Fig. 3

Changes of chromosomal level chromatin compactness. a, b Comparisons of A. thaliana chromosome 3 and A. lyrata chromosome 5 (chromosome 10 in the synthetic hybrid reference genome) are shown in (a) and (b), respectively. For each panel, data from each biological replicate are shown on the left and the Hi-C maps from combined replicates are shown on the right. The plot on the left shows interaction decay exponents, calculated from Hi-C maps at 20-kb resolution, which are shown on the right. For each curve, the contact frequency at 20-kb distance is set to 1. To make colors in the two Hi-C maps comparable, values in each normalized Hi-C map were divided by the average value indicative of interactions between bins 20 kb apart. c, d FISH experiments. c A 5.3-Mb region (highlighted in green in the sketch) of the A. thaliana genome can be specifically detected with a BAC probe mixture. Scale bars, 2 μm. d Space volume occupied by the probed A. thaliana genomic region in the hybrid and the parent nuclei. p values mean results of Wilcoxon–Mann–Whitney tests. e Analysis of chromatin compactness derived from Hi-C maps at 5-kb resolution. Pericentromeric regions in A. thaliana are excluded