Transcriptome analysis reveals the immunosuppression in Chinese mitten crab (Eriocheir sinensis) under Metschnikowia bicuspidate infection

• Comprehensive transcriptome analysis of Eriocheir sinensis ’s immune response to Metschnikowia bicuspidate . • Immunity-related pathways were significantly enriched based on the enrichment analysis of down-regulated DEGs. • The expression of immunity-related genes significantly increases at early stage of infection, and gradually decreases as the infection duration prolonged. • Immune response of E. sinensis may be suppressed during the intermediate stage of M. bicuspidate infection. “milky disease” is a recently emerging disease in Chinese mitten crab ( Eriocheir sinensis ), and its pathogen has been confirmed as Metschnikowia bicuspidate . High lethality of the disease causes great economic losses in the E. sinensis aquaculture industry. No effective treatment is currently available. Aquatic animals resist pathogen invasion through their immune systems . Evaluation of the immune responses of E. sinensis to M. bicuspidate is essential for control of “milky disease” in farmed animals. In this study, the transcriptomic profiles of E. sinensis were sequenced and analyzed on the 10th day after M. bicuspidate infection. Differential expression analysis revealed the existence of 1129 significantly differentially expressed genes (DEGs), with 520 genes upregulated and 609 genes downregulated. GO functional analysis and KEGG pathway analysis revealed DEGs, which were mostly related to metabolism and immunity. Immunity-related pathways (Lysosome, Peroxisome, Histidine metabolism, and Xenobiotics biodegradation and metabolism) were significantly enriched based on the enrichment analysis of down-regulated DEGs. Further analysis via quantitative real-time PCR revealed that some immune-related genes, such as catalase ( CAT ), superoxide dismutase ( SOD ), acid phosphatase ( ACP ), and alkaline phosphatase ( ALP ), were significantly up-regulated in the early stage of the infection, but significantly decreased in the middle stage of the infection in infected crabs. Furthermore, histological analysis revealed that M. bicuspidate can cause damage to the hepatopancreas at the cellular level. These results showed that immune genes such as CAT, SOD, ACP and ALP play crucial roles in the innate immunity of E. sinensis in response to M. bicuspidate in the early stage of infection, and the immune response of E. sinensis may be suppressed during its middle stage. Collectively, the results will be helpful to more comprehensively understand the immune mechanism of E. sinensis against M. bicuspidate infection, and provide a theoretical basis for the prevention and treatment of “milky disease” in E. sinensis .