Research article
Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain
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* Corresponding author: Ian N Clarke inc@soton.ac.uk
1 Molecular Microbiology Group, University Medical School, Southampton General Hospital, Southampton, SO16 6YD, UK
2 The Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
3 Department of Clinical Microbiology, Malmo University Hospital, SE 205 02 Malmo, Sweden
4 Health Protection Agency South East, Southampton General Hospital, Southampton, SO16 6YD, UK
5 Department of Obstetrics and Gynaecology, Malmo University Hospital, SE 205 02, Malmo, Sweden
6 Viral Diseases Programme, Medical Research Council PO Box 273, Banjul, The Gambia
7 Clinical Research Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
BMC Genomics 2009, 10:239 doi:10.1186/1471-2164-10-239
Published: 21 May 2009Additional files
Additional file 1:
Comparison of the Plasticity Zone between several strains, visualised by the Artemis Comparison Tool. The grey lines indicate forward and reverse reading frames of sequenced genomes, with predicted coding sequences superimposed. The red bars indicate regions of 97–100% nucleotide identity. Brown CDSs denote pseudogenes. The cytotoxin locus is reduced in D/UW-3/CX, yet produces an active cytotoxin. It is further deleted in strain L2/434/BU. The phospholipase D locus contains pseudogenes in all strains. The trp operon is complete in strains D/UW-3/CX and L2/434/BU, but has pseudogene components in the serotype A and B strains: trpB in B/TZ1A828/OT and A/HAR-13, and trpA in Jali20 and A/HAR13.
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Additional file 2:
Pseudogene differences between strains B/TZ1A828/OT, B/Jali20, A/HAR-13 and L2/434/BU. Pseudogenes (Ψ) are highlighted in brown, and the CDSs contained within the plasticity zone are shown in mauve.
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Additional file 3:
Variable CDSs, comparing strains B/TZ1A828/OT, B/Jali20 and L2/434/BU. CDSs with significant variability between the strains are listed, with brief description of variation.
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Additional file 4:
Custom primers used for amplification and sequencing of C. trachomatis plasmids.
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