Fig. 4.

Long-range interactions between the proximal and distal regulatory regions. a An example of long-range interactions on Chr08 in G. thurberi and G. davidsonii. b Distribution of long-range interactions in each chromosome. c The long-range interactions were divided into the P-P, P-D, and D-D interactions. d Comparison of all interactions between G. thurberi and G. davidsonii. e Comparison of P-D interactions between G. thurberi and G. davidsonii. f Violin plots for long-range interactions in G. thurberi and G. davidsonii. The center red line in plot indicates the median, and the black lines indicate the upper and lower quartiles of insertion time. g Summary of the number of P–D interaction with variable distances in G. thurberi and G. davidsonii. h Comparison of expression level for genes interacting or not interacting with chromatin interactions (**P < 0.0001, a two-sided Wilcoxon signed-rank test). i Transcriptional status for genes with or without chromatin interactions. “Inactive” represents gene with FPKM < 0.1; “Active” represents gene with FPKM ≥ 0.1. “w” indicates genes with chromatin interactions; “w/o” indicates genes without chromatin interactions. j An example of one D interacted with two P in G. davidsonii. In the upper panel, the orange and blue lines represent Hi-C links in G. thurberi and G. davidsonii. respectively, and the blue boxes represent the genes locating in the interaction loop. The middle panel indicates the gene (Gd07G24850) around the P1 and P2. The lower panel is the read coverage generated by mRNA-seq