Fig. 7
Chromatin accessibility of TEs and neighboring genes. a DNS scores by genome for TE superfamilies located within and outside of 2-kb promoter regions of the genes for Gypsy superfamily (Mann-Whitney U test: WA = 85,484,000, WB = 81,997,000, WD = 6,067,000; all p values < 2.2 × 10−16), Copia superfamily (WA = 60,126,000, WB = 60,412,000, WD = 56,955,000; all p values < 2.2 × 10−16), and CACTA superfamily (WA = 91,146,000, WB = 113,700,000, WD = 86,315,000; all p values < 2.2 × 10−16). b DNS scores across gene bodies for all genes that have a TE located within 2 kb of gene or more than 2 kb from a gene. Distributions are given for all TEs (W = 39,630,000, p value < 2.2 × 10−16), class 1 TEs (W = 8,089,200, p value = 2.7 × 10−05), and class 2 TEs (W = 7,616,500, p value < 2.2 × 10−16). p values are denoted by red stars above boxplot for each comparison: *0.05 < p < 10−5; **10−5 < p < 10−10; ***10−10 < p < 10−16; NS = p > 0.05. c Log10 gene expression values for all genes that have a TE located within 2 kb of gene or more than 2 kb from a gene. Distributions are given for all TEs (W = 4,768,500, p value = 1.5 × 10−07), class 1 TEs (W = 94,150, p value = 0.11), and class 2 TEs (W = 908,540, p value = 2.5 × 10−8)