Fig. 3: Quantitative analysis of synteny reveals hotspots of rearrangements.
a Synteny diversity along each chromosome: (100 kb sliding windows with a step-size of 50 kb in blue; 5 kb sliding windows with a step-size of 1 kb in grey). Red bars: R gene clusters. Gray rectangles: centromeres. The dashed green and red lines indicate thresholds for synteny diversity values of 0.25 and 0.50. The labelled arrow (A) indicates a 2.48 Mb inversion in the Sha genome. The labelled arrow (B) indicates the location of the example shown in d. b Gene and TE densities in 10,331 syntenic (SYN) and 576 hotspots of rearrangements (HOT) regions. c The number of variable copy-number alleles in 10,331 syntenic (SYN) and 576 rearrangements (HOT) regions. d An example of a HOT region including the RPP4/RPP5 R gene cluster. The upper panel shows the distribution of synteny diversity (blue curve), nucleotide diversity (gray background) and haplotype diversity (pink background) in a 5 kb sliding window with a step-size of 1 kb. Both the nucleotide diversity and the haplotype diversity were calculated based on informative markers (MAF ≥ 0.05, missing rate < 0.2) from the 1001 Genomes Project8. The marker density is shown as the heatmap on top. The green and red dashed lines indicate the value 0.25 and 0.50 of synteny diversity, respectively. The schematic in the lower part shows the annotated protein-coding genes (colored rectangles). Blue rectangles: non-resistance genes. Other colored rectangles: resistance genes where genes with the same color belong to the same gene family. The gray links between the rectangles indicate the homologous relationships between non-resistance genes. e A dot plot of Col-0 and C24 sequence from the HOT region shown in d. Red lines: homologous regions between the two genomes. f The distribution of synteny diversity values in 1 kb sliding windows around and in 576 HOT regions. In box plots b, c and f, centre line: median, bounds of box: 25th and 75th percentiles, whiskers: 1.5 * IQR (IQR: the interquartile range between the 25th and the 75th percentile). Source Data are provided as a Source Data file.
