Whole Genome Sequences of Three Treponema pallidum ssp. pertenue Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence
Publication Date
January 24, 2012
Journal
PLOS Neglected Tropical Diseases
Authors
Darina Čejková, Marie Zobaníková, Lei Chen, Petra Pospíšilová, et al
Volume
6
Issue
1
Pages
e1471
DOI
https://dx.plos.org/10.1371/journal.pntd.0001471
Publisher URL
http://journals.plos.org/plosntds/article?id=10.1371%2Fjournal.pntd.0001471
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/22292095
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3265458
Europe PMC
http://europepmc.org/abstract/MED/22292095
Web of Science
000300416100021
Scopus
84856566939
Mendeley
http://www.mendeley.com/research/whole-genome-sequences-three-treponema-pallidum-ssp-pertenue-strains-yaws-syphilis-treponemes-differ
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Mendeley | Further Information

{"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", "type"=>"journal", "authors"=>[{"first_name"=>"Darina", "last_name"=>"Čejková", "scopus_author_id"=>"23099215700"}, {"first_name"=>"Marie", "last_name"=>"Zobaníková", "scopus_author_id"=>"36718450800"}, {"first_name"=>"Lei", "last_name"=>"Chen", "scopus_author_id"=>"56415315900"}, {"first_name"=>"Petra", "last_name"=>"Pospíšilová", "scopus_author_id"=>"37085412600"}, {"first_name"=>"Michal", "last_name"=>"Strouhal", "scopus_author_id"=>"23029368000"}, {"first_name"=>"Xiang", "last_name"=>"Qin", "scopus_author_id"=>"57037659400"}, {"first_name"=>"Lenka", "last_name"=>"Mikalová", "scopus_author_id"=>"36717991200"}, {"first_name"=>"Steven J.", "last_name"=>"Norris", "scopus_author_id"=>"7103213612"}, {"first_name"=>"Donna M.", "last_name"=>"Muzny", "scopus_author_id"=>"6603763638"}, {"first_name"=>"Richard A.", "last_name"=>"Gibbs", "scopus_author_id"=>"7202068919"}, {"first_name"=>"Lucinda L.", "last_name"=>"Fulton", "scopus_author_id"=>"56439179500"}, {"first_name"=>"Erica", "last_name"=>"Sodergren", "scopus_author_id"=>"6701578232"}, {"first_name"=>"George M.", "last_name"=>"Weinstock", "scopus_author_id"=>"7005387907"}, {"first_name"=>"David", "last_name"=>"Šmajs", "scopus_author_id"=>"6603422324"}], "year"=>2012, "source"=>"PLoS Neglected Tropical Diseases", "identifiers"=>{"sgr"=>"84856566939", "doi"=>"10.1371/journal.pntd.0001471", "pui"=>"364192312", "pmid"=>"22292095", "scopus"=>"2-s2.0-84856566939", "issn"=>"19352727", "isbn"=>"10.1371/journal.pntd.0001471"}, "id"=>"7a28bfab-78fe-3ef6-8c1a-c6c878cee014", "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.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: 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.\\n\\nCONCLUSIONS/SIGNIFICANCE: 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.", "link"=>"http://www.mendeley.com/research/whole-genome-sequences-three-treponema-pallidum-ssp-pertenue-strains-yaws-syphilis-treponemes-differ", "reader_count"=>64, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>24, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>3, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>24, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>4, "Other"=>4, "Student > Master"=>3, "Student > Bachelor"=>14, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>36, "Medicine and Dentistry"=>15, "Social Sciences"=>2, "Computer Science"=>1, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>15}, "Social Sciences"=>{"Social Sciences"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>36}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "United Kingdom"=>2, "Mexico"=>1, "Switzerland"=>1, "Spain"=>1, "Indonesia"=>1}, "group_count"=>1}

