Fig. 5

Fine-scale chromatin interaction variations associated with genomic rearrangements in G. kirkii vs. G. arboreum and G. kirkii vs. G raimondii. a Inter-chromosomal translocated fragments between ancestral Chr01 and Chr02 constitute the current Chr01 in G. arboreum. Beneath the mosaic fragments of ancestral Chr01 and Chr02 (in gray and brown, respectively) and on the left side of overall interaction map, the A/B compartment status and compositional gene density for Chr01 in G. arboreum are denoted. Within the zoomed-in diagonal interaction map beneath the overall interaction map, the green box denotes the disrupted diagonal interaction breakpoint corresponding to a synteny break. b Additional chromosomal inversion within the translocated ancestral Chr01 fragment is denoted. This introduced another synteny break into the current Chr02 in G. arboreum, denoted by the green box encompassing the disrupted diagonal interaction breakpoint. c The fused chromosomal fragments integrating ancestral Chr02 (brown), Chr04 (purple), and the unknown chromosomal fragments (yellow) in KI_2_4 of G. kirkii. d The fused chromosomal fragments integrating ancestral Chr02 (brown), Chr04 (purple), and Chr06 (orange) in KI_06 of G. kirkii. e In chromosome KI_06, the in-cis interactions between mosaic segments are illustrated in the upper diagram. The in-cis interactions (y-axis represents the intrachromosomal interactions that have been normalized using ICE and HiCNorm strategies) between chromosomal bins of the same chromosomal origins (as revealed in comparisons of G. kirkii vs. G. arboreum and G. kirkii vs. G. raimondii), summarized in terms of their bin-to-bin distance (x-axis), were statistically stronger than those between the segments of different chromosomal origins