Fig. 4

Gene variations in specific transcription modules of spider venom glands. a Heatmap of Spearman correlation coefficients between specific modules of glandular tissues. Venom gland-specific modules contain 166 orthologs found through the isa2 method. venom, venom gland; silk, silk gland; saliva, salivary gland; others, other glands, including the prothoracic, hypopharyngeal, and lymph glands of insects. b REVIGO clusters of the significantly enriched GO terms for venom gland-specific modules. Bubble sizes indicate the number of GO terms in each cluster, and the colors represent the corrected enrichment P-value on a log₁₀ scale. Similar clusters plot closer to each other. c Differential expression analysis shows up- and downregulated genes in spider venom glands. The venom glands were compared with spider silk glands (green box and circle) and all salivary glands (orange box and circle). False discovery rates (FDR) ≤ 0.01 are indicated by blue dots, while FDRs > 0.01 are indicated by black dots. Red dots signify the positively selected genes at the ancestor branch of spiders, as well as the genes in specific transcription modules. Digits in the Venn diagrams represent differentially expressed gene numbers in each group. Ptp36E, protein tyrosine phosphatase 36E; msps, mini spindles; DUGs, differentially upregulated genes; DDGs, differentially downregulated genes. d Time tree of ten species across arthropods. Yellow branches indicate the spiders used in our study; the red dot signifies the spider ancestor. MYA, million years ago. e GO enrichment of fourteen positively selected genes at the ancestral branch of spiders. These genes were contained in the venom gland-specific transcription modules and were differentially upregulated in the venom glands. Digits in the circles indicate the gene numbers enriched in the terms. f Specific mutation of the gene Ptp36E. Two sites (orange) of this gene were positively selected at the spider ancestor branch. This gene was under relaxed selection at three spider branches