Figure 7. hox genes expressed across cell lineages within the sox10:GFP⁺ atlas.

(A) Dot plot shows both the mean expression (color) as well as percent of cells (size) per lineage for zebrafish hox genes in the first eight paralogy groups (PG). The full list of hox gene expression profiles per lineage can be found in Figure 7—figure supplement 1. Discrete hox profiles discern specific cell types, which is particularly evident in the enteric neuronal cluster. (B) Clustering of atlas lineages based hox expression profiles groups highlights robust core neural signature, which distinguishes the neural lineages from the remainder of the clades. Neural and glial progenitors formed an intermediate clade between the low-hox expressing lineages and the main neural branch. Additionally, the fin bud mesenchyme, which also has a highly distinctive hox profile, also forms a distinct clade. Subtle variations in hox expression by remaining lineages are further reflected in the remaining portion of the dendrogram; however, these are far less distinct. (C–D) Pairwise comparison of the fraction of cells in either the autonomic neural progenitor lineage (C) or the enteric neurons (D) for the first eight parology groups. Intersection of the gene pairs reflect the fraction of cells with expression for both genes with a log2 Fold change values > 0, with the identical gene intersections along the primary diagonal representing the total number of cells which express that gene in the lineage. Enteric neural hox signature was not only specific to this cell population, but also was abundantly co-expressed. (E) Summary panel describing the specific autonomic and enteric hox signatures detected. A common hox expression profile, referred to as the core signature, was found that is then modified across the specific lineages. (F–M) In situ validation of the chief enteric neural hox signature via HCR. phox2bb (F–J) labels enterically fated neurons at the level of the midgut in larval stage embryos fixed at 70–72hpf. White arrows highlight specific cells of interest. Key hox signature constituents hoxb5a (G) and hoxb5b (H) or hoxd4a (K) and hoxa5a (L) were found to be co-expressed within phox2bb expressing cells (White Arrows). Scale bars in (I,M): 50 μm.

Figure 7—figure supplement 1. Comprehensive overview of hox expression profiles within the atlas.

(A) Similar to Figure 7A,a comprehensive dot plot shows both the mean expression (color) as well as percent of cells per lineage (size) for zebrafish all hox genes. Discrete hox profiles discern specific cell types, which is particularly evident in the enteric neuronal cluster, as well as the fin bud mesenchyme. (B–I) Hindbrain expression patterns for enteric hox profiles. Autonomic neural marker phox2bb clearly marks the midbrain and hindbrain (hb) domains, as well as the pharyngeal arches (pa). Enterically fated cells can also clearly be seen along the tract of the gut (dash region), starting the foregut (fg). Anterior domains for hoxb5a (C), hoxb5b (D), hoxd4a (G), and hoxa5a (H) are represented by a vertical line. Overlapping regions can be approximated by the merged images (E, I). Scale in (B, F): 50 μm; dorsoventral-rostrocaudal axis defined in (F). (J) UMAP of the atlas demonstrating pervasive hox expression throughout the dataset. Expression was defined as having a log2 fold change >0. Approximately 85% of cells contained expression for at least one hox gene. (K–R) Feature plots representing the expression of selected hox genes within the atlas UMAP. hoxd4a (K), hoxa5a (L), hoxb5a (M), hoxb5b (N) all localize in varying degrees to the enteric neural signature, though hoxd4a also marks the mesenchymal clusters, as seen (A). hoxa4a (O) highlights its pervasive expression among the clusters. hoxa13b (P) and hoxa11b (Q) are key markers denoting the fin bud mesenchyme. Alternative neural populations are further identified by their hoxa9a (R) expression profile, contrasting with the enteric populations.