Genome comparison of M. marinum strain M and M. ulcerans haplotypes in selected RDs. Only selected RDs that contribute to the understanding of the M. ulcerans phylogeny are shown. Dashed lines represent sequence identity; Δ = deletion; :: = substitution; shaded boxes are IS2404 and IS2606 as indicated. M. ulcerans MRCA = most recent common ancestor. Since the Mexican strains showed either deletions expanding the whole RD or did not show any significant microarray hit in other RDs, the Mexican haplotype was only included in the illustration of RD11 where it revealed informative differences. a) Alignment of the members of the African/Australian haplotype shows sequence identity in the tested crucial genome regions. b) Haplotype Australia 5142/47 is identical in all regions except for RD3C as indicated; here the breakpoints differ from deletion RD3B in the South American haplotype.