Extended Data Fig. 7: Analysis of the single-copy pan-genome.

a, Pipeline used to select single-copy k-mers in PAVs as markers for genome-wide association scan analysis. b, Summary of single-copy sequence in 20 genome assemblies and results of their clustering. c, Copy number of single-copy sequences in a diversity panel comprising 200 domesticated and 100 wild accessions. Frequency ranges from blue (low) to red (high). d–g, Comparison of PCA on the basis of PAV and SNP variants in whole-genome shotgun data of 200 diverse accessions (d, e) and 19,778 varieties of domesticated barley⁹ (f, g). Top panels show PCA results from 160,716 PAVs; bottom panels show PCA results from 779,503 of genotyping-by-sequencing SNPs. The accessions are coloured according to geographical origin and row type (using the colour code defined in Extended Data Fig. 1).