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Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity

Luke J Mappley12*, Michael L Black23, Manal AbuOun1, Alistair C Darby4, Martin J Woodward2, Julian Parkhill5, A Keith Turner56, Matthew I Bellgard2, Tom La7, Nyree D Phillips7, Roberto M La Ragione18 and David J Hampson28

Author Affiliations

1 Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Reading University, Addlestone, Surrey, KT15 3NB, UK

2 Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire, RG6 6AP, UK

3 School of Medical Sciences, Edith Cowan University, Perth, WA, 6027, Australia

4 Institute of Integrative Biology, School of Biological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK

5 The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

6 Discuva Ltd, Cambridge Science Park, Milton Road, Cambridge, CB4 0WE, UK

7 School of Veterinary and Biomedical Science, Murdoch University, Perth, WA, 6150, Australia

8 Faculty of Health and Medical Sciences, University of Surrey, Guilford, Surrey, GU2 7XH, UK

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BMC Genomics 2012, 13:454  doi:10.1186/1471-2164-13-454

Published: 5 September 2012

Additional files

Additional file 1:

Type and copy number of mobile genetic elements (MGE) in the genomes ofB. pilosicoli 95/1000, B2904 and WesB. A combination of protein markov cluster analysis and reciprocal blast searches against the conserved domain database (CDD) was used to determine the copy number of each type of MGE across the three B. pilosicoli genomes, using a cut-off e-value of 1e-20. The ORF number, position, and size of all MGEs identified in each of the B. pilosicoli genomes is displayed.

Format: XLS Size: 54KB Download file

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Additional file 2:

Conserved and shared protein clusters between the six genome-sequencedBrachyspira strains. B. hyodysenteriae WA1 (H), B. intermedia PWS/AT (I), B. murdochii 56-150T (M) and B. pilosicoli 95/1000 (Pa), B2904 (Pb) and WesB (Pc)a strains we included in the protein cluster analysis. A cut-off e-value of 1e-20 was used.

Format: XLS Size: 18KB Download file

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Additional file 3:

Comparison of the utilisation of unique carbon sources byB. pilosicoli95/1000, B2904 and WesB. Biolog Phenotype MicroArray™ (PM) technology was employed for these studies and OmniLog apparatus was used to detect formazan formation and hence, respiration due to utilisation of the carbon source; +, able to utilise the compound; -, unable to utilise the compound.

Format: XLS Size: 31KB Download file

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