Fig. 6

Secondary metabolite genes are more polymorphic than others. a Circos plot showing genomic coordinates of the 80 putative secondary metabolite biosynthetic genes (outer track in green); percentage of 50 KB windows annotated as repeat (second track in red); number of genes with presence / absence polymorphisms (third track in turquoise); number of high impact polymorphisms (fourth track in black); and, number of single nucleotide polymorphisms (SNPs) in blue. The grey dashed lines are sites fewer than 300 KB from chromosomes, defined as subtelomeric. b The x axis shows the average percentage of each gene that was covered by Illumina reads in a panel of 25 isolates. The y axis shows distance to nearest transposable element sequence. Non-biosynthetic gene cluster (BGC) genes are in black and BGC-genes are in white. This illustrates the enrichment of presence / absence polymorphisms among BGC genes. c Sequence diversity of BGC genes and non-BGC genes. The x axis shows nucleotide diversity and the y axis shows haplotype diversity. The curved lines represent kernel density of Non-BGC genes (grey) and BGC genes (black). The horizontal and vertical dashed lines represent median haplotype and nucleotide diversity, respectively, of non-BGC and BGC genes in grey and black, respectively