RNA-seq analysis uncovers effects of ammonia on metabolism, oxidant-antioxidant equilibrium and apoptosis in the red swamp crayfish (Procambarus clarkii)

•Ammonia stress significantly altered the metabolism.•Purine metabolism was reduced and deamination of AMP was increased to cope with the influence of ammonia stress.•Ammonia stress could destabilize oxidant-antioxidant equilibrium and cause apoptosis in P. clarkii. Ammonia, as one of the major environmental pollutants in aquaculture, can lead to negative impacts on health and production of farmed animals. However, the underlying molecular mechanism of ammonia in crayfish remains unclear. In this study, the transcriptomics of hemolymph, gill and hepatopancreas of Procambarus clarkii subjected to ammonia stress were analyzed through comparison with a control group. After assembly and annotation, a total of 87,674 unigenes were obtained with an average length of 1283 bp. A total of 5062 differentially expressed genes (DEGs) were detected, including 2140 significantly upregulated DEGs and 2922 significantly downregulated DEGs. The expression of these DEGs was verified by 10 randomly selected genes using the RT-qPCR technique. Many genes related to the purine metabolism pathway, such as adenylate kinase (ADK), adenosine deaminase (ADA), purine nucleoside phosphorylase (PNP), and allantoinase (ALN), were downregulated, whereas the expression of adenosine monophosphate deaminase (AMPD) was upregulated. Genes related to oxidant-antioxidant equilibrium, such as Cu/Zn superoxide dismutase (SOD), peroxiredoxin-1(PRDX1), and catalase (CAT), were significantly downregulated. cytochrome C (Cyt-C) and cathepsins, which play important roles in apoptosis, were significantly upregulated. Collectively, ammonia stress significantly changed purine metabolism pathway, destabilized the oxidant-antioxidant equilibrium, and caused apoptosis in P. clarkii. To maintain normal life activities, P. clarkii reduced purine metabolism and increased deamination of AMP to cope with the influence of ammonia stress. These results lay a foundation for further study on the mechanisms of the response of P. clarkii to ammonia stress and provide theoretical guidance for the sustainable aquaculture of this species.