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/687814"], "description"=>"<p>Newly annotated genes for each TPE strain are shown in comparison with resequenced and reannotated Nichols genes. Gene names were modified according to the GenBank instructions from the previously published ones <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Mikalov1\" target=\"_blank\">[19]</a>. The TP0126.1, TP0126.2, TP0126.4, and TP0126.5 genes were renamed as TP0126a, TP0126b, TP0126c and TP0126d, respectively.</p>", "links"=>[], "tags"=>["schematic", "chromosomal", "tp0126", "tp0127"], "article_id"=>358285, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_schematic_representation_of_the_chromosomal_TP0126_and_TP0127_region_/358285", "title"=>"A schematic representation of the chromosomal TP0126 and TP0127 region.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-24 02:18:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/688071"], "description"=>"a<p>highly divergent <i>tprD</i> and <i>tprK</i> were excluded from the analysis.</p>b<p>calculated from the complete genome sequences.</p>", "links"=>[], "tags"=>["nucleotide", "divergence", "tpa", "tpe", "strains"], "article_id"=>358538, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.t007", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Calculated_nucleotide_diversity_and_divergence_among_and_between_TPA_and_TPE_strains_and_subspecies_/358538", "title"=>"Calculated nucleotide diversity and divergence among and between TPA and TPE strains and subspecies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/687943"], "description"=>"<p>Differences shown in 5 kb-long intervals along the treponemal chromosome. Please note that the numbers of nucleotide changes (shown in bp) are for 7 intervals artificially terminated at 100 nt; the real values are shown next to corresponding vertical columns.</p>", "links"=>[], "tags"=>["nucleotide", "differences", "investigated"], "article_id"=>358421, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_nucleotide_differences_consistently_found_between_all_investigated_pertenue_and_pallidum_genomes_/358421", "title"=>"Number of nucleotide differences consistently found between all investigated <i>pertenue</i> and <i>pallidum</i> genomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-01-24 02:20:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/688207"], "description"=>"<p><i>T. p.</i> ssp. <i>pertenue</i> (TPE) genes encoding proteins with predicted cell function containing six or more amino acid changes and/or major sequence changes between all studied <i>T. p.</i> ssp. <i>pertenue</i> and all <i>T. p.</i> ssp. <i>pallidum</i> strains are shown.</p>a<p>D, deletion; fr. mut., frameshift mutation; I, insertion; MSC (major sequence changes) are defined in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd-0001471-t001\" target=\"_blank\">Table 1</a>; rev. fr. mut., reverted frameshift mutation; S, substitution.</p>b<p>Gene expression rate in Nichols strain grown in rabbits. The gene expression rates were taken from <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-majs2\" target=\"_blank\">[58]</a>.</p>c<p>The gene was shown to contain frameshift mutations or MSC in the genome of <i>Treponema paraluiscuniculi</i> Cuniculi A <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-majs1\" target=\"_blank\">[33]</a>.</p>d<p>Detected recombination within the gene or previously identified recombination <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Gray1\" target=\"_blank\">[56]</a>.</p>e<p>The corresponding protein was identified as an antigen <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-McKevitt1\" target=\"_blank\">[54]</a>.</p>f<p>The corresponding protein was identified as a lipoprotein <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Setubal1\" target=\"_blank\">[55]</a>.</p>g<p>The selection test was calculated using the Kumar model <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Nei1\" target=\"_blank\">[47]</a> using MEGA4 <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Tamura1\" target=\"_blank\">[48]</a> software.</p>", "links"=>[], "tags"=>["genes", "containing", "changes", "encoding", "proteins"], "article_id"=>358676, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.t004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TPE_genes_containing_major_sequence_changes_encoding_proteins_with_predicted_cell_function_/358676", "title"=>"TPE genes containing major sequence changes encoding proteins with predicted cell function.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:24:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/688302"], "description"=>"a<p>AE000520.1.