Cross-species comparison of amniote single-cell transcriptomes reveals evolutionary conservation and divergence in the chicken immune system

The molecular characterization of chicken cells provides insight into avian physiology and vertebrate evolution. Here we present a single-cell RNA-sequencing (scRNA-seq) atlas of the chicken, encompassing 1.57 million cells across 157 cell types from 36 tissues from 16 chickens, as well as spatial transcriptomes from 1 chicken embryo. We further acquire scRNA-seq data from 3 turtles (230 thousand cells, 14 tissues) and 2 ducks (22 thousand cells, 3 tissues), and integrated our data with publicly available human scRNA-seq data (960 thousand cells, 32 tissues) to explore their evolutionary conservation, particularly of immune cells. In chicken, follicular dendritic cells, unlike in mammals, exhibit myeloid rather than stromal origins and help promote B cell proliferation and migration in the bursa of Fabricius. γδ T cell subsets vary across species, reflecting the evolution of pathogen recognition and signaling mechanisms among amniotes. Our transcriptomics data thus provide a resource to study chicken cell biology and amniote evolution, highlighting immune cell similarities and distinctions arising from evolutionary divergence. Molecular characteristics of amniote lineages can inform evolutionary inference. Here, the authors present a single-cell RNA-sequencing atlas of the chicken, which is applied to compare immune cells of chicken, turtle, duck and human, determining similarities and distinctions across amniote immune system evolution.