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Journal Articles

Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis

Open Access
Berivan Temiz, Michael Meier, Megan J. Wilson
Journal: Development
Development (2025) 152 (20): dev204265.
https://doi.org/10.1242/dev.204265
Published: 17 June 2025
View articletitled, Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis
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Includes: Supplementary data
Journal Articles

An interview with Mansi Srivastava

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Journal: Development
Development (2025) 152 (20): dev204952.
https://doi.org/10.1242/dev.204952
Published: 17 June 2025
View articletitled, An interview with Mansi Srivastava
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The study system: Botrylloides diegensis. (A) Simplified phylogeny showing the position of tunicates (Orders in orange) as the closest chordate group to vertebrates (based on Kocot et al., 2018). (B) A colony of B. diegensis attached to a glass slide. (C) Illustration of B. diegensis orange morphs with vascular networks (red lines) and elliptical vascular termini (ampulla). Zooids are arranged side-by-side in a ladder-like configuration within the gelatinous tunic. (D) Simplified external anatomy of a mature zooid in a lateral view. A vascular network [blood vessels (bv) with terminal ampullae (a)] connects the zooids throughout the colony. (E) Example schematic of a section through a mature zooid showing structures that are often present. These include the branchial chamber (bc), endostyle (end), peribranchial chamber (pbc), intestine (in) and stomach (sm). (F,G) Section of a primary bud (F) and developmental stages of a budlet (G). The dashed arrow indicates the progression of budlet development. nc, neural complex; go, gonad; be, branchial epithelium; tt, testis; o, ovary; bd, bud disc.

The study system: Botrylloides diegensis . (A) Simplified phylogeny showi...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 1. The study system: Botrylloides diegensis . (A) Simplified phylogeny showing the position of tunicates (Orders in orange) as the closest chordate group to vertebrates (based on Kocot et al., 2018 ). (B) A colony of B. diegensis attached to a glass slide. (C) Illustration of B. diegen... More about this image found in The study system: Botrylloides diegensis . (A) Simplified phylogeny showi...
Images
Overview of the experimental pipeline and clustering results. (A) Single cells were prepared using the acetic methanol (ACME) maceration method (García-Castro et al., 2021). Cells were stained with DRAQ5 and sorted by FACS. Cells were captured in droplets using a 10x Chromium system. Single-cell libraries were prepared and sequenced. After mapping the transcripts to the genome, clustering analysis was performed to identify the cell types. (B) UMAP clustering analysis revealed 29 single-cell clusters. Each cluster was color-coded. (C) Heatmap of the top five marker genes in each cluster.

Overview of the experimental pipeline and clustering results. (A) Single c...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 2. Overview of the experimental pipeline and clustering results. (A) Single cells were prepared using the acetic methanol (ACME) maceration method ( García-Castro et al., 2021 ). Cells were stained with DRAQ5 and sorted by FACS. Cells were captured in droplets using a 10x Chromium system. S... More about this image found in Overview of the experimental pipeline and clustering results. (A) Single c...
Images
Identification of B. diegensis digestive tract clusters. (A) Schematics illustrating an internal view of a single zooid, highlighting the digestive tract and its appearance in a transverse section (right) (dotted line on the left). (B) Stacked violin plot for Tubb, Cnfn, Ctrb1 and Kng1 transcripts, the expression of which was examined by in situ hybridization. (C) Cluster expression for Tubb identified this gene as a top marker gene for clusters 10 and 11 (B), although it was expressed by cells found in several other clusters. Tubb mRNA was found in the inner stomach folds (blue arrows), outer stomach folds (black arrow; inset), stigmata (green arrows) and intestine. (D) In situ expression of Ctrb1 mRNA was observed in the cells on the outer side of each stomach fold. (E) Kng1+ cells are located in the longitudinal stomach folds and blood cells within the circulation (right panels). (F) Single-cell cluster expression profile for Cnfn (g04846), the top marker gene for cluster 11 (B). The Cnfn probe-stained cells are found in rows (asterisks) that line the branchial chamber, known as stigmata cells. No staining was observed in other tissues, such as the endostyle and intestine (right panel). (G) Based on the in situ results, an illustration of a stomach fold showing the location of Tubb+, Ctrb1+ and Kng1+ cells in the stomach epithelium. end, endostyle; stm, stomach; isf, inner stomach fold; osf, outer stomach fold; sti, stigmata; t, tunic; int, intestine; bv, blood vessel; sti, stigmata.

