Fig. 3

P. mammillata vPNS candidate genes identification by RNA-seq analysis on whole embryos. A Schematic representation of the experimental design and treatments for DGE analysis at late gastrula, initial tailbud II, mid tailbud I and late tailbud II stages. B Quantification of significantly (p-value <0.05 calculated by DESeq2) differentially expressed genes (in percentage of the total gene number which is 19,467 genes) from DGE analysis. For each RNA-seq experiment, upregulated genes are indicated in green and downregulated genes in red in the histograms. C Differential gene expression of vPNS genes. Log2 fold change of known (yellow backdrop) or candidate (blue backdrop) vPNS genes are shown for samples treated with BMP4 (light blue to dark blue histograms for early to late stages respectively) or BMP4+DAPT (purple histograms for late tailbud stages) compared to control levels. D–L In situ hybridization at selected developmental stages for P. mammillata candidate genes identified from our RNA-seq data and expressed in the vPNS: Hes.a (D), Id.b (E), Id.c (F), Bmp2/4 (G), Phmamm.g00001319 (H), Nherf.a (I), Selectin (J), Slc9a3r1 (K) and Slc6a12 (L). Genes expressed in the VML are represented by a blue circle and genes expressed in ventral ESNs by a purple circle. Embryos are shown in lateral view with dorsal to the top and anterior to the left. Scale bar: 50 μm