Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme
Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hier...
Gespeichert in:
| Veröffentlicht in: | PloS one 2013-06, Vol.8 (6), p.e66567-e66567 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | e66567 |
|---|---|
| container_issue | 6 |
| container_start_page | e66567 |
| container_title | PloS one |
| container_volume | 8 |
| creator | Li, Yanjun Cui, Yujun Cui, Baizhong Yan, Yanfeng Yang, Xianwei Wang, Haidong Qi, Zhizhen Zhang, Qingwen Xiao, Xiao Guo, Zhaobiao Ma, Cong Wang, Jing Song, Yajun Yang, Ruifu |
| description | Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.
Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.
Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis. |
| doi_str_mv | 10.1371/journal.pone.0066567 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_plos_</sourceid><recordid>TN_cdi_plos_journals_1370366605</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A478182346</galeid><doaj_id>oai_doaj_org_article_85c2d2024af444808f6896dd218968d8</doaj_id><sourcerecordid>A478182346</sourcerecordid><originalsourceid>FETCH-LOGICAL-c692t-ce70dd8a652740def8595b6beafe63ba668f133250f8894775119b15456a89073</originalsourceid><addsrcrecordid>eNqNk99r1TAUx4sobl79D0QDgujDveZHm6YvwphuuzAcbHPgU0jT09tc2qYm7dj-e1NvN25lD9KHlJPP-Z6cb3Ki6C3BK8JS8mVrB9eqetXZFlYYc57w9Fl0SDJGl5xi9nzv_yB65f0W44QJzl9GB5QJnFDGD6O7E1D94MAjW6Ib5YzKa0A_hiYHN4auVVtAgy6hC5xHpkW_wHnTGoU68L3xKACorwB9g1uobddA24-JCp0ZcMrpymhVo1NobX_fmXaDrnQFDbyOXpSq9vBmWhfRz5Pv18dny_OL0_Xx0flS84z2Sw0pLgqheELTGBdQiiRLcp6DKoGzXHEuSsIYTXApRBanaUJIlpMkTrgSGU7ZInq_0-1q6-VkmpfBQsw458GSRbTeEYVVW9k50yh3L60y8m_Auo1Urje6BikSTQuKaazKOI4FFiUXGS8KSsIiChG0vk7VhryBQgcznKpnovOd1lRyY28lC0Kp4EHg0yTg7O8hOCwb4zXUtWrBDuHcaUbSmFOeBfTDP-jT3U3URoUGTFvaUFePovIoTgURlMVj2dUTVPjC5RsdXlhpQnyW8HmWEJge7vqNGryX66vL_2cvbubsxz22AlX3lbf10Bvb-jkY70DtrPcOykeTCR77Jw9uyHFA5DQgIe3d_gU9Jj1MBPsDnLEJ3g</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1370366605</pqid></control><display><type>article</type><title>Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme</title><source>Public Library of Science (PLoS) Journals Open Access</source><source>MEDLINE</source><source>DOAJ Directory of Open Access Journals</source><source>EZB-FREE-00999 freely available EZB journals</source><source>PubMed Central</source><source>Free Full-Text Journals in Chemistry</source><creator>Li, Yanjun ; Cui, Yujun ; Cui, Baizhong ; Yan, Yanfeng ; Yang, Xianwei ; Wang, Haidong ; Qi, Zhizhen ; Zhang, Qingwen ; Xiao, Xiao ; Guo, Zhaobiao ; Ma, Cong ; Wang, Jing ; Song, Yajun ; Yang, Ruifu</creator><contributor>Cloeckaert, Axel</contributor><creatorcontrib>Li, Yanjun ; Cui, Yujun ; Cui, Baizhong ; Yan, Yanfeng ; Yang, Xianwei ; Wang, Haidong ; Qi, Zhizhen ; Zhang, Qingwen ; Xiao, Xiao ; Guo, Zhaobiao ; Ma, Cong ; Wang, Jing ; Song, Yajun ; Yang, Ruifu ; Cloeckaert, Axel</creatorcontrib><description>Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.
Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.
Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0066567</identifier><identifier>PMID: 23805236</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acinetobacter baumannii ; Analysis ; Bacillus anthracis ; Biodiversity ; Biology ; Capillary electrophoresis ; Deoxyribonucleic acid ; Disease prevention ; DNA ; Epidemics ; Epidemiology ; Evolution (Biology) ; Forensic engineering ; Forensic science ; Francisella tularensis ; Genetic aspects ; Genetic diversity ; Genetic Loci ; Genetic Variation ; Genomes ; Genomics ; Genotype ; Genotyping ; Genotyping Techniques - methods ; Glycerol ; Hospitals ; Laboratories ; Loci ; Medicine ; Microorganisms ; Multiculturalism & pluralism ; Mutation ; Mutation rates ; Mycobacterium tuberculosis ; Nitrates ; Pathogens ; Phylogenetics ; Polymorphism ; Quarantine ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Strains (organisms) ; Studies ; Tandem Repeat Sequences ; Tuberculosis ; Yersinia pestis ; Yersinia pestis - classification ; Yersinia pestis - genetics</subject><ispartof>PloS one, 2013-06, Vol.8 (6), p.e66567-e66567</ispartof><rights>COPYRIGHT 2013 Public Library of Science</rights><rights>2013 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2013 Li et al 2013 Li et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-ce70dd8a652740def8595b6beafe63ba668f133250f8894775119b15456a89073</citedby><cites>FETCH-LOGICAL-c692t-ce70dd8a652740def8595b6beafe63ba668f133250f8894775119b15456a89073</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689786/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689786/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/23805236$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Cloeckaert, Axel</contributor><creatorcontrib>Li, Yanjun</creatorcontrib><creatorcontrib>Cui, Yujun</creatorcontrib><creatorcontrib>Cui, Baizhong</creatorcontrib><creatorcontrib>Yan, Yanfeng</creatorcontrib><creatorcontrib>Yang, Xianwei</creatorcontrib><creatorcontrib>Wang, Haidong</creatorcontrib><creatorcontrib>Qi, Zhizhen</creatorcontrib><creatorcontrib>Zhang, Qingwen</creatorcontrib><creatorcontrib>Xiao, Xiao</creatorcontrib><creatorcontrib>Guo, Zhaobiao</creatorcontrib><creatorcontrib>Ma, Cong</creatorcontrib><creatorcontrib>Wang, Jing</creatorcontrib><creatorcontrib>Song, Yajun</creatorcontrib><creatorcontrib>Yang, Ruifu</creatorcontrib><title>Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.
Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.
Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.</description><subject>Acinetobacter baumannii</subject><subject>Analysis</subject><subject>Bacillus anthracis</subject><subject>Biodiversity</subject><subject>Biology</subject><subject>Capillary electrophoresis</subject><subject>Deoxyribonucleic acid</subject><subject>Disease prevention</subject><subject>DNA</subject><subject>Epidemics</subject><subject>Epidemiology</subject><subject>Evolution (Biology)</subject><subject>Forensic engineering</subject><subject>Forensic science</subject><subject>Francisella tularensis</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genetic Loci</subject><subject>Genetic Variation</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>Genotyping Techniques - methods</subject><subject>Glycerol</subject><subject>Hospitals</subject><subject>Laboratories</subject><subject>Loci</subject><subject>Medicine</subject><subject>Microorganisms</subject><subject>Multiculturalism & pluralism</subject><subject>Mutation</subject><subject>Mutation rates</subject><subject>Mycobacterium tuberculosis</subject><subject>Nitrates</subject><subject>Pathogens</subject><subject>Phylogenetics</subject><subject>Polymorphism</subject><subject>Quarantine</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Strains (organisms)</subject><subject>Studies</subject><subject>Tandem Repeat Sequences</subject><subject>Tuberculosis</subject><subject>Yersinia pestis</subject><subject>Yersinia pestis - classification</subject><subject>Yersinia pestis - genetics</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNk99r1TAUx4sobl79D0QDgujDveZHm6YvwphuuzAcbHPgU0jT09tc2qYm7dj-e1NvN25lD9KHlJPP-Z6cb3Ki6C3BK8JS8mVrB9eqetXZFlYYc57w9Fl0SDJGl5xi9nzv_yB65f0W44QJzl9GB5QJnFDGD6O7E1D94MAjW6Ib5YzKa0A_hiYHN4auVVtAgy6hC5xHpkW_wHnTGoU68L3xKACorwB9g1uobddA24-JCp0ZcMrpymhVo1NobX_fmXaDrnQFDbyOXpSq9vBmWhfRz5Pv18dny_OL0_Xx0flS84z2Sw0pLgqheELTGBdQiiRLcp6DKoGzXHEuSsIYTXApRBanaUJIlpMkTrgSGU7ZInq_0-1q6-VkmpfBQsw458GSRbTeEYVVW9k50yh3L60y8m_Auo1Urje6BikSTQuKaazKOI4FFiUXGS8KSsIiChG0vk7VhryBQgcznKpnovOd1lRyY28lC0Kp4EHg0yTg7O8hOCwb4zXUtWrBDuHcaUbSmFOeBfTDP-jT3U3URoUGTFvaUFePovIoTgURlMVj2dUTVPjC5RsdXlhpQnyW8HmWEJge7vqNGryX66vL_2cvbubsxz22AlX3lbf10Bvb-jkY70DtrPcOykeTCR77Jw9uyHFA5DQgIe3d_gU9Jj1MBPsDnLEJ3g</recordid><startdate>20130621</startdate><enddate>20130621</enddate><creator>Li, Yanjun</creator><creator>Cui, Yujun</creator><creator>Cui, Baizhong</creator><creator>Yan, Yanfeng</creator><creator>Yang, Xianwei</creator><creator>Wang, Haidong</creator><creator>Qi, Zhizhen</creator><creator>Zhang, Qingwen</creator><creator>Xiao, Xiao</creator><creator>Guo, Zhaobiao</creator><creator>Ma, Cong</creator><creator>Wang, Jing</creator><creator>Song, Yajun</creator><creator>Yang, Ruifu</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130621</creationdate><title>Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme</title><author>Li, Yanjun ; Cui, Yujun ; Cui, Baizhong ; Yan, Yanfeng ; Yang, Xianwei ; Wang, Haidong ; Qi, Zhizhen ; Zhang, Qingwen ; Xiao, Xiao ; Guo, Zhaobiao ; Ma, Cong ; Wang, Jing ; Song, Yajun ; Yang, Ruifu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-ce70dd8a652740def8595b6beafe63ba668f133250f8894775119b15456a89073</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Acinetobacter baumannii</topic><topic>Analysis</topic><topic>Bacillus anthracis</topic><topic>Biodiversity</topic><topic>Biology</topic><topic>Capillary electrophoresis</topic><topic>Deoxyribonucleic acid</topic><topic>Disease prevention</topic><topic>DNA</topic><topic>Epidemics</topic><topic>Epidemiology</topic><topic>Evolution (Biology)</topic><topic>Forensic engineering</topic><topic>Forensic science</topic><topic>Francisella tularensis</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>Genetic Loci</topic><topic>Genetic Variation</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Genotyping</topic><topic>Genotyping Techniques - methods</topic><topic>Glycerol</topic><topic>Hospitals</topic><topic>Laboratories</topic><topic>Loci</topic><topic>Medicine</topic><topic>Microorganisms</topic><topic>Multiculturalism & pluralism</topic><topic>Mutation</topic><topic>Mutation rates</topic><topic>Mycobacterium tuberculosis</topic><topic>Nitrates</topic><topic>Pathogens</topic><topic>Phylogenetics</topic><topic>Polymorphism</topic><topic>Quarantine</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>Strains (organisms)</topic><topic>Studies</topic><topic>Tandem Repeat Sequences</topic><topic>Tuberculosis</topic><topic>Yersinia pestis</topic><topic>Yersinia pestis - classification</topic><topic>Yersinia pestis - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Yanjun</creatorcontrib><creatorcontrib>Cui, Yujun</creatorcontrib><creatorcontrib>Cui, Baizhong</creatorcontrib><creatorcontrib>Yan, Yanfeng</creatorcontrib><creatorcontrib>Yang, Xianwei</creatorcontrib><creatorcontrib>Wang, Haidong</creatorcontrib><creatorcontrib>Qi, Zhizhen</creatorcontrib><creatorcontrib>Zhang, Qingwen</creatorcontrib><creatorcontrib>Xiao, Xiao</creatorcontrib><creatorcontrib>Guo, Zhaobiao</creatorcontrib><creatorcontrib>Ma, Cong</creatorcontrib><creatorcontrib>Wang, Jing</creatorcontrib><creatorcontrib>Song, Yajun</creatorcontrib><creatorcontrib>Yang, Ruifu</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Opposing Viewpoints</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing & Allied Health Database</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Meteorological & Geoastrophysical Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Agricultural Science Collection</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>Meteorological & Geoastrophysical Abstracts - Academic</collection><collection>ProQuest Engineering Collection</collection><collection>ProQuest Biological Science