Dynamic alternative polyadenylation in ovaries of Muscovy ducks across different laying stages based on full-length transcriptomics

Alternative polyadenylation (APA) is a critical post-transcriptional regulatory mechanism, yet its role in follicular development and atresia in waterfowl remains poorly understood. To address this, we performed full-length transcriptome sequencing using Oxford Nanopore Technologies (ONT) on ovarian tissues from Muscovy ducks (Cairina moschata) at distinct laying stages: pre-ovulation, consecutive ovulation and inconsecutive ovulation. Our analysis identified dynamically regulated APA events across these stages. Differentially used APA sites were enriched in pathways governing cell cycle regulation/division, ubiquitin-mediated proteasomal degradation, and energy metabolism. Functional interrogation of associated genes demonstrated that stage-specific APA events may contribute to the expression of genes involved in lipid metabolism and purine metabolism pathways, ultimately influencing ovulation patterns. Furthermore, we integrated mRNA-miRNA networks and identified two hub miRNAs, gga-miR-1770_L-2R-1_1ss4CA and cgr-miR-149-5p_R + 3, with significant regulatory functions on follicular dynamics. This study provides the first comprehensive characterization of stage-specific APA mechanisms underlying follicular development and atresia in Muscovy ducks, offering novel insights into post-transcriptional regulation of avian reproduction.