Identification and comparative profiling of ovarian and testicular microRNAs in the swimming crab Portunus trituberculatus.

MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA, known as key post-transcriptional regulators for development and function of reproductive organ in animals. However, limited information is currently available on the regulatory roles of miRNAs in crustacean reproduction. In the present study, we performed small RNA deep sequencing in ovary and testis tissues of the swimming crab Portunus trituberculatus, which is a commercially important species in East Asian countries, to identify and characterize the miRNAs in gonads. We obtained 187 and 225 miRNAs from ovary and testis, respectively, including 188 known and 65 novel miRNAs. Expression profiling of the identified miRNAs indicated that ovary and testis shared the same six most abundant miRNAs (let-7, let-7c, let-7f, mir-2, mir-184 and mir-276), which accounted for a large proportion of total reads in gonads (35.78% for ovary and 37.01% for testis) and indicated that they may play essential roles in gonadal development and function. Statistically, 75 miRNAs showed differential expression level between ovary and testis tissues, and the putative target genes of these miRNAs were significantly enriched in 14 KEGG pathways, including several pathways important in reproduction, such as GnRH signaling pathway, Wnt signaling pathway, ovarian steroidogenesis and TGF-beta signaling pathway. Further analysis found that the differentially expressed miRNAs exhibited stage-specific expression during ovarian and testicular development, suggesting their potential roles in reproductive development. Our study provided the first insight into regulatory roles of gonadal miRNAs and would serve as a valuable resource for investigating miRNA-mediated mechanisms of reproduction regulation in P. trituberculatus and other crustaceans.