</p>", "links"=>[], "tags"=>["genomic"], "article_id"=>358786, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.t002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_the_genomic_features_of_the_three_T_pallidum_ssp_pertenue_strains_/358786", "title"=>"Summary of the genomic features of the three <i>T. pallidum</i> ssp. <i>pertenue</i> strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:26:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/350897", "https://ndownloader.figshare.com/files/350950", "https://ndownloader.figshare.com/files/350992", "https://ndownloader.figshare.com/files/351121", "https://ndownloader.figshare.com/files/351182", "https://ndownloader.figshare.com/files/351237"], "description"=>"<div><h3>Background</h3><p>The yaws treponemes, <em>Treponema pallidum</em> ssp. <em>pertenue</em> (TPE) strains, are closely related to syphilis causing strains of <em>Treponema pallidum</em> ssp. <em>pallidum</em> (TPA). Both yaws and syphilis are distinguished on the basis of epidemiological characteristics, clinical symptoms, and several genetic signatures of the corresponding causative agents.</p> <h3>Methodology/Principal Findings</h3><p>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 (<em>d<sub>A</sub></em>) 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.</p> <h3>Conclusions/Significance</h3><p>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.</p> </div>", "links"=>[], "tags"=>["genome", "sequences", "yaws", "syphilis", "treponemes"], "article_id"=>129360, "categories"=>["Biological Sciences", "Cancer", "Genetics"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>["https://dx.doi.org/10.1371/journal.pntd.0001471.s001", "https://dx.doi.org/10.1371/journal.pntd.0001471.s002", "https://dx.doi.org/10.1371/journal.pntd.0001471.s003", "https://dx.doi.org/10.1371/journal.pntd.0001471.s004", "https://dx.doi.org/10.1371/journal.pntd.0001471.s005", "https://dx.doi.org/10.1371/journal.pntd.0001471.s006"], "stats"=>{"downloads"=>19, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Whole_Genome_Sequences_of_Three_Treponema_pallidum_ssp_pertenue_Strains_Yaws_and_Syphilis_Treponemes_Differ_in_Less_than_0_2_of_the_Genome_Sequence/129360", "title"=>"Whole Genome Sequences of Three <em>Treponema pallidum</em> ssp. <em>pertenue</em> Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-01-24 02:36:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/688268"], "description"=>"a<p>Resequencing of selected Nichols genes (unpublished results) resulted in similar fusions (with the exceptions of TP0126, TP0126a; TP0314, TP0315; and TP0859, TP0860) as in the Samoa D genome. Gene names with underscored dash indicate fusions.</p>b<p>Genes are fused only in the Samoa D and SS14 genomes, not in other <i>pertenue</i> or <i>pallidum</i> tested genomes.</p>c<p>Genes are fused only in the Nichols genome and separated in all further 6 investigated genomes (Samoa D, CDC-2, Gauthier, SS14, Chicago, DAL-1).</p>", "links"=>[], "tags"=>["fusions", "observed", "tpe", "samoa", "genome", "tpa", "nichols"], "article_id"=>358734, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.t003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_fusions_observed_between_TPE_Samoa_D_genome_and_TPA_Nichols_genome_/358734", "title"=>"Gene fusions observed between TPE Samoa D genome and TPA Nichols genome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:25:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/688115"], "description"=>"a<p>CHP, conserved hypothetical protein; HP, hypothetical protein; OMP, outer membrane protein; TCHMP, treponemal conserved hypothetical membrane protein; TCHOMP, treponemal conserved hypothetical outer membrane protein; TCHP, treponemal conserved hypothetical protein.</p>b<p><i>tprD</i> sequence was not included in the analysis.</p>", "links"=>[], "tags"=>["changes", "tpe", "compared", "sequenced"], "article_id"=>358588, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.t006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genetic_changes_specific_for_individual_TPE_strain_compared_to_the_other_two_sequenced_TPE_strains_/358588", "title"=>"Genetic changes specific for individual TPE strain compared to the other two sequenced TPE strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:23:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/688160"], "description"=>"<p><i>T. p.