Identification and Potential Functions of MicroRNAs Involved in Freshwater Adaptation in Aquatic Firefly Aquatica leii

Aquatic insects are well-adapted to freshwater habitats; however, the contribution of miRNA-mediated post-transcriptional regulation to freshwater adaptation remains unexplored. Here, 12 miRNAomes for larval and adult aquatic (Aquatica leii) and terrestrial (Pyrocoelia praetexta) fireflies were generated for comparative analyses. In total, 20 differentially expressed miRNAs (DEMs) specific to A. leii were screened as aquatic adaptation-related miRNAs via intraspecific and interspecific comparisons. A functional enrichment analysis of target genes showed that these miRNAs significantly (false discovery rate, FDR < 0.05) regulate 10 pathways associated with key biological processes, such as energy metabolism (oxidative phosphorylation, 2-oxocarboxylic acid metabolism, pantothenate and CoA biosynthesis, valine, leucine and isoleucine biosynthesis, and insulin secretion pathway), defense/detoxification response (drug metabolism—cytochrome P450), neural signal transduction (serotonergic synapse and sphingolipid metabolism), as well as development and lifespan (hedgehog signaling pathway-fly and longevity regulating pathway). A miRNA–target–pathway network uncovered a broad post-transcriptional regulatory mechanism related to freshwater adaptation in fireflies. The roles of two randomly selected miRNA–mRNA pairs were validated through in vivo and in vitro experiments using miRNA mimics. The current study is the first to explore a miRNA-mediated potentially regulatory network for aquatic adaptation in fireflies and even insects, providing key insights into miRNA-mediated post-transcriptional regulation contributing to survival in freshwater environments.