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In this study, we performed single-cell RNA sequencing (scRNA-seq) of an entire B. diegensis colony, including zooids, buds and vascular tunics, to resolve cellular heterogeneity and to identify cell and tissue markers. We identified 29 major cell clusters within the colony and used in situ hybridization to examine the spatial expression of cluster marker genes. Numerous tissue types were identified at the molecular level, including blood cells and zooid tissues, such as the branchial epithelium, stomach and endostyle. Distinct cluster markers were identified for specific regions of the stomach epithelium, highlighting the specialization of these regions and the strength of using scRNA-seq to explore their functionality. Cell trajectory projections highlighted the early appearance of progenitor clusters, whereas more differentiated zooid-related tissues appeared later in the developmental path. This study provides a valuable resource for understanding the development, tissue function and regeneration of B. diegensis. It demonstrates the power of scRNA-seq to define cell types and tissues in complex colonial organisms.<\/jats:p>","DOI":"10.1242\/dev.204265","type":"journal-article","created":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T10:16:43Z","timestamp":1747995403000},"source":"Crossref","is-referenced-by-count":2,"title":["Single-cell transcriptomic profiling of the whole colony of <i>Botrylloides diegensis<\/i>: insights into tissue specialization and blastogenesis"],"prefix":"10.1242","volume":"152","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0499-8301","authenticated-orcid":false,"given":"Berivan","family":"Temiz","sequence":"first","affiliation":[{"name":"Otago School of Biomedical Sciences, University of Otago 1 Developmental Biology and Genomics Laboratory, Department of Anatomy , , PO Box\u00a056, Dunedin 9054 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Meier","sequence":"additional","affiliation":[{"name":"Otago School of Biomedical Sciences, University of Otago 1 Developmental Biology and Genomics Laboratory, Department of Anatomy , , PO Box\u00a056, Dunedin 9054 ,","place":["New Zealand"]},{"name":"University of Otago 2 Department of Pathology , , Dunedin 9054 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3425-5071","authenticated-orcid":false,"given":"Megan J.","family":"Wilson","sequence":"additional","affiliation":[{"name":"Otago School of Biomedical Sciences, University of Otago 1 Developmental Biology and Genomics Laboratory, Department of Anatomy , , PO Box\u00a056, Dunedin 9054 ,","place":["New Zealand"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2025,6,17]]},"reference":[{"key":"2025062510040823800_DEV204265C1","doi-asserted-by":"publisher","first-page":"2651","DOI":"10.1002\/jemt.24119","article-title":"Localization of vasoactive intestinal peptide and toll-like receptor 2 immunoreactive cells in endostyle of urochordate Styela plicata (Lesueur, 1823)","volume":"85","author":"Alesci","year":"2022","journal-title":"Microsc. 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