Fig. 1: Phased potato pangenome reference (PPG-v.1.0).

a, PCA from 193 potato accessions; the 31 selected accessions are highlighted with solid dots. b, Assessment of genome contiguity by contig N50 for haplotype 1 (solid lines) and haplotype 2 (dashed lines). The N_x value represents x% of the total contigs length that is covered by the shortest contig length. c, Assessment of correctness by switch errors and Hamming errors for each diploid assembly. d, Reliability of the 29 diploid assemblies (excluding 2 inbred lines). For each haplotype-resolved assembly, the left bar represents haplotype H1 and the right bar represents H2. Regions identified as haploid are considered trustworthy (green). The y axis is broken to illustrate both the prominence of the reliable haploid component and the stratification of the unreliable segments. e, Pangenome growth curves for wild, cultivated, and wild plus cultivated groups. Pie charts represent conserved sequence (present in at least 90% of the haplotypes) and variable sequence in the PGGB pangenome graph. Numbers in the pie charts represent sequence length (Mb). f, Non-reference nodes (>50 bp) in the potato PGGB pangenome were annotated as four primary types, including TEs, satellite repeats, low-complexity (simple repeats) and non-repetitive sequences. Six different TE families were identified.