Integrated mRNA and miRNA Expression Profile Analysis of Female and Male Gonads in Acrossocheilus fasciatus

SIMPLE SUMMARY: Gonadal development and sex differentiation are important research contents of aquaculture, which are regulated by complex and precise networks, such as mRNA–miRNA regulatory networks. Acrossocheilus fasciatus is an important economic fish in the south of China, and females grow faster than males. However, it is damaged by overfishing and water environment, and artificial breeding has become a concern. mRNA sequencing and miRNA sequencing were used to study the internal mechanism of sex control in A. fasciatus. Differentially expressed genes and miRNAs were identified and their potential biological functions were analyzed. In addition, through target gene prediction and dual-luciferase reporter assay, the interaction between 3 miRNAs and their target genes was confirmed. Our findings will contribute to the sex control of A. fasciatus and provide new ideas for aquaculture. ABSTRACT: MicroRNAs (miRNAs) are regarded as key regulators in gonadal development and sex determination in diverse organisms. However, the functions of miRNAs in gonads of Acrossocheilus fasciatus, an economically important freshwater species in the south of China, are still unclear. Here, high-throughput sequencing was performed to investigate the mRNA and miRNAs on gonads of A. fasciatus. In total, 49,447 unigenes were obtained, including 11,635 differentially expressed genes (DEGs), among which 4147 upregulated genes and 7488 downregulated genes in the testis compared to the ovary, while 300 (237 known, and 63 novel) miRNAs with 36 differentially expressed miRNAs (DEMs) were identified, from which 17 upregulated and 19 downregulated DEMs. GO and KEGG enrichment analysis were performed to analyze the potential biological functions of DEGs and DEMs. Using qRT-PCR, 9 sex-related genes and 9 miRNAs were selected to verify the sequencing data. By dual-luciferase reporter assay, miR-22a-5p and miR-22b-5p interaction with piwil1, and miR-10d-5p interaction with piwil2 were identified. These findings could provide a reference for miRNA-regulated sex control of A. fasciatus and may reveal new insights into aquaculture and breeding concepts.