</i> ssp. <i>pertenue</i> (TPE) genes encoding hypothetical proteins containing six or more amino acid changes and/or major sequence changes between all studied <i>T. p.</i> ssp. <i>pertenue</i> and all <i>T. p.</i> ssp. <i>pallidum</i> strains are shown. CHP, conserved hypothetical protein; HP, hypothetical protein; TCHMP, treponemal conserved hypothetical membrane protein; TCHOMP, treponemal conserved hypothetical outer membrane protein; TCHP, treponemal conserved hypothetical protein.</p>a<p>D, deletion; fr. mut., frameshift mutation; I, insertion; MSC (major sequence changes) are defined in <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd-0001471-t001\" target=\"_blank\">Table 1</a>; S, substitution.</p>b<p>Gene expression rate in Nichols strain grown in rabbits. The gene expression rates were taken from <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-majs2\" target=\"_blank\">[58]</a>.</p>c<p>The gene was shown to contain frameshift mutations or MSC in the genome of <i>Treponema paraluiscuniculi</i> Cuniculi A <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-majs1\" target=\"_blank\">[33]</a>.</p>d<p>The corresponding protein was identified as an antigen <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-McKevitt1\" target=\"_blank\">[54]</a>.</p>e<p>The corresponding protein was identified as a lipoprotein <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Setubal1\" target=\"_blank\">[55]</a>.</p>f<p>Detected recombination.</p>g<p>The selection test was calculated using the Kumar model <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Nei1\" target=\"_blank\">[47]</a> using MEGA4 <a href=\"http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0001471#pntd.0001471-Tamura1\" target=\"_blank\">[48]</a> software.</p>", "links"=>[], "tags"=>["genes", "containing", "changes", "encoding", "hypothetical"], "article_id"=>358634, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.t005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_TPE_genes_containing_major_sequence_changes_encoding_hypothetical_proteins_/358634", "title"=>"TPE genes containing major sequence changes encoding hypothetical proteins.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:23:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/688361"], "description"=>"<p>Genetic differences were characterized in 983 similarly annotated genes and pseudogenes in both <i>T. p.</i> ssp. <i>pertenue</i> (TPE; Samoa D, CDC-2, and Gauthier) and <i>T. p.</i> ssp. <i>pallidum</i> strains (TPA; Nichols, DAL-1, SS14, Chicago). Only changes present in all investigated TPE strains when compared to all investigated TPA strains are shown in this table.</p>a<p>statistically significant results when compared to the genes encoding components of general metabolism. The p-value was corrected using Bonferroni correction for multiple comparisons to p = 0.008 and p-values lower than 0.008 were considered as statistically significant. p-values lower than 0.05 are also shown.</p>b<p>MSC (major sequence changes) were defined as 15 or more dispersed amino acid substitutions, indels longer than 10 amino acids, truncated and full length proteins (results of frameshift and reverted frameshift mutations, nonsense and start codon changing mutations).</p>c<p>not statistically significant.</p>", "links"=>[], "tags"=>["differences", "tpa", "tpe", "proteins", "encoded"], "article_id"=>358837, "categories"=>["Biological Sciences", "Genetics", "Infectious Diseases"], "users"=>["Darina Čejková", "Marie Zobaníková", "Lei Chen", "Petra Pospíšilová", "Michal Strouhal", "Xiang Qin", "Lenka Mikalová", "Steven J. Norris", "Donna M. Muzny", "Richard A. Gibbs", "Lucinda L. Fulton", "Erica Sodergren", "George M. Weinstock", "David Šmajs"], "doi"=>"https://dx.doi.org/10.1371/journal.pntd.0001471.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_identified_differences_between_TPA_and_TPE_proteins_encoded_by_different_functional_gene_groups_/358837", "title"=>"Distribution of identified differences between TPA and TPE proteins encoded by different functional gene groups.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-01-24 02:27:17"}

PMC Usage Stats | Further Information

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Relative Metric

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