Multi-omics reveals dynamic molecular characteristics in the ovarian development of Chinese longsnout catfish Leiocassis longirostris

Leiocassis longirostris (L. longirostris) is a significant freshwater fish species in China. Due to the decline in natural populations, its market demand is now largely met through artificial breeding. However, the complex and prolonged ovarian maturation process has rendered current artificial breeding methods limited. Additionally, the molecular mechanisms underlying ovarian development in L. longirostris remain poorly understood. In this study, we conducted RNA and protein sequencing of L. longirostris ovarian samples across five developmental stages, categorized based on histological staining results. To uncover the dynamic characteristics of ovarian development, we identified differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) by comparing gene and protein expression profiles stage-by-stage (stage I to II, II to III, III to IV, and IV to V). GO and KEGG enrichment analyses of these profiles revealed significant enrichment in terms and pathways related to the endocrine system, signal transduction, and lipid metabolism, with dynamic changes observed across stages. The nine-quadrant analysis further elucidated the regulatory characteristics of DEGs and DEPs, highlighting differences in mRNA and protein-level regulation of genes and proteins involved in fat and protein digestion and absorption. Protein-protein interaction networks were further constructed from shared DEGs and DEPs profiles to evacuate candidate proteins involved in L. longirostris ovarian development. Moreover, we clustered DEGs and DEPs into ten clusters based on their expression trend. KEGG enrichment analysis of clusters showed pathways such as FoxO and MAPK signaling pathways were significantly enriched in cluster 4, where the expression increased as ovarian development. qPCR validation confirmed differential expression of genes associated with oocyte meiosis and steroid hormone biosynthesis, consistent with RNA-seq results. This study provides a foundation for understanding yolk lipids metabolism, paracrine factors, and endocrine system regulation during ovarian development and offers insights into developing efficient artificial breeding strategies for L. longirostris.