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The neural crest is a migratory population of stem-like cells that contribute to multiple traits including the bones of the skull, peripheral nervous system, and pigment. How neural crest cells differentiate into diverse cell types is a fundamental question in the study of vertebrate biology. Here, we use single-cell RNA sequencing to characterize transcriptional changes associated with neural crest cell development in the zebrafish trunk during the early stages of migration. We show that neural crest cells are transcriptionally diverse and identify pre-migratory populations already expressing genes associated with differentiated derivatives, specifically in the xanthophore lineage. Further, we identify a population of Rohon–Beard neurons in the data. The data presented identify novel genetic markers for multiple trunk neural crest cell populations and Rohon–Beard neurons providing insight into previously uncharacterized genes critical for vertebrate development.

Single-cell RNA analysis identifies pre-migratory neural crest cells expressing markers of differentiated derivatives