Integrated miRNA-mRNA transcriptomic analysis of hepatopancreas reveals molecular strategies in Chinese mitten crab ( Eriocheir sinensis ) under acute nitrite stress

Nitrite is one of the most common pollutants in high-density aquaculture or in recirculated aquaculture systems. In this study, gene and miRNA expression dynamics were investigated for unveiling the genetic regulation of Eriocheir sinensis in response to acute nitrite stress. Two groups of E. sinensis with different vitality of appendages (i.e., NG and DG) were treated with nitrite-N in 6 and 24 h, respectively. A number of differentially expressed (DE) genes and miRNAs were detected in the pairwise comparisons of the two groups. We found that the DE genes and the target genes of DE miRNAs were significantly enriched into some key pathways, such as metabolic pathways, MAPK signaling pathway, and nitrogen metabolism. Notably, the number of DE genes identified from the pairwise comparison of MNG vs. FNG (NG groups at 6 h and 12 h, respectively) was much larger than that identified from MDG vs. FDG (FG groups at 6 h and 12 h, respectively), indicating that the individuals from strong vitality group had genetic superiority for tolerance of nitrite stress. The similar trend was also observed from the identification of DE miRNAs. Some key genes (e.g., hsp70, mtnd2, act7, hspg2, cam-1) involved in signaling transduction, oxidative phosphorylation, and energy metabolism were detected in this study. Besides, several miRNAs (miR-31, miR-215, miR-142-x) that mediate the calmodulin related genes were also identified, inferring that calcium signaling pathway participates in the responses to nitrite stress in crabs. This study revealed the mRNA and miRNA expression patterns of Chinese mitten crab under sustained nitrite stress and provided the genetic basis for the molecular selective breeding.