Fig. 1

Distribution of DNS scores across the genomic regions and chromosomes. a Density of DNS scores across the whole genome in 2 Mb windows for the A (red), B (blue), and D (purple) genomes. Inset: distribution of 2 Mb-window DNS scores by genome. b Distribution of DNS scores across genomic segments, distal R1, interstitial R2a, pericentromeric C, interstitial R2b, and distal R3. The relative distribution of genomic features used for the segmentation of wheat chromosomes is shown on the left. c Distribution of DNS scores by genomic segment and genome (A—red, B—blue, D—purple); homeologous chromosome group 4 DNS values are shown as lighter colors (chr4A—light pink, 4B—powder blue, 4D—light lavender). Distal segment R1 is reduced 3.6× compared to A genome R1 segments. d Structural evolution of wheat chromosome 4A and segmentation of the ancestral (aR1, aR2a, aC, aR2b, aR3) and modern (mR1, mR2a, mC, mR2b, mR3) 4A chromosomes. TE composition of the R1 segment on modern 4A (mR1), and R1 and R2a segments of remaining chromosomes from the A genome. e Top panel: representative DNS scores for 1 Mb windows across entire chromosome 3A. Genomic segments are shown in the background as dark pink for distal segments, light pink for interstitial segments, and pale yellow for the pericentromeric region; location of the centromere is dark yellow. Bottom panel: proportion of 1 Mb windows that are considered outliers for hyper-resistant regions MRF (green) and hyper-sensitive regions MSF (red) across chromosome 3A