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Different region analysis for genotyping Yersinia pestis isolates from China.

Li Y, Dai E, Cui Y, Li M, Zhang Y, Wu M, Zhou D, Guo Z, Dai X, Cui B, Qi Z, Wang Z, Wang H, Dong X, Song Z, Zhai J, Song Y, Yang R - PLoS ONE (2008)

Bottom Line: In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China.

ABSTRACT

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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Related in: MedlinePlus

The distribution Major genomovars in natural plague foci of China.There are 15 plague foci in China. Focus A: Marmota caudate Plague Focus of the Pamirs Plateau; Focus B: Marmota baibacina-Spermophilus undulates Plague Focus of the Tianshan Mountains; Focus C: Marmota himalayana Plague Focus of the Qinghai-Gansu-Tibet Grassland; Focus D: Marmota himalayana Plague Focus of the Qilian Mountain; Focus E: Apodemus chevrieri-Eothenomys miletus Plague Focus of the highland of Northwestern Yunnan Province; Focus F: Rattus flavipectus Plague Focus of the Yunnan-Guangdong-Fujian provinces; Focus G: Marmota himalayana Plague Focus of the Gangdisi Mountains; Focus H: Spermophilus dauricus Plague Focus of the Song-Liao Plain; Focus I: Meriones unguiculatus Plague Focus of the Inner Mogolian Plateau; Focus J: Spermophilus dauricus alaschanicus Plague Focus of the Loess Plateau in Gansu and Ningxia provinces; Focus K: Marmota himalayana Plague Focus of the Kunlun Mountains; Focus L: Microtus brandti Plague Focus of the Xilin Gol Grassland; Focus M: Microtus fuscus Plague Focus of the Qinghai-Tibet Plateau; Focus N: Marmota sibirica Plague Focus of the Hulun Buir Plateau of Inner Mongonia. Focus O: Rhombomys opimus Plague Focus of the Junggar Basin of Xinjiang. B1, B2, B3 and B4 are subfoci of Focus B, K1 and K2 are subfoci of Focus K. Focus N is a silent plague focus without strains available for this study.
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pone-0002166-g002: The distribution Major genomovars in natural plague foci of China.There are 15 plague foci in China. Focus A: Marmota caudate Plague Focus of the Pamirs Plateau; Focus B: Marmota baibacina-Spermophilus undulates Plague Focus of the Tianshan Mountains; Focus C: Marmota himalayana Plague Focus of the Qinghai-Gansu-Tibet Grassland; Focus D: Marmota himalayana Plague Focus of the Qilian Mountain; Focus E: Apodemus chevrieri-Eothenomys miletus Plague Focus of the highland of Northwestern Yunnan Province; Focus F: Rattus flavipectus Plague Focus of the Yunnan-Guangdong-Fujian provinces; Focus G: Marmota himalayana Plague Focus of the Gangdisi Mountains; Focus H: Spermophilus dauricus Plague Focus of the Song-Liao Plain; Focus I: Meriones unguiculatus Plague Focus of the Inner Mogolian Plateau; Focus J: Spermophilus dauricus alaschanicus Plague Focus of the Loess Plateau in Gansu and Ningxia provinces; Focus K: Marmota himalayana Plague Focus of the Kunlun Mountains; Focus L: Microtus brandti Plague Focus of the Xilin Gol Grassland; Focus M: Microtus fuscus Plague Focus of the Qinghai-Tibet Plateau; Focus N: Marmota sibirica Plague Focus of the Hulun Buir Plateau of Inner Mongonia. Focus O: Rhombomys opimus Plague Focus of the Junggar Basin of Xinjiang. B1, B2, B3 and B4 are subfoci of Focus B, K1 and K2 are subfoci of Focus K. Focus N is a silent plague focus without strains available for this study.

Mentions: Notably, Major and Minor genomovars make sense only by combining with the concept of natural plague foci. The Major genomovar in one plague focus might be the Minor one in the other. For example, genomovar09 was the Major genomovar in Focus F, but the Minor one in Focus E. The distribution of the Major genomovar(s) in each plague focus of China was presented in Figure 2. Normally, each focus has its own characteristic Major genomovar(s). However, there were still some strains from several foci indistinguishable by the DFR profiles. For instance, strains from Foci G and H shared genomovar10, Foci K2 and I genomovar11 and Foci L and M genomovar14. This suggested the close relationship between the strains in the corresponding foci. These strains might be recently spread from one focus to another and there was no enough time for DFR varieties to accumulate. We might need other methods with higher resolution to differentiate strains from these foci. Actually, based on CRISPR(clustered regularly interspaced short palindromic repeat) and MLVA(multiple-locus VNTR analysis) analysis we are able to differentiate strains from Foci L and M, as well as K2 and I.


Different region analysis for genotyping Yersinia pestis isolates from China.

