title: Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence.
abstract: BACKGROUND
  The yaws treponemes, Treponema pallidum ssp. pertenue (TPE) strains, are closely related to syphilis causing strains of Treponema pallidum ssp. pallidum (TPA). Both yaws and syphilis are distinguished on the basis of epidemiological characteristics, clinical symptoms, and several genetic signatures of the corresponding causative agents.
  
  
  RESULTS
  To precisely define genetic differences between TPA and TPE, high-quality whole genome sequences of three TPE strains (Samoa D, CDC-2, Gauthier) were determined using next-generation sequencing techniques. TPE genome sequences were compared to four genomes of TPA strains (Nichols, DAL-1, SS14, Chicago). The genome structure was identical in all three TPE strains with similar length ranging between 1,139,330 bp and 1,139,744 bp. No major genome rearrangements were found when compared to the four TPA genomes. The whole genome nucleotide divergence (d(A)) between TPA and TPE subspecies was 4.7 and 4.8 times higher than the observed nucleotide diversity (π) among TPA and TPE strains, respectively, corresponding to 99.8% identity between TPA and TPE genomes. A set of 97 (9.9%) TPE genes encoded proteins containing two or more amino acid replacements or other major sequence changes. The TPE divergent genes were mostly from the group encoding potential virulence factors and genes encoding proteins with unknown function.
  
  
  CONCLUSIONS
  Hypothetical genes, with genetic differences, consistently found between TPE and TPA strains are candidates for syphilitic treponemes virulence factors. Seventeen TPE genes were predicted under positive selection, and eleven of them coded either for predicted exported proteins or membrane proteins suggesting their possible association with the cell surface. Sequence changes between TPE and TPA strains and changes specific to individual strains represent suitable targets for subspecies- and strain-specific molecular diagnostics.
authors.affiliation: Department of Biology, Masaryk University, Brno, Czech Republic.
authors.forename: Darina
authors.initials: D
authors.lastname: Cejková
authors.forename: Marie
authors.initials: M
authors.lastname: Zobaníková
authors.forename: Lei
authors.initials: L
authors.lastname: Chen
authors.forename: Petra
authors.initials: P
authors.lastname: Pospíšilová
authors.forename: Michal
authors.initials: M
authors.lastname: Strouhal
authors.forename: Xiang
authors.initials: X
authors.lastname: Qin
authors.forename: Lenka
authors.initials: L
authors.lastname: Mikalová
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Norris
authors.forename: Donna M
authors.initials: DM
authors.lastname: Muzny
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.forename: Lucinda L
authors.initials: LL
authors.lastname: Fulton
authors.forename: Erica
authors.initials: E
authors.lastname: Sodergren
authors.forename: George M
authors.initials: GM
authors.lastname: Weinstock
authors.forename: David
authors.initials: D
authors.lastname: Smajs
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D023061:Gene Order; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D026801:Synteny; D013587:Syphilis / Q000382:microbiology*; D014210:Treponema pallidum / Q000235:genetics* / Q000302:isolation & purification; D015001:Yaws / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial