Transcriptome Analysis Reveals Immune and Antioxidant Defense Mechanisms in the Eriocheir japonica sinensis after Exposure to Ammonia

As a key species in freshwater aquaculture, <i>Eriocheir japonica sinensis</i> was subjected to ammonia stress to assess its impact on the hepatopancreas. A total of 4007 differentially expressed genes (DEGs) were identified between control and treatment groups, comprising 1838 upregulated and 2169 downregulated genes. Following exposure to 300 mg/L of ammonia, the oxidative phosphorylation pathway was activated, while the lysosomal pathway was suppressed, thereby influencing immune functions. Thirteen DEGs from these pathways were further validated via qRT-PCR, revealing gene expression changes of one- to two-fold. Both acid phosphatase (ACP) and alkaline phosphatase (AKP) levels in the hepatopancreas and hemolymph initially increased and then decreased, indicating a disruption in immune functionality. Additionally, alanine transaminase (ALT) and triglyceride (TG) levels were measured, alongside catalase (CAT) activity, total antioxidant capacity (T-AOC), and malondialdehyde (MDA) content, all of which showed an upward trend, signifying oxidative stress and tissue damage. These results offer critical insights into the antioxidant and immune mechanisms of <i>E. j. sinensis</i> in ammonia-enriched environments.