Identification and characterization of microRNAs in the gonad of Trachinotus ovatus using Solexa sequencing

The Trachinotus ovatus (T. ovatus) reach sexual maturity as late as 4–5 years, and there are no obvious morphology differences between males and females, even at maturity, making the selection of male and female parents for selective breeding difficult. To examine the potential regulatory mechanism of sexual differentiation, we conducted a microRNAs (miRNAs) analysis on the ovaries and testes of T. ovatus. A total of 13,423,691 and 11,734,953 raw reads, representing 91,883,908 and 86,879,726 unique sequences of 18–35 nt length obtained from the ovaries and testes, respectively. After mapping to the T. ovatus transcriptome reference sequence (unpublished data), and comparing the miRNA sequences with the miRBase database, 179 known mature miRNAs and 100 novel miRNAs were identified. Expression analysis showed that, 165 miRNAs were differentially expressed between the ovary and testis. To validate the Illumina results, the expression patterns of the nine most differently expressed miRNAs (dre-miR-7a, dre-miR-7b, dre-miR-153a-3p, dre-miR-144-3p, dre-miR-301a, dre-miR-92a-3p, dre-miR-727-5p, Novel 124, and Novel 190, as well as those of five miRNAs that may relate to gonad development (dre-miR-143, dre-miR-101a, dre-miR-202-5p, dre-let-7c-5p, and dre-miR-181a-5p), were assayed with RT-qPCR. The expression trends for all the miRNAs validated with RT-qPCR were consistent with the next-generation sequencing data. The identification and characterization of the miRNAs differentially expressed between the ovary and the testis of the T. ovatus will increase our understanding of the role of miRNAs in gonad differentiation. These data also facilitate studies on miRNA regulation of teleost reproduction.