Abstract
BACKGROUND: Early embryonic development begins with a transcriptionally quiescent phase that is regulated by maternally deposited products. Developmental control subsequently shifts to the zygotic genome through zygotic genome activation (ZGA) during the maternal-to-zygotic transition. This transition represents a critical developmental window that governs embryonic timing and cell fate determination. Notably, the characteristics and temporal dynamics of ZGA occur in distinct waves and display substantial divergence across species. METHODS: Single-cell RNA sequencing data from 139 human and porcine samples, spanning developmental stages from the oocyte to the morula, were integrated using Seurat v5 with reciprocal principal component analysis. Downstream analyses included orthologous gene mapping, dimensionality reduction, differential gene expression analysis, functional enrichment analysis, and pseudotime trajectory inference using Monocle3. Transcription factor (TF) regulatory networks were reconstructed using SCENIC (v1.3.1). RESULTS: Our analyses revealed both conserved and species-specific features during embryonic development from the oocyte to the morula stage in humans and pigs. The core TFs associated with major ZGA events differed markedly between the two species, indicating species-specific regulatory programs. In contrast, chromatin remodeling–related genes were highly enriched among maternal transcripts and exhibited functional conservation across species. Furthermore, MT genes showed consistently higher average expression levels in human embryos compared with porcine embryos across all examined stages, whereas ATP8 expression demonstrated pronounced heterogeneity among pig embryos. CONCLUSION: In conclusion, early embryonic development in humans and pigs is governed by conserved regulatory mechanisms underlying key biological processes, such as chromatin remodeling and major ZGA events. However, notable differences in metabolic activity and signaling pathways suggest the presence of species-specific adaptive strategies during early development. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07904-w.