Fig. 1: Amphioxus neurula cell type atlas.

a drawings of Mediterranean amphioxus developmental stages from the egg to the larva (with one open gill slit) stage. The developmental time (hours post fertilization, hpf) is given for embryos raised at 19 °C, and we highlight the neurula stage presented in this study (21 hpf). b Two-dimensional projection of cell clusters (metacells) using a force-directed layout based on the co-clustering graphs for individual cells (see Methods). Metacells are color-coded by cell type. c Normalized fold change expression of top variable genes (rows) per metacell (columns, grouped by cell type). For each metacell, we selected up to 30 markers with a minimum fold change ≥ 2. Selected gene names from known markers, used to annotate each cell type, are indicated to the right of the heatmap. Genes in bold case are shown in panel (d). d Pie charts depicting the fraction of cells mapped to each cell type among the cell transcriptomes and the cell counting experiment (top); and the 3D reconstruction with assignment of nuclei to each germ layer (bottom). A transverse section is shown on the left, and dorsal views with anterior to the top on the right (full, without epidermis nuclei, without epidermis and neural cells nuclei. e Expression profile of previously unknown marker genes for specific cell types (neural, endoderm, anterior epidermis, presumptive cerebral vesicle, notochord, and tailbud) analyzed by in situ hybridization (ISH, top, with anterior to the left and dorsal to the top in side views, n = 10 embryos) and corresponding two-dimensional expression maps (bottom, based on the same layout as panel b). Gene expression is shown as density maps representing UMI counts (per 10,000 UMIs) in each cell.