Transcriptome analysis reveals the immune response mechanism of golden cuttlefish (Sepia esculenta) larvae exposed to ink

The golden cuttlefish (Sepia esculenta), a significant cephalopod in the Yellow and Bohai Seas of China, is highly esteemed for its exceptional medicinal and commercial value. The natural resources of the S. esculenta are currently facing depletion due to the ongoing environmental degradation and overfishing. Secreted by the ink sac of the S. esculenta, the ink contains a diverse array of nutrients and active ingredients, which can exert a substantial impact on biological immune cells' proliferation and differentiation, the occurrence of inflammation, autophagy, along with other processes pertaining to immune response, and thus affects their survival. In the actual production, the high-density artificial cultivation and transportation process of S. esculenta often leads to large-scale inkjet phenomenon, posing a significant threat to the survival of this species. The present study employed RNA-seq as the basis to investigate the mechanisms of immune response in S. esculenta larvae when exposed to ink. Conduct functional enrichment analysis (GO and KEGG) as well as protein-protein interaction (PPI) network analysis for the 1951 differentially expressed genes (DEGs). In addition, this study is the pioneering attempt to employ a combined analysis of KEGG and PPI network construction and further reveal a set of 20 key genes associated with immunity, which have higher numbers of PPI or KEGG pathway participation. It is evident that the ink exposure has an impact on the inflammatory response, immune cell propagation and specialization, transmission of signals in the immune system, and autophagy in S. esculenta larvae. Through the enrichment analysis of genes and pathway functions, we understood the impact of ink exposure on the larvae of S. esculenta exhibit immune resistance, further improved our overall comprehension regarding the immune functionality exhibited by mollusks, and contributed to improving the survival rate of S. esculenta in factory farming.