A single-cell atlas of pig gastrulation as a resource for comparative embryology

The bilaminar disc of early pig embryos closely mirrors that of humans making it a powerful model for studying gastrulation. Given the difficulties obtaining embryos in non-rodents, early cell-fate decisions during mammalian gastrulation remain ill-understood. Here we present a single-cell transcriptomic atlas of pig gastrulation and early organogenesis. We uncover the dynamics of cell fate emergence during pig peri-gastrulation and reveal conserved and species-specific transcriptional programs across different mammals. Combined with investigations in embryos and embryonic stem cells, we elucidate the spatial, molecular, and temporal events during definitive endoderm (DE) formation. We show that early FOXA2+ epiblast progenitors become DE without undergoing epithelial-to-mesenchymal transition, contrasting later emerging FOXA2/TBXT+ anterior primitive streak, which form node/notochord progenitors. We demonstrate that DE fate is driven by hypoblast-derived NODAL signalling, which is extinguished upon DE differentiation. These findings highlight the interplay between temporal and topological signalling during early cell fate decisions during mammalian gastrulation. Single-cell RNA sequencing of 62 pig embryos at 8 different time points ranging from the beginning of gastrulation (E11.5) through to the 12 somite stage (E15) using the 10X chromium platform.