Comparative genomics of closely related treponemal strains
Abstract number: 1733_413
Strouhal M., Matejkova P., [Scaron]majs D., Sodergren E., Norris S.J., Weinstock G.M.
Objectives: Genus Treponema includes several pathogenic spirochetes: Treponema pallidum ssp. pallidum (TPA) is the causative agent of sexually transmitted syphilis, Treponema pallidum ssp. pertenue (TPE) causes endemic non-veneral treponemal infections and T. paraluiscuniculi (TPAR) is the etiologic agent of veneral syphilis in rabbits and does not infect humans. These treponemes cannot be continuously cultivated under in vitro conditions and are indistinguishable by morphological and serological methods. In this study, genomes of closely related treponemes were compared.
Methods: Whole genome fingerprinting (WGF) was used to compare four treponemal strains including Nichols (TPA), SS14 (TPA), Samoa D (TPE) and Cuniculi A (TPAR). The genomes of analysed strains were divided into 97 overlapping intervals covering the whole genome and each of these segments was amplified and digested by restriction enzymes BamH I, EcoR I and Hind III. The resulting restiction profiles were used for identification of heterologous regions in chromosomal DNA.
Results: When compared to the Nichols genome the prominent indels and sequence changes were preferentially localised in tpr genes (tprD TP0131, tprE TP0313, tprF TP0316, tprG TP0317, tprI TP0620, tprJ TP0621, tprK TP0897 and tprL TP1031) and in the hypothetical genes in the vicinity of tpr genes. Differences in number of tandem repetitions within the gene TP470 and genes TP04334 (hypothetical genes) were detected in all analysed strains. In the second case fusion of both genes (TP04334) resulted in one acidic repeat protein gene (arp gene). Altogether, 2 deletions and 2 insertions, 7 deletions and 3 insertions, 12 deletions and 7 insertions were found in the strains SS14, Samoa D and Cuniculi A, respectively.
Conclusions: In this study, WGF was shown to be essential approach for verification of the whole genome assembly based on comparative genome sequencing and dideoxyterminator sequencing data. During completion of the SS14 and Samoa D genome sequences, tandem repeat regions and regions comprising paralogous genes were selectively identified by WGF.
This work was supported by the grants from the Internal Grant Agency of the Ministry of Health of the Czech Republic (NR/89674/2006) and from the Grant Agency of the Czech Republic (310/04/0021).
|Session name:||European Society of Clinical Microbiology and Infectious Diseases|
|Location:||ICC, Munich, Germany|
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