Lidong Guo, Baichuan Tong, Xiaomin Gao, Xiaodong Jia, Xiang Liu, Lei Li, Mengyang Xu, Yaolei Zhang, Jiahao Wang, Qun Liu, Kai Han, Ruihua Zhang, Zeyu Lin, Liyan He, Xiao Du, Yating Qin, Yue Song, Zengbao Yuan, Xiaobin Liu, Yao Li, Jiaxin Luo, Tao Yang, Jing Chen, Yangyang Li, Xizi Wang, Zhaona Song, Inge Seim, Long Zhao, Bin Zhang, Ruijiao Chen, Baoyu He, Changwei Shao, Huanming Yang, Xun Xu, Fengming Sun, Qingming Qu, Songlin Chen, Guangyi Fan
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.