Different region analysis for genotyping Yersinia pestis isolates from China
DFR (different region) analysis has been developed for typing Yesinia pestis in our previous study, and in this study, we extended this method by using 23 DFRs to investigate 909 Chinese Y. pestis strains for validating DFR-based genotyping method and better understanding adaptive microevolution of...
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| creator | Li, Yanjun Dai, Erhei Cui, Yujun Li, Min Zhang, Yujiang Wu, Mingshou Zhou, Dongsheng Guo, Zhaobiao Dai, Xiang Cui, Baizhong Qi, Zhizhen Wang, Zuyun Wang, Hu Dong, Xingqi Song, Zhizhong Zhai, Junhui Song, Yajun Yang, Ruifu |
| description | DFR (different region) analysis has been developed for typing Yesinia pestis in our previous study, and in this study, we extended this method by using 23 DFRs to investigate 909 Chinese Y. pestis strains for validating DFR-based genotyping method and better understanding adaptive microevolution of Y. pestis.
On the basis of PCR and Bionumerics data analysis, 909 Y. pestis strains were genotyped into 32 genomovars according to their DFR profiles. New terms, Major genomovar and Minor genomovar, were coined for illustrating evolutionary relationship between Y. pestis strains from different plague foci and different hosts. In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis. Notably, several sequenced Y. pestis strains share the same DFR profiles with Chinese strains, providing data for revealing the global plague foci expansion.
Distribution of Y. pestis genomovars is plague focus-specific. Microevolution of biovar Orientalis was deduced according to DFR profiles. DFR analysis turns to be an efficient and inexpensive method to portrait the genome plasticity of Y. pestis based on horizontal gene transfer (HGT). DFR analysis can also be used as a tool in comparative and evolutionary genomic research for other bacteria with similar genome plasticity. |
| doi_str_mv | 10.1371/journal.pone.0002166 |
| format | Article |
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On the basis of PCR and Bionumerics data analysis, 909 Y. pestis strains were genotyped into 32 genomovars according to their DFR profiles. New terms, Major genomovar and Minor genomovar, were coined for illustrating evolutionary relationship between Y. pestis strains from different plague foci and different hosts. In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis. Notably, several sequenced Y. pestis strains share the same DFR profiles with Chinese strains, providing data for revealing the global plague foci expansion.
Distribution of Y. pestis genomovars is plague focus-specific. Microevolution of biovar Orientalis was deduced according to DFR profiles. DFR analysis turns to be an efficient and inexpensive method to portrait the genome plasticity of Y. pestis based on horizontal gene transfer (HGT). DFR analysis can also be used as a tool in comparative and evolutionary genomic research for other bacteria with similar genome plasticity.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0002166</identifier><identifier>PMID: 18478120</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Antimicrobial agents ; Bacteria ; Base Sequence ; China ; Data analysis ; Data processing ; Disease control ; Disease prevention ; DNA Primers ; Drug resistance ; Epidemiology ; Evolution ; Evolution (Biology) ; Gene transfer ; Genes, Bacterial ; Genetics and Genomics/Comparative Genomics ; Genomes ; Genomics ; Genotype ; Genotyping ; Glycerol ; Hypotheses ; Information management ; Laboratories ; Microbiology/Microbial Evolution and Genomics ; Molecular Biology/Molecular Evolution ; Nitrates ; Pasteurella ; Pathogens ; Pathology/Forensic Pathology ; Phylogenetics ; Plague ; Plastic properties ; Plasticity ; Polymerase Chain Reaction ; Pseudotuberculosis ; Public health ; Public Health and Epidemiology/Infectious Diseases ; Rhombomys opimus ; Strains (organisms) ; Yersinia pestis ; Yersinia pestis - genetics ; Yersinia pseudotuberculosis ; Yersinia pseudotuberculosis - genetics ; Zoonoses</subject><ispartof>PloS one, 2008-05, Vol.3 (5), p.e2166-e2166</ispartof><rights>COPYRIGHT 2008 Public Library of Science</rights><rights>2008 Li et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (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>Li et al. 2008</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c662t-60978d13e31d7cff04c77485bb72b132bc0b28e221082172f4b0e3fbc058face3</citedby><cites>FETCH-LOGICAL-c662t-60978d13e31d7cff04c77485bb72b132bc0b28e221082172f4b0e3fbc058face3</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/PMC2367435/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367435/$$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/18478120$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Hofreiter, Michael</contributor><creatorcontrib>Li, Yanjun</creatorcontrib><creatorcontrib>Dai, Erhei</creatorcontrib><creatorcontrib>Cui, Yujun</creatorcontrib><creatorcontrib>Li, Min</creatorcontrib><creatorcontrib>Zhang, Yujiang</creatorcontrib><creatorcontrib>Wu, Mingshou</creatorcontrib><creatorcontrib>Zhou, Dongsheng</creatorcontrib><creatorcontrib>Guo, Zhaobiao</creatorcontrib><creatorcontrib>Dai, Xiang</creatorcontrib><creatorcontrib>Cui, Baizhong</creatorcontrib><creatorcontrib>Qi, Zhizhen</creatorcontrib><creatorcontrib>Wang, Zuyun</creatorcontrib><creatorcontrib>Wang, Hu</creatorcontrib><creatorcontrib>Dong, Xingqi</creatorcontrib><creatorcontrib>Song, Zhizhong</creatorcontrib><creatorcontrib>Zhai, Junhui</creatorcontrib><creatorcontrib>Song, Yajun</creatorcontrib><creatorcontrib>Yang, Ruifu</creatorcontrib><title>Different region analysis for genotyping Yersinia pestis isolates from China</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>DFR (different region) analysis has been developed for typing Yesinia pestis in our previous study, and in this study, we extended this method by using 23 DFRs to investigate 909 Chinese Y. pestis strains for validating DFR-based genotyping method and better understanding adaptive microevolution of Y. pestis.
On the basis of PCR and Bionumerics data analysis, 909 Y. pestis strains were genotyped into 32 genomovars according to their DFR profiles. New terms, Major genomovar and Minor genomovar, were coined for illustrating evolutionary relationship between Y. pestis strains from different plague foci and different hosts. In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis. Notably, several sequenced Y. pestis strains share the same DFR profiles with Chinese strains, providing data for revealing the global plague foci expansion.
Distribution of Y. pestis genomovars is plague focus-specific. Microevolution of biovar Orientalis was deduced according to DFR profiles. DFR analysis turns to be an efficient and inexpensive method to portrait the genome plasticity of Y. pestis based on horizontal gene transfer (HGT). DFR analysis can also be used as a tool in comparative and evolutionary genomic research for other bacteria with similar genome plasticity.</description><subject>Analysis</subject><subject>Antimicrobial agents</subject><subject>Bacteria</subject><subject>Base Sequence</subject><subject>China</subject><subject>Data analysis</subject><subject>Data processing</subject><subject>Disease control</subject><subject>Disease prevention</subject><subject>DNA Primers</subject><subject>Drug resistance</subject><subject>Epidemiology</subject><subject>Evolution</subject><subject>Evolution (Biology)</subject><subject>Gene transfer</subject><subject>Genes, Bacterial</subject><subject>Genetics and Genomics/Comparative Genomics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Genotyping</subject><subject>Glycerol</subject><subject>Hypotheses</subject><subject>Information management</subject><subject>Laboratories</subject><subject>Microbiology/Microbial Evolution and Genomics</subject><subject>Molecular Biology/Molecular