Identification of microRNAs from juvenile greater amberjack (Seriola dumerili) in response to marine heatwaves

Marine heatwaves (MHWs) have become more frequent in recent years, and this has had a major effect on fisheries and marine ecosystems. MicroRNAs (miRNAs) are essential regulators of the thermal stress response. Here, we identified the miRNAs involved in the response to MHWs in Seriola dumerili. A total of 10.65 M, 12.60 M, 14.51 M, and 13.96 M clean tags were acquired in the control group-4d (CG-4d), CG-13d, experimental group-4d (EG-4d), and EG-13d groups, respectively, and 889 miRNAs were identified. In the transcriptome sequencing, a total of 142,613.81 M clean data were obtained. Differentially expressed (DE) analysis of miRNA and genes showed that a total of 58 and 2313 of miRNAs and genes were differentially expressed in the short-lasting MHWs group, respectively. 67 and 3804 of miRNAs and genes were differentially expressed in the repeatedly-occurring MHWs group, respectively. Integrated analysis of DE genes (DEGs) and DE miRNAs revealed 3474 and 7035 miRNA-mRNA pairs in the short-lasting MHWs group and repeatedly-occurring MHWs group, respectively. The number of down-regulated target DEGs was higher than the number of up-regulated target DEGs in the repeatedly-occurring MHWs group, which indicated that damage induced by repeatedly-occurring MHWs in S. dumerili may be greater than that induced by short-lasting MHWs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that target DEGs were enriched in antioxidant, metabolic, protein folding, and immunological pathways. An interacted network was constructed using 15 miRNAs and 157 target DEGs from these pathways, which revealed that miR-195-x, miR-203-y, and miR-14-y play essential roles in regulating the response of S. dumerili to MHWs.