Identification of B. diegensis digestive tract clusters. (A) Schematics ...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 3. Identification of B. diegensis digestive tract clusters. (A) Schematics illustrating an internal view of a single zooid, highlighting the digestive tract and its appearance in a transverse section (right) (dotted line on the left). (B) Stacked violin plot for Tubb , Cnfn , Ctrb1 an... More about this image found in Identification of B. diegensis digestive tract clusters. (A) Schematics ...
Images
GO and pathway analyses for cell clusters associated with digestive functions. (A) Network plot of enriched biological processes from Metascape analysis. Each node represents a GO or pathway term, and edges indicate functional similarity based on shared gene content or annotation. Nodes are grouped and colored by cluster assignment and predicted tissue type, illustrating how lysosomal degradation, mitochondrial metabolism and ciliary function cluster into broader biological themes across digestive-associated cell types. (B) Heatmap showing –log10(P-value) of selected enriched GO terms in clusters associated with the digestive tract and stigmata to highlight distinct biological functions. Each row represents an enriched GO term, and each column represents the gene list for clusters 14, 4, 5, 10 and 11.

GO and pathway analyses for cell clusters associated with digestive functio...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 4. GO and pathway analyses for cell clusters associated with digestive functions. (A) Network plot of enriched biological processes from Metascape analysis. Each node represents a GO or pathway term, and edges indicate functional similarity based on shared gene content or annotation. Nodes ... More about this image found in GO and pathway analyses for cell clusters associated with digestive functio...
Images
Identification of endostyle clusters. (A) UMAP feature density plots show the highest concentration of cells expressing each of these tunicate endostyle genes. (B) GO and Pathway terms colored by P-value, as determined by Metascape. (C) Violin plot for cluster marker 3, Fbn1. (D) In situ expression pattern for the cluster 3 marker Fbn1 in zone 8 of the endostyle. (E) Tubb mRNA was detected in zone 1 cells of the endostyle. (F) Schematic showing the different zones of the endostyle, highlighting the spatial expression of Fbn1 and Tubb. z8, zone 8; z1, zone 1; st, stigmata; V, ventral; D, dorsal. Scale bars: 50 µm.

Identification of endostyle clusters. (A) UMAP feature density plots show ...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 5. Identification of endostyle clusters. (A) UMAP feature density plots show the highest concentration of cells expressing each of these tunicate endostyle genes. (B) GO and Pathway terms colored by P -value, as determined by Metascape. (C) Violin plot for cluster marker 3, Fbn1 . (D) In... More about this image found in Identification of endostyle clusters. (A) UMAP feature density plots show ...
Images
Candidate blood cell clusters. (A) A stacked violin plot representing the Seurat cluster expression of four marker genes, further examined by in situ hybridization. (B) Detection of Foxred2 mRNA by in situ hybridization identified vascular endothelium (blue arrows), and cells of the developing heart and some blood cells (asterisk). (C) Cluster 13 g11109 Gst3a marker in situ hybridization. Positive cells were found in the circulatory system and near the endostyle (asterisks). (D) Cluster 17 marker, Csmd3, mRNA-positive cells were in the vasculature, near the endostyle (asterisks) and the thin epithelium lining the tunic vessels (arrows). (E) Cluster 8 marker, g05125 (Notch-like), probes stained only a few scattered cells in the vascular circulation stained with the g05125 probe (arrows). (F) GO and Pathway heatmap showing enriched biological processes in clusters 17, 7, 25, 8 and 13. A heatmap is shown to enable direct comparison across blood-associated clusters, highlighting shared versus distinct functional associations. stm, stomach; et, vessel endothelium; bv, blood vessel; end, endostyle; ca, compartment amoebocyte; cc, compartment cell; z2, zone 2; z4, zone 4. Scale bars: 10 µm.

