Whole embryo barcoding reveals convergent origins of mesodermal cells during mammalian gastrulation

Abstract

Classical fate-mapping and recent single-cell trajectory studies have suggested that mesoderm diversification during gastrulation proceeds through progressive fate bias and branching lineage segregation. Here, we combine inducible CRISPR-based lineage recording with single-cell RNA sequencing to reconstruct clonal relationships across mouse embryos barcoded at primitive streak onset and analyzed at early organogenesis. Mesodermal clones diverged after streak formation, but their developmental outputs remained extensively overlapping, revealing a clonal architecture that is not a simple branching lineage tree. Using sampling-aware statistical models, we quantify distinct clonal origins of paraxial mesoderm across the anterior-posterior axis, show that endothelial cells arise from multiple mesoderm origins but demonstrate transcriptional differences that correspond to anatomical position and clonal lineage, and identify clonal sharing between extra-embryonic mesoderm and embryonic derivatives, including cardiac lineages and a shared hindlimb-allantois progenitor. In the heart, progenitors corresponding to classical heart fields remain multipotent, contributing both myocardial and non-myocardial cell types. Together, our findings support a model in which mesodermal diversity is assembled through spatially distinct, fate-biased progenitor pools whose descendants converge on shared cell states. Our findings challenge simple branching models of mesoderm diversification and provide a clonal framework for understanding how tissue diversity emerges in the embryo.