision. First, the male islet hormone (IAG) gene was also found in Japanese worm shrimp and showed a sequence feature that was highly homologous to worm shrimp Rohman. It is speculated that IAG also plays a male switch role in this species (Cai et al., 2023). Second, the researchers cloned the Mn-Foxl2 gene of Japanese marshmallows and found that it was expressed at high levels in female embryos while significantly inhibited in male embryos. This is different from the co-expression of Foxl2, a male or female, in M. Rohbac. Again, the presence of the Dmrt gene was also detected in Japanese marshmallows and it was confirmed that it was expressed in males than females. Dmrt is a conservative sex determinant and is responsible for activating male traits in many species. The male biased expression of Japanese marshmallow Dmrt indicates that its function may be similar to that of vertebrate Dmrt1, responsible for testicular differentiation. 8 Multiomics Integration Revealed Adaptive Evolution Mechanisms 8.1 Synergistic application of transcriptome and proteome analysis in expression regulation In functional genomics studies, single collective data are sometimes insufficient to explain complex biological phenomena. Transcriptomics provides information on mRNA levels, but only in conjunction with proteomics can we understand the status of the final product of gene expression. Integrating the two omics data can reveal the gene regulation mechanism more comprehensively. In shrimp research, the combination of transcriptome-proteome applications are gradually emerging. A typical case is a multiomic study of environmental stress responses. A 3-month salinity stress experiment was conducted using Japanese marshmallows as a model, and the transcriptome and proteome changes in the hepatopancreatic and gill tissue were monitored. The results showed that under high salt exposure, there were significant changes in mRNA levels of thousands of genes in the gills and hepatopancreas (DEGs), but only hundreds of corresponding proteins showed significant differences (DEPs). By correlating transcription and protein data, researchers found that only a small number of pathways showed consistent significant changes at both levels, including protein secretion pathways, cGMP-PKG signaling pathways, aminoglycopy, etc. (Fan et al., 2023). On the other hand, the transcriptional levels of many genes are not consistent with protein levels: for example, about 2,000 differential genes were observed in the hepatopancreas of the low-salt (7‰) group, but there was almost no significant change in the corresponding protein. This may be due to factors such as post-transcriptional regulation, protein stability or translation efficiency. This is the value of multiomic integration: it helps us filter out real significant changes in function. When there is only transcriptome data, a large number of differentially expressed genes may not have functional effects, and after binding to the proteome, it can focus on those "core genes" whose transcripts and proteins have changed. 8.2 Epigenetic mechanism: regulation of expression by DNA methylation and miRNA In addition to changes in the DNA sequence itself, epigenetic regulation plays an important role in the adaptive evolution of shrimps. Epigenetic markers such as DNA methylation and non-coding RNA (such as microRNAs, miRNAs) can regulate gene expression without changing the gene sequence, thereby achieving a rapid response to environmental or developmental signals. In recent years, breakthroughs have been made in the study of DNA methylation in shrimp. Some people used whole-genome sulfite sequencing (WGBS) to compare muscle methylation levels in individuals in the same line as Pacific white shrimp. The results showed that the 5-methylcytosine level in the entire genome of fast-growing individuals was about 2.00%, significantly lower than that of slow-growing individuals. When analyzed in conjunction with the transcriptome, it was found that elevated methylation levels were often accompanied by downregulation of expression of certain metabolic and growth-related genes. A key gene associated with muscle development is highly methylated in the promoter region in slow-growing shrimp, resulting in a significant decrease in its mRNA expression. This reveals part of the reason for growth differences at the epigenetic level: DNA methylation promotes genes by silencing growth, which inhibits the growth rate of shrimp. This study is the first experimental evidence to directly prove that DNA methylation affects crustacean growth traits, and is of milestone significance. Similarly, DNA methylation is also involved in environmental adaptation in shrimp. In addition to DNA methylation, non-coding RNAs such as
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