Integrated analysis of lncRNA-miRNA-mRNA regulatory network revealing molecular mechanisms of immune response and ion transport in Eriocheir sinensis under alkalinity stress.

High alkalinity stress threatens to aquatic animal survival. However, research on the alkalinity tolerance and adaptation mechanisms of crustaceans remains limited. This study assessed the Chinese mitten crab's (Eriocheir sinensis) tolerance to alkalinity and investigated its adaptation mechanism through physiological, histological, and whole transcriptome analysis of gills. Acute alkalinity stress experiments showed that the alkalinity 96 h-LC50 for E. sinensis was 66.97 mmol/L. The experiment constructed a high alkalinity group (33.5 mmol/L, NHC) and a control group (0 mmol/L, CL) model. The gill filaments in the NHC group exhibited structural damage, including curling, atrophy, and cell vacuolation, along with the manifestation of oxidative stress. Between the NHC group and CL group, a total of 1047 differentially expressed (DE) lncRNAs, 70 DE miRNAs, and 1191 DE mRNAs were obtained. KEGG and GO enrichment analysis found that they were mainly enriched in immune and metabolic pathways, such as the mTOR signaling pathway, TGF-beta signaling pathway, NOD-like receptor signaling pathway, carbohydrate metabolism, and amino acid metabolism pathway. Through the analysis of targeting relationships and screening of target genes related to immune responses, ion transport, and apoptosis, a total of 11 lncRNAs, 6 miRNAs, and 8 mRNAs were obtained for constructing the lncRNA-miRNA-mRNA regulatory network. The findings of this study demonstrate that under high alkaline stress conditions, both the innate immune response and ion transport are enhanced in the gills. This research elucidates the molecular mechanisms underlying gill-mediated high environmental alkalinity stress in crustaceans, which also offers a theoretical foundation for E. sinensis saline-alkaline aquaculture.