Candidate blood cell clusters. (A) A stacked violin plot representing the ...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 6. Candidate blood cell clusters. (A) A stacked violin plot representing the Seurat cluster expression of four marker genes, further examined by in situ hybridization. (B) Detection of Foxred2 mRNA by in situ hybridization identified vascular endothelium (blue arrows), and cells of th... More about this image found in Candidate blood cell clusters. (A) A stacked violin plot representing the ...
Images
Cell populations and their relationships. (A) Schematic overview of the principal tissues and organs in a B. diegensis colony and their proposed origins. Budding arises from a small group of cells in the peribranchial chamber epithelium of the immature zooid (before stigmata perforation), which forms the bud disc (Berrill, 1947). This disc separates from the parent epithelium to create a closed vesicle encased by the outer epidermis of the parental zooid. Germ cells segregate early from the inner vesicle to form oocytes and sperm. On the dorsal side of the vesicle, an invagination produces a neural placode. The heart and digestive tracts form on the posterior side, with organ primordia first appearing as outpockets of the branchial epithelium. Cells lining blood vessels, ampullae and epithelia have also been proposed to serve as hemocyte sources (Rosental et al., 2018; Rinkevich et al., 2010). (B) Representative schematic showing relationships among these tissues, placed beside a UMAP cluster plot. The arrows indicate transitory relationships between various epithelial compartments. (C) UMAP density plot illustrating the co-expression of Pitx, Otx, Nk4 and Runx within cluster 6. Cells with higher levels of co-expression are rendered in increasingly orange tones. (D) Monocle 3 trajectory analysis. The trajectory root is inferred to be the progenitor population (cluster 6), most likely corresponding to the peribranchial epithelium. end, endostyle; sti, stigmata; pbc, peribranchial chamber; bc, branchial chamber; int, intestine; stm, stomach; bd, bud disc; dt, dorsal tube.

Cell populations and their relationships. (A) Schematic overview of the pr...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 7. Cell populations and their relationships. (A) Schematic overview of the principal tissues and organs in a B. diegensis colony and their proposed origins. Budding arises from a small group of cells in the peribranchial chamber epithelium of the immature zooid (before stigmata perforatio... More about this image found in Cell populations and their relationships. (A) Schematic overview of the pr...
Images
Expression of Col24a1 (g02151) and Lgal4/7 (g08355) during colony development in B. diegensis. (A,B) UMAP plots showing Col24a1 and Lgal4/7 expression across cell clusters. (C) Violin plots highlighting the significant enrichment of these genes in cluster 6. (D) In situ hybridization for Col24a1. (i,ii) In the secondary bud (‘budlet’), a strong signal is present in the PBC (pbc)epithelium, including the blastodisc (black arrows). tt, testis; oo, ovary; dt, dorsal tube. (iii) As the branchial chamber (bc) epithelium thins, Col24a1 persists there but is absent from the endostyle (end). In the primary bud (iv,v), expression continues in the PBC and BC epithelium, and in the outer vesicle (ov) epithelium and blastodisc. sti, stigmata. In the zooid stage (vi,vii), no staining is observed in gut tissues; however, strong mRNA signal appears in cells associated with the vessel epithelium (ve) on the tunic-vessel side (contrasting the vessel-chamber side) and in the perivisceral epithelium (orange arrowheads in vi, vii). stm, stomach. (viii-x) In the hemolymph, Col24a1 localizes to smaller cells that resemble hemoblasts/stem-like cells or immature immunocytes, as well as thin vessel epithelium-lining cells (arrowheads). Mature immunocytes (morula cells; asterisks in ix, x) show no expression. T, tunic. (E) In situ hybridization with Lgal4/7 RNA probe. (i) Only faint staining is detected in the early bud. (ii,iii) Stronger expression emerges in the thinning PBC epithelium (arrows) and the outer vesicle layer (orange arrows). (iv-vii) In the primary bud (iv), Lgal4/7 marks the stigmata primordia in the BC epithelium; it is also present in the maturing stomach epithelium (v) and appears faintly in zone 8 of the endostyle (vii). Blood cells adjacent to the VE are also strongly positive (orange arrows in v and vi). (viii) Expression is seen in cells attached to the VE (blue arrows), with some detaching into the vessel lumen and others localizing in the tunic (orange arrow). (F) Expression of the marker gene Tubb (g04669) during blastogenesis. (i,ii) No expression is observed in the initial or secondary buds. (iii,iii′) Tubb appears first in the developing gut and intestine – initially in the inner stomach folds (black arrows) and then in the ciliated cells at the top of the outer stomach folds (green arrows; see also Fig. 3). (H) Expression of the cluster 4 marker Ctrb1 (g03753) in secondary and primary buds. (i,ii) No signal is detected in the early, pre-folded stomach. (iii,iii′) Once the stomach loops fold, Ctrb1 is expressed in specialized cell types of the maturing stomach (green arrow), while newly folded loops still lack this staining (green arrow, iii″). z8, zone 8. Scale bars: 10 μm in Dviii-x, Ev′,vi, Fiii′, Hiii′,iii″; 20 μm in Dvi,vii, Ei,vii,viii, Fi,ii; 50 μm in Eiii,iv,v, Fiii, Hi,ii; 100 μm in Eiii, Hiii.

