Integrated analysis of lncRNA-miRNA-mRNA networks reveals stage-specific molecular regulation of oogenesis in Chinese alligator (Alligator sinensis)

Here we integrated transcriptomic and non-coding RNA analyses to elucidate stage-specific lncRNA/miRNA-mRNA regulatory networks during oogenesis. Gonadal tissue samples were collected at three critical developmental stages: 1-day post-hatching (AH), 15-day post-hatching (BH), and 90-day post-hatching (CH). RNA sequencing revealed 568 upregulated and 222 downregulated genes during the early proliferation phase (from AH period to BH period), and 667 upregulated and 241 downregulated genes during the maturation phase (from BH period to CH period). Additionally, we identified 1,194 lncRNAs and 1,808 miRNAs dynamically expressed across these stages. During early proliferation, cell cycle genes (CCN3 - CCN Family Member 3, CDC45 - Cell Division Cycle 45) and signaling pathways (WNT - Wingless-Type MMTV Integration Site Family, FGF - Fibroblast Growth Factor) dominated, while metabolic genes (ALDOB-Aldolase B, Fructose-Bisphosphate, FABP4 - Fatty Acid Binding Protein 4) were suppressed. In the maturation phase, meiosis-related genes (STAG3 - Stromal Antigen 3, SPO11- Sporulation Protein 11 Homolog) and germ cell-specific factors (DAZL - Deleted in Azoospermia-Like, NOBOX - Newborn Ovary Homeobox) were upregulated, accompanied by miRNA-mediated suppression of non-essential functions. This study provides the first comprehensive roadmap of non-coding RNA-mediated oogenesis in reptiles, offering insights for conservation strategies in endangered species.