High-throughput sequencing reveals the regulatory role of microRNAs in the Chinese mitten crab (Eriocheir sinensis) response to heat stress

The Chinese mitten crab (Eriocheir sinensis) is the most extensively farmed crab species in China. With global climate warming leading to frequent extreme weather events, E. sinensis in the main breeding areas during summer often faces the threat of heat stress. In this study, we constructed three small RNA (sRNA) libraries for both the heat stress group and the control group of E. sinensis and obtained 32,988,452 reads from the heat stress group and 32,341,291 reads from the control group through Illumina sequencing. By aligning with miRNAs in the miRBase database and predicting novel miRNAs with software, a total of 128 miRNAs were identified in these six libraries, including 98 known miRNAs and 30 novel miRNAs. By calculating and comparing the expression levels of miRNAs in the heat stress group and the control group, nine differentially expressed miRNAs (DEMs) were identified. The target genes of miRNAs were predicted using miRanda and RNAhybrid software, and the target genes of DEMs were annotated with GO and KEGG, revealing a significant regulatory effect of DEMs on the TGF-beta signaling pathway. The novel miRNA, novel_83, might inhibit TGIF in the TGF-beta signaling pathway, delaying body growth through the TGIF-p300/SP1 complex-p15 pathway to cope with heat stress. The above results indicate that miRNAs participate in regulating the physiological response of E. sinensis to heat stress and are an important part of the regulatory network. This study lays a foundation for further exploring the role of miRNAs in crustaceans coping with environmental stresses, and provides new ideas and directions for mitigating the damage caused by heat stress to E. sinensis.