Open Access Highly Accessed Research article

On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer

Kenneth D Doig1, Kathryn E Holt1, Janet AM Fyfe3, Caroline J Lavender3, Miriam Eddyani4, Françoise Portaels4, Dorothy Yeboah-Manu5, Gerd Pluschke67, Torsten Seemann2 and Timothy P Stinear1*

Author Affiliations

1 Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia

2 Victorian Bioinformatics Consortium, Monash University, Clayton, Australia

3 Victorian Infectious Diseases Reference Laboratory, North Melbourne, Australia

4 Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium

5 Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana

6 Swiss Tropical and Public Health Institute, Molecular Immunology, Basel, Switzerland

7 University of Basel, Basel, Switzerland

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BMC Genomics 2012, 13:258  doi:10.1186/1471-2164-13-258

Published: 19 June 2012

Additional files

Additional file 1: Table S1:

Strain table and summary statistics. Isolates used in this study with sequencing summary statistics.

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Additional file 2: Figure S2:

Percentage DNA difference between isolates. Scatter Plot showing the percentages of DNA missing from references M. marinum “M” (y-axis) and M. ulcerans Agy99 and pMUM001 plasmid (x-axis). The percent missing is calculated by taking the number of zero coverage positions in the short read mapping to reference and dividing by total length of the reference. The dotted lines show the percentage missing from either reference to distinguish the M. marinum isolates from the MPM isolates. The clusterings are coloured as follows with the number in each cluster in brackets; M. marinum isolates (5) – blue, Fish and frog isolates (5) – green, Japanese isolate (1) – pink, French Guiana isolates – purple, Australian isolates (10) – gold, African Isolates (13) – red.

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Additional file 3: Table S2:

Core SNPs. Listing of core SNPs and short indels common to all M. ulcerans isolates when mapped to references M. ulcerans Agy99 and M. marinum M.

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Additional file 4: Table S3:

M. ulceransspecific CDS and features. List M. ulcerans Agy99 reference annotated features found in all M. ulcerans isolates but not found in any of the M. marinum isolates.

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Additional file 5: Table S4:

Diagnostic regions. List of nucleotide diagnostic regions distinguishing strains between various strain groups: M. marinum strains, M. ulcerans strains, African strains, Australian strains, strains from other regions, human host strains and fish or frog host strains.

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Additional file 6: Table S5:

Ancestral Pseudogenes. List of putative ancestral pseudogenes.

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Additional file 7: Table S6:

High dN/dS CDS and CDS with high non-synonymous SNPs. List of core M. marinum CDS with dN/dS > 1.0 in representative M. ulcerans isolates (Mm_1726, Mm_99/84, Mm_99/87, Mm_99/89, Mu_CC40299, Mu_JKD8071, Mu_DL045, Mu_1G897, Mu_8765, Mu_05142109, Mu_Agy99).

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Additional file 8: Table S7:

M. marinumorthologs ofM. tuberculosisT-cell antigens. List of M. tuberculosis T cell antigens with orthologs in M. marinum ‘M’ and M. ulcerans Agy99. Orthologs have > 80% amino acid identity.

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Additional file 9: Figure S1:

Work Flow. Schematic of the workflow with intermediate stages of the data shown in blue boxes. The inputs to the process are shown in red and comprise the annotated reference genomes and the short read sequencing data of the study isolates. The results are shown in green and include the phylogeny of the complex, novel CDS within each of the isolates, core and accessory genomes of the complex and putative ancestral pseudogenes.

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