Extended Data Fig. 5: Pangenome analysis and functional enrichment.

a, Comparison of different groups of grapevine accessions for the content of softcore, dispensable and private genomes. b,c, Nucleotide diversity (b), dN/dS (c) of core, softcore, dispensable genes. a–c, Significance was tested using a Kruskal–Wallis test; multiple comparisons were analyzed using a Nemenyi test. The P values were not corrected for multiple comparisons. The different lowercase letters above the box plots represent significant differences (P ≤ 0.05). For each boxplot, the box edges represent the interquartile range (IQR), with the centerline indicating the median. The whiskers extend to the most extreme data points within 1.5× IQR. d–g, GO enrichment of pangenome core genes (d), softcore genes (e), private genes (f) and dispensable genes (g) for 144 haplotype grapevine genomes. The enriched GO categories were determined using the one-sided version of Fisher’s exact test, followed by the Benjamin–Hochberg correction to obtain adjusted P values for multiple testing.