A single-cell atlas of mongolia sheep early embryo

Abstract Background The establishment of different cell types during organogenesis in mouse early embryos has been well studied. However, cell type differentiation and its molecular mechanisms in early embryo development in Mongolian sheep are not well understood. Results In this study, we present the first comprehensive single-cell transcriptomic characterization of Ujumqin sheep and Hulunbuir short-tailed sheep at E16. Thirteen major cell types were identified in Ujumqin sheep at E16, and 8 major cell types were identified in Hulunbuir short-tailed sheep at E16. Functional enrichment analysis showed that several pathways were significantly enriched in the notochord cluster, namely, the TGF-beta signaling pathway, Hippo signaling pathway, platelet activation pathway, riboflavin metabolism pathway, Wnt signaling pathway, regulation of actin cytoskeleton, and insulin signaling pathway. In contrast, glutathione metabolism, glyoxylate and dicarboxylate metabolism, citrate cycle, thyroid hormone synthesis, pyruvate metabolism, cysteine and methionine metabolism, thermogenesis, and the VEGF signaling pathway were significantly enriched in the spinal cord cluster. Steroid biosynthesis, riboflavin metabolism, cell cycle, Hippo signaling, Hedgehog signaling, FOXO signaling, JAK-STAT signaling, and Wnt signaling were significantly enriched in the paraxial mesoderm cluster. The notochord cluster, spinal cord cluster and paraxial mesoderm cluster were all strongly related to tail development. Pseudotime analysis demonstrated that mesenchyme can contribute to the notochord in Ujumqin sheep. Further molecular assays showed that the Hippo signaling pathway was enriched in Ujumqin sheep. Conclusion This comprehensive single-cell map reveals the contributions of a previously unrecognized signaling pathway and contributes to our understanding of the mechanism of tail development in short-tailed sheep.