Single-cell profiling coupled with lineage analysis reveals vagal and sacral neural crest contributions to the developing enteric nervous system

During development, much of the enteric nervous system (ENS) arises from the vagal neural crest that emerges from the caudal hindbrain and colonizes the entire gastrointestinal tract. However, a second contribution to the ENS comes from the sacral neural crest that arises in the caudal neural tube and populates the post-umbilical gut. By coupling single cell transcriptomics with axial-level specific lineage tracing in avian embryos, we compared the contributions of embryonic vagal and sacral neural crest cells to the pre-umbilical and post-umbilical chick ENS and the associated peripheral ganglia (the Nerve of Remak and pelvic plexuses) at embryonic day (E) 10. Using replication incompetent avian (RIA) retroviruses, we indelibly labeled the vagal and sacral neural crest and collected their respective lineages in the E10 gut. The ENS of pre-umbilical gut is solely derived from vagal neural crest cells, which we collected for sequencing. The post-umbilical gut receives contributions from both vagal and sacral-derived neural crest cells and we collected both populations separately from this tissue.