Collection</collection><collection>Agricultural Science Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Engineering Database</collection><collection>Nursing & Allied Health Premium</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Materials Science Collection</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Engineering Collection</collection><collection>Environmental Science Collection</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Li, Yanjun</au><au>Cui, Yujun</au><au>Cui, Baizhong</au><au>Yan, Yanfeng</au><au>Yang, Xianwei</au><au>Wang, Haidong</au><au>Qi, Zhizhen</au><au>Zhang, Qingwen</au><au>Xiao, Xiao</au><au>Guo, Zhaobiao</au><au>Ma, Cong</au><au>Wang, Jing</au><au>Song, Yajun</au><au>Yang, Ruifu</au><au>Cloeckaert, Axel</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2013-06-21</date><risdate>2013</risdate><volume>8</volume><issue>6</issue><spage>e66567</spage><epage>e66567</epage><pages>e66567-e66567</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Variable number of tandem repeats (VNTRs) that are widely distributed in the genome of Yersinia pestis proved to be useful markers for the genotyping and source-tracing of this notorious pathogen. In this study, we probed into the features of VNTRs in the Y. pestis genome and developed a simple hierarchical genotyping system based on optimized VNTR loci.
Capillary electrophoresis was used in this study for multi-locus VNTR analysis (MLVA) in 956 Y. pestis strains. The general features and genetic diversities of 88 VNTR loci in Y. pestis were analyzed with BioNumerics, and a "14+12" loci-based hierarchical genotyping system, which is compatible with single nucleotide polymorphism-based phylogenic analysis, was established.
Appropriate selection of target loci reduces the impact of homoplasies caused by the rapid mutation rates of VNTR loci. The optimized "14+12" loci are highly discriminative in genotyping and source-tracing Y. pestis for molecular epidemiological or microbial forensic investigations with less time and lower cost. An MLVA genotyping datasets of representative strains will improve future research on the source-tracing and microevolution of Y. pestis.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23805236</pmid><doi>10.1371/journal.pone.0066567</doi><tpages>e66567</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2013-06, Vol.8 (6), p.e66567-e66567 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1370366605 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Acinetobacter baumannii Analysis Bacillus anthracis Biodiversity Biology Capillary electrophoresis Deoxyribonucleic acid Disease prevention DNA Epidemics Epidemiology Evolution (Biology) Forensic engineering Forensic science Francisella tularensis Genetic aspects Genetic diversity Genetic Loci Genetic Variation Genomes Genomics Genotype Genotyping Genotyping Techniques - methods Glycerol Hospitals Laboratories Loci Medicine Microorganisms Multiculturalism & pluralism Mutation Mutation rates Mycobacterium tuberculosis Nitrates Pathogens Phylogenetics Polymorphism Quarantine Single nucleotide polymorphisms Single-nucleotide polymorphism Strains (organisms) Studies Tandem Repeat Sequences Tuberculosis Yersinia pestis Yersinia pestis - classification Yersinia pestis - genetics |
| title | Features of Variable Number of Tandem Repeats in Yersinia pestis and the Development of a Hierarchical Genotyping Scheme |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T23%3A35%3A28IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Features%20of%20Variable%20Number%20of%20Tandem%20Repeats%20in%20Yersinia%20pestis%20and%20the%20Development%20of%20a%20Hierarchical%20Genotyping%20Scheme&rft.jtitle=PloS%20one&rft.au=Li,%20Yanjun&rft.date=2013-06-21&rft.volume=8&rft.issue=6&rft.spage=e66567&rft.epage=e66567&rft.pages=e66567-e66567&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0066567&rft_dat=%3Cgale_plos_%3EA478182346%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1370366605&rft_id=info:pmid/23805236&rft_galeid=A478182346&rft_doaj_id=oai_doaj_org_article_85c2d2024af444808f6896dd218968d8&rfr_iscdi=true |