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Simple Summary: As a filter-feeding and sessile invertebrate living in estuaries and intertidal areas, Crassostrea gigas must cope with and adapt to a dynamic and changeable environment. Vibrio alginolyticus is a Gram-negative bacterium that is widespread in oceans and estuaries, and is one of the main Vibrio species that cause oyster disease. In this study, we used transcriptome sequencing to help us better understand how the giant oyster adapts to pathogen-rich environments. By focusing on the gills, which play a crucial role in the immune response, we aimed to shed light on the molecular processes underlying the interaction between the oyster and the pathogen. Over the years, oysters have faced recurring mass mortality issues during the summer breeding season, with Vibrio infection emerging as a significant contributing factor. Tubules of gill filaments were confirmed to be in the hematopoietic position in Crassostrea gigas, which produce hemocytes with immune defense capabilities. Additionally, the epithelial cells of oyster gills produce immune effectors to defend against pathogens. In light of this, we performed a transcriptome analysis of gill tissues obtained from C. gigas infected with Vibrio alginolyticus for 12 h and 48 h. Through this analysis, we identified 1024 differentially expressed genes (DEGs) at 12 h post-injection and 1079 DEGs at 48 h post-injection. Enrichment analysis of these DEGs revealed a significant association with immune-related Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To further investigate the immune response, we constructed a protein–protein interaction (PPI) network using the DEGs enriched in immune-associated KEGG pathways. This network provided insights into the interactions and relationships among these genes, shedding light on the underlying mechanisms of the innate immune defense mechanism in oyster gills. To ensure the accuracy of our findings, we validated 16 key genes using quantitative RT-PCR. Overall, this study represents the first exploration of the innate immune defense mechanism in oyster gills using a PPI network approach. The findings provide valuable insights for future research on oyster pathogen control and the development of oysters with enhanced antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Simple Summary: The health of Amphioctopus fangsiao, a species used in aquaculture or fish farming, can be greatly affected by infections. To understand how their immune system responds, we looked at the changes in their immune cells when exposed to substances that mimic these infections. By studying these responses, we were able to identify key parts of their immune system that change when faced with infection-causing threats. We also discovered important genes, including PKMYT1 (protein kinase, membrane associated tyrosine/threonine 1) and NAMPT (nicotinamide phosphoribosyltransferase), that play a crucial role in this response. Our study gives us a deeper understanding of the immune system of the Amphioctopus fangsiao. The primary influencer of aquaculture quality in Amphioctopus fangsiao is pathogen infection. Both lipopolysaccharides (LPS) and polyinosinic:polycytidylic acid (Poly I:C) are recognized by the pattern recognition receptor (PRR) within immune cells, a system that frequently serves to emulate pathogen invasion. Hemolymph, which functions as a transport mechanism for immune cells, offers vital transcriptome information when A. fangsiao is exposed to pathogens, thereby contributing to our comprehension of the species' immune biological mechanisms. In this study, we conducted analyses of transcript profiles under the influence of LPS and Poly I:C within a 24 h period. Concurrently, we developed a Weighted Gene Co-expression Network Analysis (WGCNA) to identify key modules and genes. Further, we carried out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses to investigate the primary modular functions. Co-expression network analyses unveiled a series of immune response processes following pathogen stress, identifying several key modules and hub genes, including PKMYT1 and NAMPT. The invaluable genetic resources provided by our results aid our understanding of the immune response in A. fangsiao hemolymph and will further our exploration of the molecular mechanisms of pathogen infection in mollusks. [ABSTRACT FROM AUTHOR]