Transcriptome Comparisons of Multi-Species Identify Differential Genome Activation of Mammals Embryogenesis

The identification of underlying differences is crucial for understanding the embryogenesis of species specificity. In this paper, a comparative transcriptome analysis of multi-species (CTAMS) was first developed to detect the genome activation differences of embryogenesis among human, mouse, and bovine. The annotation of intra-species and the detection of inter-species difference were separately to avoid potential batch effects. The profile clusters and Pearson correlation showed the human and bovine embryos displayed a high similarity in genome activation with a dramatic maternal to zygotic transition between 4–8 cell stages. But the mouse embryos maintained the high activity during the whole embryogenesis. Moreover, the stage-specific differentially expressed genes (DEGs) exhibited the specification of trophectoderm and inner cell mass may occur at blastocyst stage in human and bovine embryos, at morula stage in the mouse. The transcription and translation associated pathways were widely activated at morula stage in human embryos, 8-cell stage in bovine embryos and 2-cell stage in mouse embryos. The signal transduction pathways also displayed species-specific expression patterns. Finally, a probable pathway activated landscape of embryonic genome was given with the development axis.