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Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters

BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols...

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Autores principales: Pětrošová, Helena, Pospíšilová, Petra, Strouhal, Michal, Čejková, Darina, Zobaníková, Marie, Mikalová, Lenka, Sodergren, Erica, Weinstock, George M., Šmajs, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769245/
https://www.ncbi.nlm.nih.gov/pubmed/24058545
http://dx.doi.org/10.1371/journal.pone.0074319
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author Pětrošová, Helena
Pospíšilová, Petra
Strouhal, Michal
Čejková, Darina
Zobaníková, Marie
Mikalová, Lenka
Sodergren, Erica
Weinstock, George M.
Šmajs, David
author_facet Pětrošová, Helena
Pospíšilová, Petra
Strouhal, Michal
Čejková, Darina
Zobaníková, Marie
Mikalová, Lenka
Sodergren, Erica
Weinstock, George M.
Šmajs, David
author_sort Pětrošová, Helena
collection PubMed
description BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols-like strains and SS14-like strains. TPA Nichols and SS14 strains were completely sequenced in 1998 and 2008, respectively. Since publication of their complete genome sequences, a number of sequencing errors in each genome have been reported. Therefore, we have resequenced TPA Nichols and SS14 strains using next-generation sequencing techniques. METHODOLOGY/PRINCIPAL FINDINGS: The genomes of TPA strains Nichols and SS14 were resequenced using the 454 and Illumina sequencing methods that have a combined average coverage higher than 90x. In the TPA strain Nichols genome, 134 errors were identified (25 substitutions and 109 indels), and 102 of them affected protein sequences. In the TPA SS14 genome, a total of 191 errors were identified (85 substitutions and 106 indels) and 136 of them affected protein sequences. A set of new intrastrain heterogenic regions in the TPA SS14 genome were identified including the tprD gene, where both tprD and tprD2 alleles were found. The resequenced genomes of both TPA Nichols and SS14 strains clustered more closely with related strains (i.e. strains belonging to same syphilis treponeme subcluster). At the same time, groups of Nichols-like and SS14-like strains were found to be more distantly related. CONCLUSION/SIGNIFICANCE: We identified errors in 11.5% of all annotated genes and, after correction, we found a significant impact on the predicted proteomes of both Nichols and SS14 strains. Corrections of these errors resulted in protein elongations, truncations, fusions and indels in more than 11% of all annotated proteins. Moreover, it became more evident that syphilis is caused by treponemes belonging to two separate genetic subclusters.
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spelling pubmed-37692452013-09-20 Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters Pětrošová, Helena Pospíšilová, Petra Strouhal, Michal Čejková, Darina Zobaníková, Marie Mikalová, Lenka Sodergren, Erica Weinstock, George M. Šmajs, David PLoS One Research Article BACKGROUND: Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols-like strains and SS14-like strains. TPA Nichols and SS14 strains were completely sequenced in 1998 and 2008, respectively. Since publication of their complete genome sequences, a number of sequencing errors in each genome have been reported. Therefore, we have resequenced TPA Nichols and SS14 strains using next-generation sequencing techniques. METHODOLOGY/PRINCIPAL FINDINGS: The genomes of TPA strains Nichols and SS14 were resequenced using the 454 and Illumina sequencing methods that have a combined average coverage higher than 90x. In the TPA strain Nichols genome, 134 errors were identified (25 substitutions and 109 indels), and 102 of them affected protein sequences. In the TPA SS14 genome, a total of 191 errors were identified (85 substitutions and 106 indels) and 136 of them affected protein sequences. A set of new intrastrain heterogenic regions in the TPA SS14 genome were identified including the tprD gene, where both tprD and tprD2 alleles were found. The resequenced genomes of both TPA Nichols and SS14 strains clustered more closely with related strains (i.e. strains belonging to same syphilis treponeme subcluster). At the same time, groups of Nichols-like and SS14-like strains were found to be more distantly related. CONCLUSION/SIGNIFICANCE: We identified errors in 11.5% of all annotated genes and, after correction, we found a significant impact on the predicted proteomes of both Nichols and SS14 strains. Corrections of these errors resulted in protein elongations, truncations, fusions and indels in more than 11% of all annotated proteins. Moreover, it became more evident that syphilis is caused by treponemes belonging to two separate genetic subclusters. Public Library of Science 2013-09-10 /pmc/articles/PMC3769245/ /pubmed/24058545 http://dx.doi.org/10.1371/journal.pone.0074319 Text en © 2013 Pětrošová et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Pětrošová, Helena
Pospíšilová, Petra
Strouhal, Michal
Čejková, Darina
Zobaníková, Marie
Mikalová, Lenka
Sodergren, Erica
Weinstock, George M.
Šmajs, David
Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters
title Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters
title_full Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters
title_fullStr Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters
title_full_unstemmed Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters
title_short Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters
title_sort resequencing of treponema pallidum ssp. pallidum strains nichols and ss14: correction of sequencing errors resulted in increased separation of syphilis treponeme subclusters
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769245/
https://www.ncbi.nlm.nih.gov/pubmed/24058545
http://dx.doi.org/10.1371/journal.pone.0074319
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