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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.
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BMC Ecology and Evolution

ISSN: 2730-7182

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