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Different Region Analysis for Genotyping Yersinia pestis Isolates from China

BACKGROUND: 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 microe...

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Autores principales: 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
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367435/
https://www.ncbi.nlm.nih.gov/pubmed/18478120
http://dx.doi.org/10.1371/journal.pone.0002166
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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_facet 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 Li, Yanjun
collection PubMed
description BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.
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spelling pubmed-23674352008-05-14 Different Region Analysis for Genotyping Yersinia pestis Isolates from China 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 PLoS One Research Article BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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. Public Library of Science 2008-05-14 /pmc/articles/PMC2367435/ /pubmed/18478120 http://dx.doi.org/10.1371/journal.pone.0002166 Text en Li 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
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
Different Region Analysis for Genotyping Yersinia pestis Isolates from China
title Different Region Analysis for Genotyping Yersinia pestis Isolates from China
title_full Different Region Analysis for Genotyping Yersinia pestis Isolates from China
title_fullStr Different Region Analysis for Genotyping Yersinia pestis Isolates from China
title_full_unstemmed Different Region Analysis for Genotyping Yersinia pestis Isolates from China
title_short Different Region Analysis for Genotyping Yersinia pestis Isolates from China
title_sort different region analysis for genotyping yersinia pestis isolates from china
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367435/
https://www.ncbi.nlm.nih.gov/pubmed/18478120
http://dx.doi.org/10.1371/journal.pone.0002166
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