Multi-stage single-cell atlas of a chordate non-embryonic development unveils dedifferentiating bud founder cells

Colonial tunicates are the only chordates capable of forming fully functional bodies from somatic tissues through non-embryonic development, or budding. In Botryllus schlosseri , budding produces new individuals (zooids) from a portion of the peribranchial epithelium of a preexisting zooid. While the anatomy of this process has been described in detail, the cellular and molecular mechanisms underpinning bud initiation remain elusive. Here, we present a multi-stage single-cell transcriptomic atlas of a non-embryonic development in a chordate, capturing initiation and development of zooids. We identify an epithelial founder cell population that gains developmental potential through possible dedifferentiation, challenging the long-standing hypothesis that a long-lived, circulating pluripotent stem cell drives new zooid formation. Although some circulating cells exhibit stem-like expression profiles, these populations are either hematopoietic or germline restricted lineages. This atlas provides a foundational resource for understanding the cellular origin and mechanisms underlying agametic development and possibly whole-body regeneration in chordates.