A cross-vertebrate single-cell and spatial atlas reveals evolutionary trajectories of gastrointestinal cellular...

The cellular innovations underlying vertebrate gastrointestinal diversification remain largely unknown. Here, we constructed a single-cell and spatial transcriptomic atlas comprising nearly 1 million cells from 10 species, spanning 500 million years of vertebrate evolution. Analysis of conserved gene co-expression modules shows that the repurposing of existing genetic programs, together with de novo gene emergence, drives cellular evolution. We link module remodeling to lineage-specific dynamics, including ciliated cell loss and the tuft cell emergence. Furthermore, we identify lymphoid aggregates in lungfish, suggesting that intestinal immune organization may be prior to the tetrapod lineage, and demonstrate that fish oxynticopeptic cells exhibit functional polarization that prefigures mammalian gastric specialization. Our atlas provides a global view of gastrointestinal evolution, highlighting the role of regulatory repurposing in defining organ function.