Fig. 1

Cellular atlas of the anemonefish forebrain contains all expected cell types and identifies key cell types involved in reproduction. (A) Experimental design and workflow. (B) Single nuclei plotted as points in UMAP coordinate space and colored according to cluster assignment. Clusters were assigned based on transcriptomic similarity/dissimilarity with other nuclei. Parent clusters were identified with numbers (1–19), and if a parent cluster contained multiple child clusters then each child cluster was assigned a letter (a, b, c, etc.). Colored fields surround parent clusters to aid in identifying their boundaries. (C) Clusters were assigned to cell types based on expression of canonical marker genes among the cluster’s marker-DEGs. For more information on marker genes used to assign cell types, see Supplementary Excel File 1. D-E) Dotplots depict the expression of select genes within each cluster, chosen a priori due to their documented involvement in the differential regulation of reproduction between sexes. Dot size indicates the percent of cells within the cluster that expressed the given gene. Dot color indicates the average normalized expression value within the cluster. These genes fall into two general categories: those involved in steroid signaling (D), and those that mark neuronal populations that release particular neuropeptides (E). Genes associated with small molecule neurotransmitters are shown in Supplementary Fig. 4