Dynamic transcriptome analysis of the embryonic development of the mud crab <i>Scylla paramamosain</i> Estampador, 1950 (Decapoda: Brachyura: Portunidae)

Abstract The mud crab (Scylla paramamosain Estampador, 1950) holds significant economic value within China’s crab farming industry. The artificial propagation of juvenile crabs nevertheless remains in its early stages, with heavy reliance on wild-caught seed stock. Key challenges in mud crab aquaculture include the prolonged embryonic development period, the difficulty of controlling developmental processes, and a tendency toward developmental desynchronization. Gaining a thorough understanding of the embryonic development process is crucial for providing a theoretical foundation for improving the reproduction and breeding of this species. We utilized transcriptome sequencing to investigate gene expression patterns across five critical stages of embryonic development: blastula, nauplius, eyespot, heartbeating, and prehatching. Our results revealed that marked variations in gene expression during the early stages of development, with significant differences observed in the blastula, nauplius, and eyespot stages. By contrast, the gene expression profiles during the heartbeat and prehatching stages were more closely aligned. The expression patterns were categorized into six distinct clusters, highlighting the complexity of the developmental processes. Our analysis also indicated that immune-related genes and pathways were highly expressed during the early stages of development, with expression levels decreasing as development progressed. By contrast, genes related to nutrition and energy metabolism showed a gradual upregulation across the developmental stages. Our study sheds light on the dynamic changes in gene expression during the embryonic development of the mud crab, elucidating key biological processes at each stage and providing valuable insights for future breeding and cultivation strategies.