Fig. 4: Genetic SVs of Malus pan-genome.

a, A Circos plot of the ‘Fuji’ genome with genomic features. From outer to inner tracks: (1–4) chromosomes, gene density, repeat elements density and transposable element (TE) density of ‘Fuji’ genome; (5) density distribution of pan-SV features detected from 36 Malus accessions, which were combined and showcased in a pan-Malus SV set. The potential centromeric regions on each chromosome are depicted as black bars on track 1. b, The composition of SVs in each Malus accession. c, A seven-way Venn diagram showing shared and clade-specific SVs. Each clade is presented by a distinct color, and the numbers within the colored sections indicate the count of SVs specific to that clade. The number in parentheses under each clade represents the total number of detected SVs in that clade (observed in at least one haplotype of one accession in the clade). A total of 34,930 SVs are commonly detected in all seven clades. d, Trend of core- and pan-SVs; the SVs called from additional accessions in the listed order were added iteratively. e, Schematic diagram of pan-genome graph paths at the Rvi6 region of M. floribunda haplotig. Red represents the backbone reference genome. Alternative paths are shown in gray. M. floribunda-specific segments are shown in blue. The position and orientation of the HcrVf2 gene are indicated in purple.