Expression of Col24a1 (g02151) and Lgal4/7 (g08355) during colony devel...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 8. Expression of Col24a1 ( g02151 ) and Lgal4/7 ( g08355 ) during colony development in B. diegensis . (A,B) UMAP plots showing Col24a1 and Lgal4/7 expression across cell clusters. (C) Violin plots highlighting the significant enrichment of these genes in cluster 6. (D) In situ h... More about this image found in Expression of Col24a1 (g02151) and Lgal4/7 (g08355) during colony devel...
Images
Identification of potential differentiation pathways using CellRank. (A) The PAGA plot displays each cell cluster as a node, with branching lines indicating potential differentiation pathways among the clusters. (B) A tSNE projection where cells are colored by pseudotime, showing the progression of cell states over time. Darker colors represent earlier pseudotime states, whereas lighter colors represent later pseudotime states. The Cluster IDs are given for the later states. A UMAP projection is shown in Fig. S20. (C,D) Velocity plots using the tSNE projection, where arrows represent the direction of RNA velocity, indicating the predicted future states of the cells based on their transcriptional activity and pseudotime. The cells are colored using the Seurat Cluster ID. (D) An annotated version of plot C shows a detailed identification of specific cell types and their predicted differentiation pathways.

Identification of potential differentiation pathways using CellRank. (A) T...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 9. Identification of potential differentiation pathways using CellRank. (A) The PAGA plot displays each cell cluster as a node, with branching lines indicating potential differentiation pathways among the clusters. (B) A tSNE projection where cells are colored by pseudotime, showing the pro... More about this image found in Identification of potential differentiation pathways using CellRank. (A) T...
Images
Cell fate dynamics. (A) UMAP plot showing diffusion pseudotime (dpt_pseudotime). The color scale represents pseudotime, with cells colored yellow appearing later in the predicted cell trajectory pathway. (B) Fate probability UMAP, shown as terminal clusters. TS, terminal state. (C) Aggregate fate probability bar graphs. These display the probabilities of different clusters (20, 11, 15, 19 and 6) progressing toward the terminal states, as predicted by CellRank. (D) A selection of driver genes is presented alongside a gene whose expression is highest at the earliest pseudotime on the lineage towards the terminal state fate (Table S4).

Cell fate dynamics. (A) UMAP plot showing diffusion pseudotime (dpt_pseudo...

