Transcriptome analysis provides novel insights into the immune mechanisms of Macrobrachium nipponense during molting

Molting is a basic physiological behavior of the Oriental river prawn (Macrobrachium nipponense), however, the gene expression patterns and immune mechanisms during the molting process of Oriental river prawn are unclear. In the current study, the gene expression levels of the hepatopancreas of the Oriental river prawn at different molting stages (pre-molting, Prm; mid-molting, Mm; and post-molting, Pom) were detected by mRNA sequencing. A total of 1721, 551, and 1054 differentially expressed genes (DEGs) were identified between the Prm hepatopancreas (PrmHe) and Mm hepatopancreas (MmHe), MmHe and Pom hepatopancreas (PomHe) and PrmHe and PomHe, respectively. The results showed that a total of 1151 DEGs were annotated into 316 signaling pathways, and the significantly enriched immune-related pathways were "Lysosome", "Hippo signaling pathway", "Apoptosis", "Autophagy-animal", and "Endocytosis". The qRT-PCR verification results of 30 randomly selected DEGs were consistent with RNA-seq. The expression patterns of eight immune related genes in different molting stages of the Oriental river prawn were analyzed by qRT-PCR. The function of Caspase-1 (CASP1) was further investigated by bioinformatics, qRT-PCR, and RNAi analysis. CASP1 has two identical conserved domains: histidine active site and pentapeptide motif, and the expression of CASP1 is the highest in ovary. The expression levels of triosephosphate isomerase (TPI), Cathepsin B (CTSB) and Hexokinase (HXK) were evaluated after knockdown of CASP1. This research provides a valuable basis to improve our understanding the immune mechanisms of Oriental river prawns at different molting stages. The identification of immune-related genes is of great significance for enhancing the immunity of the Oriental river prawn, or other crustaceans, by transgenic methods in the future. •The hepatopancreas tissue transcriptome of Macrobrachium nipponense at different molting stages was constructed.•A total of 3326 DEGs were identified, including 1932 up-regulated genes and 1394 down-regulated genes.•Expression patterns of the 30 DEGs validated by qRT-PCR were consistent with the result of RNAseq.•Many DEGs were enriched in immune-related pathways.•The regulatory relationship between Caspase-1 and other immune-related genes was studied by RNAi.