Comparison of single-cell landscapes among three amniotes reveals conservation and innovation in avian 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 149 cell types, along with a spatial transcriptomic map of the embryo. By integrating it with 1.2 million single cells from humans and turtles, 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. Overall, our study provides an invaluable resource to study chicken cell biology and avian evolution and shines light on the evolutionary and cellular characteristics of immune cells across amniotes.