In silico identification and characterization of microRNAs from rotifers, cladocerans, and copepods

MicroRNAs (miRNAs) are short non-coding RNA molecules that regulate post-transcription and influence various biological processes across species. Despite various studies of miRNAs in vertebrates, plants, and other organisms, miRNA data in aquatic invertebrates are insufficient. In this study, we identified miRNAs from four aquatic invertebrate species that are widely used in aquatic toxicology: the rotifer Brachionus koreanus, the water flea Daphnia magna, the cyclopoid copepod Paracyclopina nana, and the harpacticoid copepod Tigriopus japonicus, using next-generation sequencing and in silico analysis. We identified total 188, 41, 47, and 100 miRNAs from each species, and target genes were predicted based on 3'-untranslated region information. Target prediction and functional annotation results provided the biological processes of these miRNAs in various development-related mechanisms, signaling transduction, and metabolism-related pathways. Moreover, the network between the miRNAs and their targets concerning defense-related and antioxidant genes suggests the suitability of miRNAs as biomarkers in ecotoxicological studies.