Fig. 3

Inter-chromosomal interactions of 1RS/1BL in AK58. a Circos plot presenting the inter-chromosomal interactions between chromosome 1RS/1BL and the other chromosomes in AK58. The centromere region is indicated with a black line. Chromosome 1RS/1BL is enlarged (right), with the inter-chromosomal interaction loci of 1RS and 1BL indicated by blue bars. b Comparison of the extent of the inter-chromosomal interactions detected for 1RS and 1BL in AK58. The interaction density of 1RS was significantly lower than that of 1BL (P < 2.2E−16, Welch’s two-sample t-test). c Circos plot presenting the inter-chromosomal interactions between chromosome 1B and the other chromosomes in the non-1RS/1BL variety Chinese Spring (CS). d Comparison of the extent of the inter-chromosomal interactions detected for 1BS and 1BL in CS (P = 0.6014, Welch’s two-sample t-test). e Synteny plot presenting the sequence homology across chromosomes 1A, 1B, and 1D. Homologous regions are connected by ribbons. f Proportion of TE subfamilies in the short and long arms of chromosomes 1A, 1B, and 1D. g DNA methylation distribution across chromosomes 1A, 1B, and 1D in three contexts. Each chromosome was divided to 200 consecutive bins, and the DNA methylation level was recorded and plotted for each bin. h Box plot showing the DNA methylation levels across 1AS, 1RS, and 1DS. T-test was used for pair-wise comparison