Transcriptomic Analysis Reveals Functional Interaction of mRNA-lncRNA-miRNA in Steroidogenesis and Spermatogenesis of Gynogenetic Japanese Flounder ( Paralichthys olivaceus )

Teleost fishes exhibit extraordinary diversity, plasticity and adaptability with their sex determination and sexual development, and there is growing evidence that non-coding RNAs (ncRNAs) are emerging as critical regulators of reproduction. Japanese flounder ( ) is an important marine cultured fish that presents significant sexual dimorphism with bigger females, in which gynogenesis has been applied for aquaculture industry. In order to reveal the regulatory mechanisms of sexual development in gynogenetic female and sex-reversed neo-male , the lncRNA-miRNA-mRNA interactions were investigated using high-throughput sequencing. A total of 6772 differentially expressed mRNAs (DEmRNAs), 2284 DElncRNAs, and 244 DEmiRNAs were obtained between gynogenetic female ovaries and sex-reversed neo-male testes. Genes in the steroid hormone biosynthesis and secretion pathway were enriched and mostly significantly upregulated in neo-male testes. Subsequently, network analysis uncovered high functional specificity for gynogenetic sperm motility, as co-expressed DEmRNAs were significantly enriched in microtubule and cytoskeleton-related biological processes. Clustered miRNAs were characterized in the genome with examples of the largest conserved clusters. The 20 members are distributed in 11 clusters and may not transcribe together with their neighboring , with repressing and repressing , both as key steroidogenesis pathway genes. In summary, this study provides comprehensive insights into the mRNA-miRNA-lncRNA functional crosstalk in teleost sexual development and gametogenesis and will expand our understanding of ncRNA biology in teleost gynogenesis.