Fig. 2: The syntenic pan-genome constructed from the 27 B. oleracea genomes.

a, The number of syntenic pan and core gene families in the 27 genomes. b, Composition of the syntenic pan-genome. The histogram shows the frequency distribution of syntenic gene families shared by different numbers of genomes. The pie chart shows the proportion of different groups of syntenic gene families. c, Percentage of different groups of syntenic gene families in each of the 27 genomes. d, Presence and absence information of all syntenic gene families in the 27 genomes. e,f, The average number of TE insertions in genes and the expression level of genes in different groups of syntenic gene families (two-sided Student’s t test; centerline, median; box limits, first and third quartiles; whiskers, 1.5× IQR). Different lowercase letters above the box plots represent significant differences (P < 0.05). g, Functional analysis (gene ontology) of lost genes in the syntenic softcore or dispensable gene families, in different B. oleracea morphotypes, highlighting strong function enrichment associated with specific metabolites. The number of lost genes in different morphotypes is provided in the tree diagram. h, Syntenic gene families were separated into three groups corresponding to the numbers of homoeologs (single-, two- or three-copy) retained from the Brassica mesohexaploidization event. The percentage of gene families in different pan-genome classes for these groups is shown in each of the 27 B. oleracea genomes. IQR, interquartile range.