Morphological and transcriptomic analyses reveal the embryonic development of Macrobrachium rosenbergii

Macrobrachium rosenbergii is one of the most economically important crustacean species in global aquaculture. However, the molecular regulatory networks governing its embryonic development remain largely unexplored. In this study, we performed comprehensive transcriptome sequencing of eight embryonic developmental stages, from fertilized egg to pre‑hatching (Groups A to H), to characterize the dynamic gene expression profiles throughout embryogenesis. Time‑series clustering identified 13 significant expression profiles, with several large clusters showing distinct temporal expression patterns across developmental stages. The A→B comparison exhibited the largest transcriptomic shift, with 17,710 downregulated and 12,640 upregulated genes. This pattern might reflect extensive transcriptional reprogramming during early embryogenesis and was potentially consistent with a maternal-to-zygotic transition. However, it did not directly demonstrate maternal RNA clearance or zygotic genome activation. KEGG enrichment analysis of the A→B DEGs revealed significant overrepresentation of genes associated with metabolic pathways, including fat digestion and absorption and fatty acid biosynthesis, as well as conserved developmental signaling pathways, including the Wnt, Hippo, and TGF-β signaling pathways. The transition from stage B to stage C (cleavage to blastula) exhibited enrichment of pluripotency‑related pathways as well as melanogenesis and tyrosine metabolism, suggesting that eye-related transcriptional programs may begin to emerge at this stage. Notably, the F to G transition (primitive heart tube to regular strong heartbeat) showed enrichment of cardiac muscle contraction, adrenergic signaling, and neuroactive ligand‑receptor interaction pathways, along with sensory‑related GO terms including phototransduction and visual perception, consistent with concurrent transcriptional changes associated with cardiac, neural, and sensory development. qRT‑PCR analysis of six selected DEGs showed expression trends consistent with the RNA‑seq results for these genes. Our findings provide a transcriptomic resource for M. rosenbergii embryogenesis and identify stage-associated expression patterns and enriched pathways. These results broaden the molecular description of crustacean embryogenesis and may inform future studies relevant to hatchery management and selective breeding.