Integrated analysis of mRNA-seq and miRNA-seq reveal the dynamics of the sexual differentiation of Procypris mera

The Chinese ink carp ( Procypris mera ), a primitive species within the Cyprinidae family, exhibits sexual dimorphism in growth, with females growing significantly faster than males. Due to the depletion of wild resources and limitations in breeding technology, its commercial viability has become concerning. Research into all-female breeding and germplasm resource recovery is crucial for addressing these challenges, with sex control intervention playing a pivotal role. In this study, we conducted histological observations of P. mera gonads using Hematoxylin-Eosin (HE) staining and identified four key stages of gonadal differentiation (60 dph, 95 dph, 110 dph, and 150 dph,) for transcriptome sequencing. Additionally, miRNA sequencing was performed at the late differentiation stage (150 dph). Our results indicate that gonadal differentiation in P. mera is largely completed by 150 dph. During ovarian differentiation, the estrogen synthesis rate-limiting gene cyp19a1a is promoted by foxl2 , facilitating estrogen production to drive ovarian differentiation while antagonizing male pathway genes. In contrast, during testicular differentiation, genes such as dmrt1 , sox9-b , and fgf1 are upregulated across all four stages, inhibiting the expression of female pathway genes dominated by foxl2 and cyp19a1a to ensure commitment to testis differentiation. Furthermore, miRNAs also play a critical role in gonadal differentiation and maturation during the later stages. The miR-200 family regulates multiple genes associated with gonadal differentiation, potentially serving as core regulators. Additionally, some newly identified miRNAs (novell-m0207, novell-m0123-5P, and novell-m0122-5P) may also contribute to the regulation of gonadal differentiation processes. Overall, this study may provide valuable insights into the gonadal differentiation process and its underlying molecular regulatory network in P. mera . These findings offer a solid foundation for improving production performance and advancing aquaculture practices for this species.