Biology subjects

Scully, T. D.

Publications and source records attributed to Scully, T. D..

3 recordsLinked to original sources

bioRxiv2025

Multi-stage single-cell atlas of Botryllus schlosseri asexual 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, known as budding. In Botryllus schlosseri, this agametic process, termed peribranchial budding, generates new zooids in a stereotyped, cyclical manner from a cluster of cells within the peribranchial epithelium. Despite detailed morphological characterization, the molecular and cellular underpinnings of budding initiation remain poorly understood. Here, we present the first single-cell transcriptomic atlas of B. schlosseri peribranchial budding, encompassing multiple stages from pre-budding to near-mature zooid. This high-resolution atlas captures the diversity of cell types involved in budding and their dynamics enabling precise cluster annotation and lineage trajectory inference. While circulating mesenchymal cells exhibit transcriptional hallmarks of stem-like states, we found no definitive evidence of broad contribution to bud onset and early morphogenesis beyond hematopoietic and gonadal lineages. Instead, we identified a distinct founder cell population arising from peribranchial epithelium, marked by a unique transcriptional profile and progressive acquisition of developmental potency. This supports a model in which budding is initiated by dedifferentiation of committed epithelial cells rather than activation of multi- or pluripotent stem cells. Furthermore, we highlight signaling pathways, including GNRHR-like receptors, that may couple metabolic state with developmental progression. Altogether, our data suggest that peribranchial budding in B. schlosseri is driven by potential reprogramming within epithelial tissues. This work provides a foundational resource for studying non-embryonic development and the evolution of regenerative strategies in chordates.

developmental biology↗

bioRxiv2025

Immune cell type divergence in a basal chordate

Evolutionary adaptations often occur at the level of cell types and cellular function. Innate immune cells are a promising system for studying cell type evolution, as they are widespread across metazoans, have several conserved functions, and are under selective pressure from pathogens. However, molecular characterizations of invertebrate immune cells are limited, and it remains unclear whether invertebrate immune cell types are homologous to those in vertebrates. Here we use single-cell RNA sequencing, in situ hybridization, and live reporters to define the identity of blood cell states from a basal chordate, Ciona robusta. We find evidence that C. robusta circulating blood contains a differentiation hierarchy that gives rise to at least eight major morphotypes, constituting approximately half of mature blood cell states. The mature cell states include phagocytes, as well as cells variously expressing vanadium-binding proteins, carbonic anhydrases, pattern recognition receptors, cytokines, and complement factors. Despite the expression of homologs to vertebrate immune components, extensive divergence between tunicate and vertebrate immune cells obscures cell state homology. Altogether, this work modernizes blood cell classifications in C. robusta and extends the known repertoire of immune cells within chordates.

evolutionary biology↗

bioRxiv2023

A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells

Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most marine organisms, however, cells are viable at a higher salinity than is compatible with scRNA-seq, impacting data quality and cell representation. We show that a low-salinity phosphate buffer supplemented with D-mannitol (PBS-M) enables higher-quality scRNA-seq of blood cells from the tunicate Ciona robusta. Using PBS-M reduces cell death and ambient mRNA, revealing cell states not otherwise detected. This simple protocol modification could enable or improve scRNA-seq for the majority of marine organisms.

genomics↗