Figure S3 in Large-scale snake genome analyses provide insights into vertebrate development

Figure S3. Snake-specific genome structural variations (SSSVs), snake-diverged conserved non-coding elements (SD-CNEs that were diverged in snakes but were still conserved in the outgroup) (SD-CNEs), and orthologous genes used for evolutionary analysis, related to Figure 3 and STAR Methods (A) SSSVs distribution in different genome regions. (B) Genomic reads coverage of the snake-specific lost gene GHRL across four lizards (green anole [Acar], Anan's rock agama [Lsac], Komodo dragon [Vkom],and viviparous lizard [Zviv]), and 14 newly sequenced snakes. (C) Z-score cut off of SD-CNEs. (D) The enriched MGI terms that related to snake phenotypes for genes with SD-CNE (adjusted p value <0.05). SD-CNEs (dots) are located around the transcription start site of the genes enriched in eye, eyelid, ear, lung, mandible, maxillary, sternum, and tooth development-related terms. (E) Enriched GO terms (adjusted p value <0.05) for the newly evolved coding genes in snakes. Those related to dietary excess, protein digestion, and olfactory receptor activity were colored in red, blue, and brown, respectively. (F) Enriched GO terms (adjusted p value <0.05) for snake-specific coding genes that were lost. Red, blue, orange, and green were used to indicate the terms involved in vision, lens development, appetite, and bile acid biosynthetic process, respectively. (G) SSSV deletion in the potential regulatory region of RP1. (H) Counts of orthologous genes used for evolutionary analysis among 27 selected species.