Evolution</subject><subject>Nitrates</subject><subject>Pasteurella</subject><subject>Pathogens</subject><subject>Pathology/Forensic Pathology</subject><subject>Phylogenetics</subject><subject>Plague</subject><subject>Plastic properties</subject><subject>Plasticity</subject><subject>Polymerase Chain Reaction</subject><subject>Pseudotuberculosis</subject><subject>Public health</subject><subject>Public Health and Epidemiology/Infectious Diseases</subject><subject>Rhombomys opimus</subject><subject>Strains (organisms)</subject><subject>Yersinia pestis</subject><subject>Yersinia pestis - genetics</subject><subject>Yersinia pseudotuberculosis</subject><subject>Yersinia pseudotuberculosis - genetics</subject><subject>Zoonoses</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2008</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>eNqNkl2LEzEUhgdR3HX1H4gOCAtetJ4kM0l6Iyz1q1BY8Au8Cpn0ZJoyTbrJjNh_b3Y7aiteSC4STp7znuTlLYqnBKaECfJqE4bodTfdBY9TAKCE83vFOZkxOuEU2P2j81nxKKUNQM0k5w-LMyIrIQmF82L5xlmLEX1fRmxd8KXOovvkUmlDLFv0od_vnG_LbxiT806XO0x9vnYpdLrHzMWwLedr5_Xj4oHVXcIn435RfHn39vP8w2R5_X4xv1pODOe0n3CYCbkiDBlZCWMtVEaIStZNI2hDGG0MNFQipQQkJYLaqgFkNpdrabVBdlE8P-juupDUaERShBFKpSD1LBOLA7EKeqN20W113KugnborhNgqHXtnOlSgOUiphbVGVobUmmHVcI7QMEvpndbrcdrQbHFlsldRdyeipzferVUbvivKuKhYnQUuR4EYbobsntq6ZLDrtMcwJCVAMAACGXzxF_jvv00PVKvz8523IU81ea1w60xOg3W5flUJymvgjOeGlycNmenxR9_qISW1-PTx_9nrr6fs5RG7Rt316xyKoc8xSqdgdQBNDClFtL_NI6Buw_zrn-o2zGoMc257dmz8n6Yxvewn_jbvzg</recordid><startdate>20080514</startdate><enddate>20080514</enddate><creator>Li, 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region analysis for genotyping Yersinia pestis isolates from China</title><author>Li, Yanjun ; Dai, Erhei ; Cui, Yujun ; Li, Min ; Zhang, Yujiang ; Wu, Mingshou ; Zhou, Dongsheng ; Guo, Zhaobiao ; Dai, Xiang ; Cui, Baizhong ; Qi, Zhizhen ; Wang, Zuyun ; Wang, Hu ; Dong, Xingqi ; Song, Zhizhong ; Zhai, Junhui ; Song, Yajun ; Yang, Ruifu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c662t-60978d13e31d7cff04c77485bb72b132bc0b28e221082172f4b0e3fbc058face3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2008</creationdate><topic>Analysis</topic><topic>Antimicrobial agents</topic><topic>Bacteria</topic><topic>Base Sequence</topic><topic>China</topic><topic>Data analysis</topic><topic>Data processing</topic><topic>Disease control</topic><topic>Disease prevention</topic><topic>DNA Primers</topic><topic>Drug resistance</topic><topic>Epidemiology</topic><topic>Evolution</topic><topic>Evolution (Biology)</topic><topic>Gene transfer</topic><topic>Genes, Bacterial</topic><topic>Genetics and Genomics/Comparative Genomics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Genotyping</topic><topic>Glycerol</topic><topic>Hypotheses</topic><topic>Information management</topic><topic>Laboratories</topic><topic>Microbiology/Microbial Evolution and Genomics</topic><topic>Molecular Biology/Molecular Evolution</topic><topic>Nitrates</topic><topic>Pasteurella</topic><topic>Pathogens</topic><topic>Pathology/Forensic Pathology</topic><topic>Phylogenetics</topic><topic>Plague</topic><topic>Plastic properties</topic><topic>Plasticity</topic><topic>Polymerase Chain Reaction</topic><topic>Pseudotuberculosis</topic><topic>Public health</topic><topic>Public Health and Epidemiology/Infectious Diseases</topic><topic>Rhombomys opimus</topic><topic>Strains (organisms)</topic><topic>Yersinia pestis</topic><topic>Yersinia pestis - genetics</topic><topic>Yersinia pseudotuberculosis</topic><topic>Yersinia pseudotuberculosis - genetics</topic><topic>Zoonoses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Li, Yanjun</creatorcontrib><creatorcontrib>Dai, Erhei</creatorcontrib><creatorcontrib>Cui, Yujun</creatorcontrib><creatorcontrib>Li, Min</creatorcontrib><creatorcontrib>Zhang, Yujiang</creatorcontrib><creatorcontrib>Wu, Mingshou</creatorcontrib><creatorcontrib>Zhou, Dongsheng</creatorcontrib><creatorcontrib>Guo, Zhaobiao</creatorcontrib><creatorcontrib>Dai, Xiang</creatorcontrib><creatorcontrib>Cui, Baizhong</creatorcontrib><creatorcontrib>Qi, Zhizhen</creatorcontrib><creatorcontrib>Wang, Zuyun</creatorcontrib><creatorcontrib>Wang, Hu</creatorcontrib><creatorcontrib>Dong, Xingqi</creatorcontrib><creatorcontrib>Song, Zhizhong</creatorcontrib><creatorcontrib>Zhai, Junhui</creatorcontrib><creatorcontrib>Song, Yajun</creatorcontrib><creatorcontrib>Yang, 