Fig. 3: Potato domestication enhanced haplotype divergence.
From: Leveraging a phased pangenome for haplotype design of hybrid potato
a, Genomic length affected by haplotype-specific (heterozygous) variants by comparing haplotype H1 to H2 across 29 diploid potato accessions. b, GHSL in wild and cultivated potatoes. The boxes represent 75% and 25% quartiles, the central line indicates the median and the whiskers extend to 1.5 times the interquartile range; P = 2.6 × 10−4, two-tailed Student’s t-test, n = 19 (cultivated) and 10 (wild). c, PCA of chromosome 1 haplotypes, with dotted lines connecting paired haplotypes in heterozygous diploid potatoes. d, The phylogeny of 63 haplotypes for chromosome 1 was constructed using the maximum-likelihood method based on 1,074 single-copy genes. Dashed lines (right) connect the paired haplotypes in each diploid genome. RH, RH89-039-16. S. lycopersicum, Solanum lycopersicum; S. etuberosum, Solanum etuberosum; S. wrightii, Solanum wrightii. e, Unfolded site frequency spectrum of four types of SVs and non-synonymous single nucleotide polymorphisms (nSNPs) compared to putatively neutral synonymous SNPs (sSNPs) across cultivated potatoes.
