Single-cell transcriptomics reveals diversity and conservation of chicken lymphocytes.

The domestic chicken (Gallus gallus) is a critical model for immunology and a major agricultural species, yet a comprehensive single-cell census of its immune architecture is lacking. Here, we constructed a high-resolution single-cell transcriptome atlas of three primary immune organs (thymus, bursa of Fabricius, and spleen) from chickens. Our analysis identified 24 distinct immune and stromal cell types, mapping their organ-specific distributions: B cells were predominantly localized to the bursa of Fabricius, while T cell subsets were enriched in the thymus. We delineated developmental trajectories and identified key transcription factors governing lineage commitment, including TCF12 for CD4⁺CD8⁺ T cells and SOX13 for T helper 2 cells. Further analysis revealed potential sexually dimorphic immune maturation, where B cells exhibited sex-biased gene expression primarily in early differentiation stages, whereas T cell differences were most pronounced during proliferation. Cross-species comparison demonstrated remarkable conservation of core immunoregulatory circuits, with transcription factors like MEF2C, LEF1, and GATA3 playing conserved roles in avian and mammalian immunity. This resource provides a foundational framework for understanding avian immune defense, advancing poultry disease-resistant breeding, and offers evolutionary insights into vertebrate immunology.