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Xingqi</au><au>Song, Zhizhong</au><au>Zhai, Junhui</au><au>Song, Yajun</au><au>Yang, Ruifu</au><au>Hofreiter, Michael</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Different region analysis for genotyping Yersinia pestis isolates from China</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2008-05-14</date><risdate>2008</risdate><volume>3</volume><issue>5</issue><spage>e2166</spage><epage>e2166</epage><pages>e2166-e2166</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>DFR (different region) analysis has been developed for typing Yesinia pestis in our previous study, and in this study, we extended this method by using 23 DFRs to investigate 909 Chinese Y. pestis strains for validating DFR-based genotyping method and better understanding adaptive microevolution of Y. pestis.
On the basis of PCR and Bionumerics data analysis, 909 Y. pestis strains were genotyped into 32 genomovars according to their DFR profiles. New terms, Major genomovar and Minor genomovar, were coined for illustrating evolutionary relationship between Y. pestis strains from different plague foci and different hosts. In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis. Notably, several sequenced Y. pestis strains share the same DFR profiles with Chinese strains, providing data for revealing the global plague foci expansion.
Distribution of Y. pestis genomovars is plague focus-specific. Microevolution of biovar Orientalis was deduced according to DFR profiles. DFR analysis turns to be an efficient and inexpensive method to portrait the genome plasticity of Y. pestis based on horizontal gene transfer (HGT). DFR analysis can also be used as a tool in comparative and evolutionary genomic research for other bacteria with similar genome plasticity.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>18478120</pmid><doi>10.1371/journal.pone.0002166</doi><tpages>e2166</tpages><oa>free_for_read</oa></addata></record> |
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| recordid | cdi_plos_journals_1312287159 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Antimicrobial agents Bacteria Base Sequence China Data analysis Data processing Disease control Disease prevention DNA Primers Drug resistance Epidemiology Evolution Evolution (Biology) Gene transfer Genes, Bacterial Genetics and Genomics/Comparative Genomics Genomes Genomics Genotype Genotyping Glycerol Hypotheses Information management Laboratories Microbiology/Microbial Evolution and Genomics Molecular Biology/Molecular Evolution Nitrates Pasteurella Pathogens Pathology/Forensic Pathology Phylogenetics Plague Plastic properties Plasticity Polymerase Chain Reaction Pseudotuberculosis Public health Public Health and Epidemiology/Infectious Diseases Rhombomys opimus Strains (organisms) Yersinia pestis Yersinia pestis - genetics Yersinia pseudotuberculosis Yersinia pseudotuberculosis - genetics Zoonoses |
| title | Different region analysis for genotyping Yersinia pestis isolates from China |
| 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%3A43%3A04IST&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=Different%20region%20analysis%20for%20genotyping%20Yersinia%20pestis%20isolates%20from%20China&rft.jtitle=PloS%20one&rft.au=Li,%20Yanjun&rft.date=2008-05-14&rft.volume=3&rft.issue=5&rft.spage=e2166&rft.epage=e2166&rft.pages=e2166-e2166&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0002166&rft_dat=%3Cgale_plos_%3EA472650636%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=1312287159&rft_id=info:pmid/18478120&rft_galeid=A472650636&rft_doaj_id=oai_doaj_org_article_0a6088a7ffc84c15a3e4b66e0b3f2259&rfr_iscdi=true |