Developmental atlas reveals mortality mechanisms in Trachinotus blochii blastula-gastrula transition

Embryonic mortality during the hatching phase significantly decreases hatchability in Trachinotus blochii , limiting the development of the aquaculture industry. To explore embryonic development and uncover the molecular mechanisms underlying early embryogenesis and stage-specific mortality, this research analyzed 200 embryos collected at each developmental stage under standard conditions (28 °C, 30‰ salinity) through transcriptome sequencing. Seven developmental stages (encompassing 27 phases) were identified, revealing that peak mortality occurs during the transition from the blastula to the gastrula stage, a period marked by oil droplet dispersion and embryo deformation. Cluster analysis of six key developmental stages revealed three developmental modules: early embryogenesis with active genomic and cellular proliferation; mid-embryogenesis focused on morphogenesis and metabolic adaptation; and late-stage development with organ functional specialization. Enrichment analyses of these modules showed that key molecular mechanisms include the coordinated actions of Wnt/Hippo signaling pathways, nucleocytoplasmic transport systems, and energy metabolism networks. Transcriptomic analysis during peak mortality periods revealed that although blastula-stage lethal embryos upregulated genes related to energy production and structural integrity, systemic dysregulation also affected hindbrain proliferation and proteostasis. Crucially, disruption of the ECM-receptor and PI3K-Akt pathways led to dysregulated proliferation and apoptosis balance. During the gastrula stage, while upregulated genes appeared to support compensatory cellular proliferation, concurrent dysregulation of core regulatory networks was observed alongside AP-1-associated inflammatory responses and apoptotic abnormalities. These correlated events coincided with the surpassing of embryonic tolerance thresholds and subsequent mortality. Twenty genes including those both upregulated and downregulated from the mortality stage were validated via RT-qPCR, with results consistent with those from transcriptome sequencing. Building upon these findings, a targeted supplementation strategy involving iron-sulfur cluster precursors and glycogen has been proposed, offering a viable pathway to overcome critical bottlenecks in large-scale aquaculture production. • A modular regulatory map was constructed of embryonic development in T. blochii. • High blastula-gastrula mortality in T. blochii : dead embryos are non-spherical with dispersed oil droplets. • Blastula stage embryonic mortality was centered on the failure of [4Fe-4S] cluster-dependent OXPHOS reprogramming. • Gastrula stage embryonic mortality was characterized by ECM dynamic dysfunction as the core defect.