Fig. 1: T2T genome assemblies and the construction of Grapepan v.1.0.

a, NGx plot showing the assembly continuity of the 18 newly assembled haplotypes compared with the published PNT2T assembly. Two haplotypes (haplotype 1 and haplotype 2) of the same individual are distinguished. b, Assessment of the assembly for nine sequenced grape accessions (BMNG, HMNG, MH, WG, MF, PN, SM, TS and BM). The quality values demonstrate the base-level accuracy of each sample. The phasing accuracy is indicated by the percentages of switch errors and hamming errors. c, Comparative genomics of 27 (published genomes only selected the primary haplotype) assemblies and one assembly of Muscadinia rotundifolia as outgroup for chromosome 1. d, Total length of MC pangenome sequences with different numbers of haplotypes; M represents megabase pairs and G represents gigabase pairs. e, Validation of pangenome deletions and insertions involved counting SVs of varying lengths and calculating the accuracy. f, PCA of the first two components of the 466 sequenced grape accessions. Different grape groups are distinguished by different colors. The samples used to construct Grapepan v.1.0 represent a wide range of genetic diversity. PC, principal component. g, The decay of LD was calculated based on three different datasets: SVs, SNPs and SVs + SNPs.