Comprehensive transcriptomic analysis reveals insights into the gill response to hypoxia and Poly I:C in Qihe crucian carp Carassius auratus

Hypoxia occurrence is potentiated by eutrophication caused by human activities and it may be the most dramatically increasing environmental factor as a result of the climate change-led increasing temperatures. The crucian carp Carassius auratus is an important aquaculture economical freshwater species and is also a potential model for the study of physiological adaptation. However, the transcriptomics and genomics data available for this species are still scarce. The gills of fish are the major organ of hypoxia and other stresses. In this study, we studied the effect of the exposure to hypoxia (1.0 mg O2/L for 7 d) and 2 mg/mL Poly I:C on the gene expression of the gills of Carassius auratus using the Illumina sequencing platform. Comparison of the gene expression levels between the experimental and control groups showed differentially expressed genes (DEGs). The DEGs were mainly annotated into glycolysis, oxidative phosphorylation and immune system categories based on the KEGG database. In glycolysis pathway, lactate dehydrogenase, malate dehydrogenase, glyceraldehyde 3-phosphate dehydrogenase, enolase and succinate dehydrogenase were identified. In addition, the DEGs were enriched in the immune-related pathway functions, including pattern recognition receptor (PRR), antigen processing and presentation, B cell and T cell receptor signaling pathways, natural killer (NK) cell mediated cytotoxicity, Fc gamma R-mediated phagocytosis, and the JAK-STAT, p53 and cytokines signaling pathways. This study also produced potential hypoxia biomarkers including FOS, JUN B, lysosomal acid lipase, and HIF-1 alpha. HIF-1 signaling pathway was significantly down-regulated after hypoxia and Poly I: C exposure. Hence, the data generated here may offer a valuable resource information for the further study of the immune response and also provide improved strategies against hypoxia and Poly I:C in teleost fish.