Extended Data Fig. 7: Pangenome analysis of H. bulbosum.

(a) Heatmap showing the similarity of k-mer hashes of H. vulgare and H. bulbosum genome sequences. (b) The cumulative size of single-copy regions in genome assemblies of 10 H. bulbosum genomes. The curves trace the growth of non-redundant single-copy sequences as sample size increases. Error bars derived from 100 ordered permutations each. The central line represents the median; the box spans the interquartile range (IQR), from the first quartile to the third quartile. Whiskers extend to the most extreme values within 1.5 × IQR from the quartiles. (c) Composition of core, shell, and cloud single-copy sequences in the haplotype-level pangenomes. (d) Summary of the H. bulbosum graph pangenome constructed by the Minigraph-Cactus pangenome pipeline. (e) Composition of core, shell, and cloud sequences in the haplotype-level graph-based pangenome. (f) Bar chart illustrating the proportion of genes contained in core, shell and cloud OGs (see Methods for details) by genotype. (g) Bar chart illustrating the number of H. bulbosum genotypes represented in the individual OGs. The x-axis gives the number of genotypes included in an OG. The pie chart provides ratios of conserved and variable genes for all 10 genotypes.