Li Y, Dai E, Cui Y, Li M, Zhang Y, Wu M, Zhou D, Guo Z, Dai X, Cui B, Qi Z, Wang Z, Wang H, Dong X, Song Z, Zhai J, Song Y, Yang R - PLoS ONE (2008)

The distribution Major genomovars in natural plague foci of China.There are 15 plague foci in China. Focus A: Marmota caudate Plague Focus of the Pamirs Plateau; Focus B: Marmota baibacina-Spermophilus undulates Plague Focus of the Tianshan Mountains; Focus C: Marmota himalayana Plague Focus of the Qinghai-Gansu-Tibet Grassland; Focus D: Marmota himalayana Plague Focus of the Qilian Mountain; Focus E: Apodemus chevrieri-Eothenomys miletus Plague Focus of the highland of Northwestern Yunnan Province; Focus F: Rattus flavipectus Plague Focus of the Yunnan-Guangdong-Fujian provinces; Focus G: Marmota himalayana Plague Focus of the Gangdisi Mountains; Focus H: Spermophilus dauricus Plague Focus of the Song-Liao Plain; Focus I: Meriones unguiculatus Plague Focus of the Inner Mogolian Plateau; Focus J: Spermophilus dauricus alaschanicus Plague Focus of the Loess Plateau in Gansu and Ningxia provinces; Focus K: Marmota himalayana Plague Focus of the Kunlun Mountains; Focus L: Microtus brandti Plague Focus of the Xilin Gol Grassland; Focus M: Microtus fuscus Plague Focus of the Qinghai-Tibet Plateau; Focus N: Marmota sibirica Plague Focus of the Hulun Buir Plateau of Inner Mongonia. Focus O: Rhombomys opimus Plague Focus of the Junggar Basin of Xinjiang. B1, B2, B3 and B4 are subfoci of Focus B, K1 and K2 are subfoci of Focus K. Focus N is a silent plague focus without strains available for this study.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2367435&req=5

pone-0002166-g002: The distribution Major genomovars in natural plague foci of China.There are 15 plague foci in China. Focus A: Marmota caudate Plague Focus of the Pamirs Plateau; Focus B: Marmota baibacina-Spermophilus undulates Plague Focus of the Tianshan Mountains; Focus C: Marmota himalayana Plague Focus of the Qinghai-Gansu-Tibet Grassland; Focus D: Marmota himalayana Plague Focus of the Qilian Mountain; Focus E: Apodemus chevrieri-Eothenomys miletus Plague Focus of the highland of Northwestern Yunnan Province; Focus F: Rattus flavipectus Plague Focus of the Yunnan-Guangdong-Fujian provinces; Focus G: Marmota himalayana Plague Focus of the Gangdisi Mountains; Focus H: Spermophilus dauricus Plague Focus of the Song-Liao Plain; Focus I: Meriones unguiculatus Plague Focus of the Inner Mogolian Plateau; Focus J: Spermophilus dauricus alaschanicus Plague Focus of the Loess Plateau in Gansu and Ningxia provinces; Focus K: Marmota himalayana Plague Focus of the Kunlun Mountains; Focus L: Microtus brandti Plague Focus of the Xilin Gol Grassland; Focus M: Microtus fuscus Plague Focus of the Qinghai-Tibet Plateau; Focus N: Marmota sibirica Plague Focus of the Hulun Buir Plateau of Inner Mongonia. Focus O: Rhombomys opimus Plague Focus of the Junggar Basin of Xinjiang. B1, B2, B3 and B4 are subfoci of Focus B, K1 and K2 are subfoci of Focus K. Focus N is a silent plague focus without strains available for this study.
Mentions: Notably, Major and Minor genomovars make sense only by combining with the concept of natural plague foci. The Major genomovar in one plague focus might be the Minor one in the other. For example, genomovar09 was the Major genomovar in Focus F, but the Minor one in Focus E. The distribution of the Major genomovar(s) in each plague focus of China was presented in Figure 2. Normally, each focus has its own characteristic Major genomovar(s). However, there were still some strains from several foci indistinguishable by the DFR profiles. For instance, strains from Foci G and H shared genomovar10, Foci K2 and I genomovar11 and Foci L and M genomovar14. This suggested the close relationship between the strains in the corresponding foci. These strains might be recently spread from one focus to another and there was no enough time for DFR varieties to accumulate. We might need other methods with higher resolution to differentiate strains from these foci. Actually, based on CRISPR(clustered regularly interspaced short palindromic repeat) and MLVA(multiple-locus VNTR analysis) analysis we are able to differentiate strains from Foci L and M, as well as K2 and I.

Bottom Line: In silico DFR profiling of the completed or draft genomes shed lights on the evolutionary scenario of Y. pestis from Y. pseudotuberculosis.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.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Beijing, China.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus