Fig. 4

Single-cell transcriptome analysis showed that Ciona GH6-1 and CesA expression correspond to epidermal cell identity. A A dimension-reduction plot shows a representation of late tailbud stage I embryonic cells, separated into 30 clusters (numbered 0 to 29). Dimensions were reduced by the uniform manifold approximation and projection (UMAP) technique in the Seurat package. Each dot represents the transcriptome of a single cell. Cells in the same cluster have similar gene expression profiles. Numbers and color labels denote cluster identities. B–D Violin plots showing expression levels of three genes. X-axis: cell cluster identifier. Y-axis: normalized expression level of each gene. B The IF-C gene (KY.Chr3.1290) was selected as an epidermal marker of cell identity of clusters. It was highly expressed in cells in clusters No. 1 and 5 and to a lesser extent in cluster 0. C, D GH6-1-expressing cells and CesA-expressing cells were mostly identified in clusters 0, 1, and 5. E Scatterplots showing relationships of normalized expression of IF-C, GH6-1, and CesA. Each dot represents the transcriptome of a cell and cells are colored by cluster identity. The X- and Y-axes represent normalized expression levels. Pearson correlation between the two features is displayed above each plot. F UMAP-dimension-reduction plots showing normalized expression levels of GH6-1 and CesA genes. Although expression of these two genes appeared mostly in the same cell clusters 0, 1, and 5, only a few cells show high expression of both genes (yellow dots). The enlarged, dashed rectangular area is shown as an insert at the bottom-right. Note that KY gene models (2019 version, KY.ChrX.yyyy) were used in the original analysis and the corresponding KY21 gene models (the latest version) are described in the main text