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Table 1 Genomic properties of M. ulcerans haplotypes as compared to the M. marinum strain M sequence in the twelve RDs

From: Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans

  deletions only insertions only b deletion::insertion b fragments dislocated fragments inverted fragments rearranged involving IS2404
  size (kb) in RD quantity (qualifier) in RD size (kb) in RD quantity in RD quantity in RD quantity in RD
  5.0 RD2           
  0.8 a RD3A           
      11.1::IS2404 c RD1       
  1.8 RD4           
M. ulcerans South America      3.8::IS2404 RD3B       
  7.3 RD7      1 RD12 1 RD12   
      17.2::14.7 d RD7       
  0.5 RD10           
      30.5::IS2404 RD9B       
  3.9 a RD12A           
  27.5 RD12B           
  0.8 a RD3A           
  60.7 RD5,10           
M. ulcerans Mexico      4.6::IS2404 RD11A       
  51.5 RD8           
  3.9 a RD12A           
  0.8 a RD3A           
  24.1 RD9A           
  3.6 RD9           
M. ulcerans Asia      4.6::IS2404 RD11A       
  3.4 RD10           
  3.9 a RD12A           
  42.0 RD12C           
    3 (IS2404) RD1         
    1 (IS2404) RD3         
    1 (IS2404) RD10         
    2 (IS2404) RD5         
    2 (IS2404) RD6         
    1 (IS2404) c RD7 1.7::IS2404/2606 RD1       
        2 RD2 1 RD2   
  0.8 a RD3A 1 (IS2404) RD8        1 RD2
        3 RD5,10 2 RD5,10   
M. ulcerans Africa/Australia 2.5 RD8A 3 (IS2404) RD12 2.1::0.3 d RD2      3 RD5,10
        1 RD6 2 RD6   
  1.8 RD9C 2 (IS2606) RD2 1.0::15.7 d RD6      1 RD6
        2 RD8 1 RD8   
  3.9 a RD12A 1 (IS2606) RD10 6.9::IS2404 RD8      2 RD8
        1 RD9 1 RD9   
    5 (IS2606) RD7 4.2::IS2404 RD9D       
    1 (IS2606) RD8         
    1 (IS2606) RD11         
    1 (IS2404/2606) RD2         
    1 (IS2404/2606) RD6         
    2 (IS2404/2606) RD12         
M. ulcerans Australia 5142/47 as above, additionally: 3.5 (RD3C) as above as above as above as above as above
  1. a: these two deletions are common for all investigated M. ulcerans strains
  2. b: inserts consist of complete IS elements plus some additional flanking nucleotides
  3. c: this insertion consists of one functional IS2404 element and an additional truncated IS2404 fragment
  4. d: the inserted DNA stretches are not represented in the M. marinum strain M genome sequence; gene bank blast and fasta searches identified sequences of i) bacteria other than mycobacteria with about 60% nucleotide identity over up to 3100 bp for the InDel in RD7; ii) mammalia with about 68% identity over 320 bp for the InDel in RD2; and iii) mycobacteria and other environmental or pathogenic bacteria with identities between 57 and 83% over 600–1900 bp, most of them grouping into insertion sequences and phages, for the InDel in RD6.