AI-Driven Cross-Species Embryo Insights: Transcriptomics Expose Conserved Genes in Homo sapiens and Bos taurus Morula-to-Blastocyst Transition

Preimplantation embryogenesis in mammals is critical for advancing reproductive biology and assisted reproductive technologies. This study presents a comparative transcriptomic analysis of preimplantation embryogenesis in Homo sapiens and Bos taurus, focusing on differential gene expression (DEG) patterns and regulatory pathways during the morula-to-blastocyst transition. Using RNA-seq data, machine learning models (LSTM and FNN), and pathway enrichment, we identified conserved and species-specific mechanisms. DEGs analysis in humans showed that between the 1-cell stage and morula, 9589 genes showed differential expression, including 9706 genes in the 1-cell and blastocyst stage, reflecting extensive transcriptional reprogramming. Bos taurus demonstrated a reduced number of differentially expressed genes (115). Principal Component Analysis (PCA) highlighted stage-specific transcriptional factors in humans, with PC1 (83% variance) distinguishing developmental progression. LSTM models outperformed FNNs in predicting stage-specific genes (ROC-AUC: 0.98–1.00), identifying critical conserved genes (6 in humans, 5 in Bos taurus) and integrated LOC783399 as a newly identified candidate gene in Bos taurus, emphasizing its role in developmental pathways. Homo sapiens prioritized stress resilience, nucleic acid binding, and implantation readiness, while Bos taurus emphasized lipid metabolism and rapid developmental kinetics. These findings underscore evolutionary trade-offs between regulatory precision and metabolic efficiency, with implications for assisted reproductive technologies.