Fig. 3: Characteristics of structural variations identified in the 27 B. oleracea genomes.

a, The distribution of GC content (33–41%), gene numbers (0–200 Mb⁻¹) and TE density (20–100%) in the T10 reference genome, the nonredundant SVs (presence, 2–100 kb/Mb; absence, 20–400 kb/Mb and all SVs, 10–400 kb Mb⁻¹) among 27 genomes, as well as the SNPs (10–40 kb⁻¹) and InDels (10–30 kb Mb⁻¹) identified in the 704 B. oleracea accessions. b, The number of different types of SVs from the nonredundant set of SVs in individual B. oleracea genomes. c, The number of SVs present in different numbers of query genomes. The bottom lines colored in light blue, light orange and light green mark these accessions from the wild/ancestral group, the AIL and the LHL, respectively. The sample IDs colored in light orange and light green denote accessions from broccoli/cauliflower and cabbage, respectively. The red rectangle marks the accessions of broccoli/cauliflower, highlighting the lower number of SVs in broccoli/cauliflower compared to the other accessions. d, The number of private SVs in wild B. oleracea, broccoli/cauliflower and cabbage genomes, showing significantly more private SVs in wild B. oleracea than in others (n = 7 versus 5 versus 7; two-sided Wilcoxon rank-sum test; centerline, median; box limits, first and third quartiles; whiskers, 1.5× IQR). e, The frequency distribution of SVs in the following five different genomic regions: upstream (within −3 kb), exon, intron, downstream (within +3 kb) and intergenic regions. The SV ratios in the five regions were calculated for each of the 27 genomes, and these values were then sorted and plotted from small to large for each of the five regions. f, The density of SV sequences per 100 bp in gene bodies and 5 kb flanking regions in the 27 B. oleracea genomes. The area plots mark the maximum and minimum values across the 27 B. oleracea genomes, and the lines denote average values.