Alignment of temporal differentiation flow models between distinct mammalian gastrulation strategies

Mammalian gastrulation is a highly conserved process that initiates cell fate acquisition and generates the basic body plan. Most mammalian embryos, including human and rabbit begin gastrulation as a planar embryonic disc as opposed to the cup-shaped mouse embryo. Such gross structure disparity is expected to have dramatic effects on gastrulation by shaping cellular mechanics and spatiotemporal interactions. Recently, we generated a highly rich temporally resolved transcriptional atlas of mouse gastrulation. Sequencing single cells from individual embryos allowed ordering them sequentially according to developmental time, facilitating the inference of hierarchical transitions. Similar to the mouse, rabbits have a large litter size consisting of asynchronous embryos. Moreover, up to organogenesis both species develop along a very similar timeline. To directly compare mouse and rabbit gastrulation, we hereby introduce a time-resolved atlas of rabbit gastrulation, densely sampling 160K single cells from 120 individual embryos between gestation days 6.0-8.5. Cross-species manifold alignment demonstrates remarkable rabbit-mouse conservation in nearly all gastrulation states though some cell states such as those of the trophoblast and PGCs are dramatically different. Using comparative analysis of differentiation flows, we find some highly synchronized developmental trajectories, such as somitogenesis, whereas others such as the allantois are more divergent by gene expression and timing. Similarly, expression is also analyzed between cell types over time to identify common genes, and uncover those which were repurposed during evolution. This study for the first time directly compares developmental trajectories, expanding our understanding of mammalian gastrulation, with potential implications across additional species.