| Summary: | <i>Sepia esculenta</i> is an economically important mollusk distributed in the coastal waters of China. Juveniles are more susceptible to stimulation by the external environment than mature individuals. The ocean salinity fluctuates due to environmental changes. However, there is a lack of research on the salinity adaptations of <i>S. esculenta</i>. Therefore, in this study, we investigated the differential expression of genes in <i>S. esculenta</i> larvae after stimulation by low salinity. RNA samples were sequenced and 1039 differentially expressed genes (DEGs) were identified. Then, enrichment analysis was performed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Finally, a protein–protein interaction network (PPI) was constructed, and the functions of key genes in <i>S. esculenta</i> larvae after low-salinity stimulation were explored. We suggest that low salinity leads to an excess proliferation of cells in <i>S. esculenta</i> larvae that, in turn, affects normal physiological activities. The results of this study can aid in the artificial incubation of <i>S. esculenta</i> and reduce the mortality of larvae.
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