Figure 3

Linear genomic comparison of sections within RDs. Comparisons are made with three sequences each using ACT (the Artemis Comparison Tool software release 5) over at least 30 kb: M. marinum M on top, M. ulcerans Agy99 at the bottom, and M. ulcerans of either haplotype, the Asian (RD2 and RD5) or the South American (RD9 and RD10) in the middle. Regions of sequence conformity are shown in parallel light grey plains, inverted DNA segments are depicted in dark grey and inverted surfaces, and white areas represent non-homologous regions like deletions and insertions. Some sequence displacements are visualized as grey areas displaying across the panels. Cut-off value for inclusion of sequence identity was 100 bp. The principal genetic backbone of the Asian and South American haplotypes (both members of the ancestral lineage) is identical for each alignment shown, but – as a matter of how the RDs were found – the particular excluded haplotypes reveal deletions in the respective RDs. Although showing the same genetic backbone as M. marinum in the marginal parts, the Mexican strains disclose large deletions over their respective RDs and are therefore not included in this computational analysis. The sequence regions were retrieved by scanning the contigs by PCR, and by cloning and sequencing of critical segments.