Extended Data Fig. 10: Definition and calculation of genomic homozygosity and similarity.

a, Diagrammatic illustration of the strategy used in calculating ‘genomic homozygosity’, which is defined as the proportion of homozygous segments across the entire genome. The genome is divided into discrete 5-Kb bins, and the proportion of homozygous segments is determined based on diagnostic SNP-stratified genotyping data. For example, within a 1-Mb region comprising 200 bins, the genomic composition of each bin is calculated based on genotyping data (see Supplementary Methods in Supplementary Information for details). The homozygosity of this 1-Mb region was calculated to be 50% if it contains 100 homozygous bins (homoeolog ratios of 4:0 or 0:4) and 100 heterozygous bins (homoeolog ratios of 3:1, 1:3 or 2:2). b, Schematic depiction of the calculation of genome similarity using a 1-Mb segment of chromosome 1. The gray areas represent syntenic regions, which are conserved genomic segments shared between the two genomes. The different colored blocks within these syntenic regions indicate the various kinds of sequence variations, such as insertions, deletions, or SNPs. Genome similarity is quantified by comparing the extent of sequence conservation and variation within these syntenic regions. Panel b was generated using BioRender with permission.