Transcriptome analysis and discovery of genes involved in immune pathways in large yellow croaker (Larimichthys crocea) under high stocking density stress

The large yellow croaker, Larimichthys crocea, is an economically important maricultured species in southeast China. Owing to the importance of stocking densities in commercial fish production, it is crucial to establish the physiological responses and molecular mechanisms that govern adaptation to crowding in order to optimize welfare and health. In the present study, an extensive immunity-related analysis was performed at the transcriptome level in L. crocea in response to crowding stress. Over 145 million high-quality reads were generated and de novo assembled into a final set of 40,123 unigenes. Gene Ontology and genome analyses revealed that molecular function, biological process, intracellular, ion binding, and cell process were the most highly enriched pathways among genes that were differentially expressed under stress. Among all of the pathways involved, 16 pathways were related to the immune system, among which the complement and coagulation cascades pathway was the most enriched for differentially expressed immunity-related genes, followed by the chemokine signaling pathway, toll-like receptor signaling pathway, and leukocyte transendothelial migration pathway. The consistently high expression of immune-related genes in the complement and coagulation cascades pathway (from 24 to 96 h after being subjected to stress) suggested its importance in both response to stress and resistance against bacterial invasion at an early stage. These results also demonstrated that crowding can significantly induce immunological responses in fish. However, long-term exposure to stress eventually impairs the defense capability in fish.