FIG. 1. Developmental dynamics of the ascidian embryo: lineage, geometry, and single-cell gene expression data.

(A) Early development of the ascidian Phallusia mammillata. Representative morphologies (top) shown along with right side of lineage tree (bottom) with the left being mirror symmetric. Cell fates at the larval stage indicated in blue for each 64-cell stage cell (adapted from Ref. [12]). Time is in hours post fertilization at 18° [18]. (B) Representative cell geometry for the 16-cell stage (top), together with the cell-cell contact graph (bottom). Colors indicate transcriptomically distinct cell-states, as discovered in Fig. 2, which are also conserved across embryos. The animal-vegetal, anterior-posterior, and left-right axes form the 3 morphological axes of the embryo. (C) Experimental set up of Ref. [16], where large numbers of embryos at each cell-stage are first dissociated and then single-cell RNA sequencing at high-depth was performed. The precise identity of each cell is lost after dissociation, but the embryonic identity is retained through barcoding [16]. The resultant cell-by-gene expression matrix is shown for the 16-cell stage and for genes that are differentially expressed across the embryo (Methods).