Comparative transcriptome profiles across distinct developmental stages in mud crab Scylla paramamosain embryos

Abstract Background Embryogenesis is a critical process that governs the development, growth, and survival of Scylla paramamosain, a commercially important mud crab species in Southeast Asia, particularly China. Despite its aquaculture value, the molecular mechanisms underlying its embryonic development remain poorly understood. To address this gap, we sequenced and compared the transcriptome profiles of three key embryonic stages (D1, D5, and D9) to characterize stage-specific gene expression dynamics. Results A total of 21,285,306 high-quality reads were generated, identifying 42,706 differentially expressed genes (DEGs). Gene Ontology (GO) enrichment analysis revealed significant (P < 0.05) associations with catalytic activity, signal transduction, and transport processes. Several development-related pathways, including the hedgehog, Wnt, and MAPK signaling pathways, showed notable up-regulation, and selected DEGs were validated using qRT-PCR. The transcriptomic patterns support the hypothesis that gene expression variability is tightly linked to developmental progression, with highly expressed DEGs enriched in morphogenesis-related pathways. Conclusions This study provides transcriptomic insights into early embryogenesis of Scylla paramamosain, generating foundational gene expression data that contribute to understanding crustacean developmental biology. The findings highlight key pathways potentially regulating early morphogenesis, and future comparative analyses of later developmental stages are recommended to clarify the transition from maternal to embryonic genomic control.