Fig. 9

Three notable examples of genes revealed by combined analyses of the RNA-seq and ATAC-seq datasets. A–C Normalized ATAC-seq signal of stage-3 wild-type, fuchi pRNAi, and Pt-hh pRNAi embryo at the g1125 (A), Pt-hh (g4322) (B), and Pt-GATA5 (g8337) (C) loci. Line with ticks at the top represents the scaffold sequence, below which annotated exons (pink boxes) and introns (black lines) are shown. fuchi-dependent peak regions are indicated by open rectangles. Arrows indicate the orientation of the gene. D Amino acid sequence alignment of the g1125 protein and its homologs detected in the genomes of two other spider species Araneus ventricosus (GBO06802.1) and Argiope bruennichi (KAF8764632.1). Residues identical across all proteins are presented with a yellow background. Residues shown in red indicate regions predicted as transmembrane domains by InterProScan version 5.53–87.0 [108]. E, F Detection of Pt-GATA5 transcript and DNA (E', F') in stage-5 (E) and stage-7 (F) embryos using chromogenic WISH. E1, E2, F1, F2 High magnification of the boxed areas in E and F, along with counter staining for DNA (E1’, E2’, F1’, F2’). The focal plane is at two different depths; the plane shown in E2 and F2 is deeper than that in E1 and F1, respectively. Signals are observed in cEND, CM, and pEND cells, which are located below the germ-disc epithelial layer, and in evenly distributed endoderm (END) cells, which are located below the germ band epithelial layer. Scale bars, 100 µm