Fig. 3.

Methylation features of 3D chromatin. a–c Methylation level, TE ratio, and gene density in A and B compartments in G. thurberi and G. davidsonii. A two-sided Wilcoxon signed-rank indicates there were significant differences at **P < 0.001. d Methylation feature around TAD boundaries. The methylation levels in TAD boundaries (orange lines) flanking 100 kb was compared with those methylation levels in random genome regions (blue lines). The lines on the right side (0 to 100 kb) indicate TAD regions, and the lines on the left side (− 100 to 0 kb) indicate TAD regions when TADs were organized consecutively or non-TAD regions when one TAD was not closely adjacent to the others. e Gene distribution around the TAD boundaries. The method for extracting genomic regions around boundaries was the same as that in panel d. f A-B compartment switching between G. thurberi (D₁) and G. davidsonii (D₃) or between G. raimondii (D₅) and G. davidsonii (D₃). g Comparison of TAD boundaries between G. thurberi and G. davidsonii (D₁_Vs_D₃) or G. raimondii and G. davidsonii (D₅_Vs_D₃)