Open Access
in Single-cell transcriptomic profiling of the whole colony of Botrylloides diegensis : insights into tissue specialization and blastogenesis > Development
Published: 17 June 2025
Fig. 10. Cell fate dynamics. (A) UMAP plot showing diffusion pseudotime (dpt_pseudotime). The color scale represents pseudotime, with cells colored yellow appearing later in the predicted cell trajectory pathway. (B) Fate probability UMAP, shown as terminal clusters. TS, terminal state. (C) Aggr... More about this image found in Cell fate dynamics. (A) UMAP plot showing diffusion pseudotime (dpt_pseudo...
Journal Articles

Dynamic WT1 expression during gastrulation specifies peritoneal smooth muscle fate independently from mesothelial fate

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Suad H. Alsukari, Huei Teng Ng, Lilly Lang, Sharna Lunn, Shanthi Beglinger, Lauren Carr, Michael Boyes, David A. Turner, Bettina Wilm
Journal: Development
Development dev.204332.
https://doi.org/10.1242/dev.204332
Published: 17 June 2025
View articletitled, Dynamic WT1 expression during gastrulation specifies peritoneal smooth muscle fate independently from mesothelial fate
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In preprints: rethinking the foundations of the ovarian reserve

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In preprints
Andrea Rix, Binyam Mogessie
Journal: Development
Development (2025) 152 (12): dev204939.
https://doi.org/10.1242/dev.204939
Published: 16 June 2025
View articletitled, In preprints: rethinking the foundations of the ovarian reserve
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Journal Articles

Mesenchymal SLMAP coordinates with MST3 to govern gut elongation during development

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Yuwei Pan, Shiyang Wang, Wuqi Yang, Xi Wu, Hanfu Zhang, Sujuan Du, Mingxin Zhang, Liyuan Hou, Maksim V. Plikus, Jianwei Shuai, Cong Lv, Lu Yu, Zhengquan Yu
Journal: Development
Development dev.204483.
https://doi.org/10.1242/dev.204483
Published: 16 June 2025
View articletitled, Mesenchymal SLMAP coordinates with MST3 to govern gut elongation during development
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Serotonin neuromodulation directs optic nerve regeneration

Open Access
Kristian Saied-Santiago, Melissa Baxter, Jaffna Mathiaparanam, Michael Granato
Journal: Development
Development dev.204334.
https://doi.org/10.1242/dev.204334
Published: 16 June 2025
View articletitled, Serotonin neuromodulation directs optic nerve regeneration
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Polyphenisms: a developmental perspective

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Peter K. Dearden
Journal: Development
Development (2025) 152 (12): dev204693.
https://doi.org/10.1242/dev.204693
Published: 13 June 2025
... in evolutionary innovation . Proc. Biol. Sci. 278 , 2705 - 2713 . 10.1098/rspb.2011.0971 Mutti , N. S. , Dolezal , A. G. , Wolschin , F. , Mutti , J. S. , Gill , K. S. and Amdam , G. V. (2011). IRS and TOR nutrient-signaling pathways act via juvenile hormone to influence...
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Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus

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Olga Lanzetta, Marchesa Bilio, Johannes Liebig, Katharina Jechow, Foo Wei Ten, Rosa Ferrentino, Ilaria Aurigemma, Elizabeth Illingworth, Christian Conrad, Soeren Lukassen, Claudia Angelini, Antonio Baldini
Journal: Development
Series: REVIEW COMMONS TRANSFER
Development (2025) 152 (12): dev204524.
https://doi.org/10.1242/dev.204524
Published: 13 June 2025
View articletitled, Tbx1 stabilizes differentiation of the cardiopharyngeal mesoderm and drives morphogenesis in the pharyngeal apparatus
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Includes: Supplementary data
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KDM6B is a conserved activator at the top of the male sex determination pathway

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Shannon M. Dupont, Alexandra Garcia-Moreno, Eleanore V. O'Neil, Blanche C. Capel
Journal: Development
Development (2025) 152 (12): dev204724.
https://doi.org/10.1242/dev.204724
Published: 13 June 2025
View articletitled, KDM6B is a conserved activator at the top of the male sex determination pathway
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Includes: Supplementary data
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In preprints: unpicking chemical and mechanical crosstalk for axonal pathfinding

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Dionn Hargreaves, Sarah Woolner
Journal: Development
Development (2025) 152 (12): dev204948.
https://doi.org/10.1242/dev.204948
Published: 13 June 2025
View articletitled, In preprints: unpicking chemical and mechanical crosstalk for axonal pathfinding
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