Integration of transcriptome and metabolome reveals molecular mechanisms responsive to cold stress in gynogenetic mrigal carp (Cirrhinus mrigala)

Cold stress is a major environmental stimulus affecting the physiological and metabolic activities of farmed fish. In our previous study, we obtained gynogenetic mrigal carp (Cirrhinus mrigala, GMC) with significantly improved cold tolerance compared with the wild individuals. To gain a comprehensive and unbiased understanding of the molecular mechanism of cold tolerance in GMC, transcriptomes and metabolomics of liver tissues were comparatively analysed. After cold treatment at 14 °C for 48 h, histology analysis revealed that the hepatocyte nucleus was shifted, blurred and disintegrated; the terminus of the gill filament was enlarged; and the number of mucus cells and their secretions were increased. A total of 4844 differentially expressed genes (DEGs), including 2420 upregulated and 2424 downregulated genes, were identified. The upregulated KEGG pathways were mainly involved in oxidative phosphorylation, the proteasome and the citrate cycle, while the downregulated pathways were involved in staphylococcus aureus infection, systemic lupus erythematosus and leishmaniasis. A total of 160 differential metabolites (DMs) were identified, including 39 increased and 121 reduced metabolites. The KEGG pathway analysis revealed significant enrichment in retinol metabolism and folate biosynthesis. KEGG function analysis showed that the DEGs and DMs were both highly enriched in purine metabolism, neuroactive ligand–receptor interaction and galactose metabolism. Correlation analysis between DEGs and DMs revealed that multiple pathways were active and strongly related to immunity and disease, metabolism and growth under cold stress. This study can facilitate our understanding of the molecular mechanisms of fish response to cold stress and provide insight into the application of gynogenesis in farmed fish.