Divergence of immune cell types in chordate blood

Tal D. Scully¹, C. J. Pickett², Nicolas A. Gort-Freitas¹, Bradley Davidson², Allon M. Klein¹*

¹Dept. of Systems Biology, Harvard Medical School, Boston, MA, USA

²Dept. of Biology, Swarthmore College, Swarthmore, PA, USA

*Corresponding author: Allon_Klein@hms.harvard.edu

Abstract

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 in Ciona robusta, a member of the tunicate subphylum, the sister group to vertebrates. We find evidence that C. robusta circulating blood contains a differentiation hierarchy, with at least five major lineages, constituting more than 75% of circulating cells. 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.

Current Biology, Nov 13 2025. doi:10.1016/j.cub.2025.10.032

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Interactively explore the data using SPRING

SPRING is a tool for interactive exploration of single-cell data. The integrated C. robusta blood cell data can be viewed here.

Gene nomenclature

• KY21 Gene IDs are listed for each gene.
• If the gene is a transcription factor, the name is written in parentheses, e.g. "KY21.Chr3.726 (Cebpa)".
• If the gene is not a transcription factor and has homology to human genes detected by OrthoFinder, the human homologs are listed in parentheses, e.g. "KY21.Chr2.1280 (MKI67)".
• If there are no detected OrthoFinder homologs, but there are human genes with good BLAST similarity, the top human BLAST hit is listed (see Methods section "" for more detail), e.g. "KY21.Chr9.653 (best hit: FN1)".
• Otherwise, if there is no known homology, the gene ID is listed alone, e.g. "KY21.Chr8.361".

Cell state name abbreviations

BLC, blebbing-like cell; GA, granular amoebocyte; HA, hyaline amoebocyte; ICC, irregular compartment cell; LGH/MC, large granules hemocyte/morula cell; ND, not determined; RA, refractile amoebocyte; RC, round cell; RSC, round spreading cell; SGH, small granules hemocyte; SRC, signet ring cell; URG, unilocular refractile granulcoyte; cLRP, candidate lineage-restricted progenitor; cMPP, candidate multipotent progenitor.