Cross-species comparison of single-cell landscapes reveals conservation and innovation in chicken immune systems

Molecular characterization of chicken cells is essential for understanding avian physiology and vertebrate evolution, yet an organism-wide single-cell atlas in chicken is still lacking. Here we describe a comprehensive reference atlas of the chicken, encompassing 1.57 million cells across 157 cell types from 36 tissues, along with a spatial transcriptomic map of the embryo. By integrating it with 0.23 newly generated and 0.97 million single cells from 14 and 32 tissues in turtle and humans, respectively, we systematically explored the evolutionary rates of various cell types, particularly immune cells. The rapid evolution of chicken cells was generally characterized by changes in their gene regulatory networks and subsequent functional adaptations. In chicken, follicular dendritic cells emerge at the early development stage and exhibit myeloid rather than stromal origins, unlike in mammals. These cells share a regulatory network with mononuclear phagocytes and promote B cell proliferation and migration in the chicken-specific bursa of Fabricius. The observed variation in subtypes and proportions of γδ T cells across the three species reflected the evolution of pathogen recognition and signaling mechanisms among amniotes. These findings were further supported by generating 21,798 single cells from 3 tissues in ducks. Overall, we provides an invaluable resource to study chicken cell biology and evolution, as well as shines light on the evolutionary and cellular characteristics of immune cells across amniotes.