Genetic Characterization of the Cell Types in Developing Feathers, and the Evolution of Feather Complexity

Feathers are the most complex and diverse epidermal appendages found in vertebrates. Their unique hierarchical organization and development is based on a diversity of cell types and morphologies. Despite these presumptive feather cell types being well characterized morphologically, little is known about how gene regulation contributes to their development. Here, we use single cell and single nuclear RNA sequencing with in situ hybridization to identify and characterize cells types in embryonic chicken feathers. We show that the distinct cell morphologies correspond to feather cell types with distinct gene expression profiles. We also describe a previously unidentified cell type, the barb ridge basal epithelium, which appears to play a role alongside the marginal plate in barb ridge differentiation. A cell-cell signaling analysis provides evidence of important roles for the barb ridge basal epithelium and marginal plate signaling to the barb ridge. Furthermore, we analyze RNA velocity trajectories of developing feather cells and find distinct developmental trajectories for epidermal cells that constitute the mature feather and those that function only in feather development. Finally, we produce an evolutionary tree of feather cell types based on transcription factor expression as a test of the prior developmental hypotheses about feather evolution. Our tree is consistent with the developmental model of feather evolution, and sheds light on the influence of ancestral epidermal stratification on feather cell evolution. This transcriptomic approach to studying feather cell types helps lay the ground work for understanding the developmental evolutionary complexity and diversity of feathers.