Transcriptome analysis identifies key regulatory genes and temporal expression dynamics during embryonic development...

The Japanese eel (Anguilla japonica), a commercially important species, has experienced severe population declines in the wild, underscoring the urgent need to improve artificial breeding techniques. However, the complexity of embryonic development and the limited understanding of its molecular regulatory mechanisms have constrained progress in artificial reproduction. To elucidate the dynamics of gene expression during early development, we conducted a comprehensive transcriptomic analysis of eight key embryonic stages using RNA-Seq. A total of 16,728 differentially expressed genes (DEGs) were identified, with the most pronounced pluripotency-related changes observed during the multicellular-blastula and differentiation-related changes in gastrula-embryo body transitions. Functional enrichment revealed distinct stage-specific pathways: early stages (multicellular) dominated by Notch and Wnt signaling, involved early developmental decisions; mid-stages (blastula to gastrula), with enriched pathways like Cell cycle, supporting rapid cell division; mid-late stages (embryo-body-formation to somite appearance) featured extracellular matrix receptor (ECM-receptor) interaction and focal adhesion, contributing to cell connectivity and tissue morphogenesis; and late stages (muscle-effect to newly-hatched-larvae) highlighted calcium signaling and metabolic pathways, providing signaling and energy support for organogenesis and functional maturation. Weighted gene co-expression network analysis (WGCNA) identified four stage-specific modules that correlated with developmental progression. Additionally, key members of the Sox, Hox, and Wnt transcription factor families were screened and found to exhibit dynamic, stage-specific expression patterns. These factors likely form a synergistic regulatory network that coordinates the entire developmental progression. Collectively, these findings delineate the molecular landscape of A. japonica embryogenesis and establish a crucial baseline transcriptomic resource that will facilitate future investigations into the molecular regulation of early development in this species.