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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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The microevolution scenario of Orientalis strains based on the gain-and-loss of DFRs.Orientalis strains evolved from genomovar07 Antiqua strains of Focus E, by acquiring DFR13, and then evolved as different genomovars by losing certain DFRs. A virtual genomovarX was proposed to illustrate the step-by-step reductionism evolution.
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pone-0002166-g003: The microevolution scenario of Orientalis strains based on the gain-and-loss of DFRs.Orientalis strains evolved from genomovar07 Antiqua strains of Focus E, by acquiring DFR13, and then evolved as different genomovars by losing certain DFRs. A virtual genomovarX was proposed to illustrate the step-by-step reductionism evolution.

Mentions: By Comparing DFR profiles of the 6 sequenced Orientalis strains and the tested Orientalis strains in China, we deduced the microevolutionary pattern of Orientalis strains based reductionism (Figure 3). We also proposed a virtual genomovarX as the missing link of genomovar09 to MG05-1020 and IP275. Interestingly, MG05-1020 and IP275 were both isolated in Madagascar. It is hopeful that we can find this genomovar in Madagascar or elsewhere, which will be of great help for better understanding the spreading of the third plague pandemics.


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 microevolution scenario of Orientalis strains based on the gain-and-loss of DFRs.Orientalis strains evolved from genomovar07 Antiqua strains of Focus E, by acquiring DFR13, and then evolved as different genomovars by losing certain DFRs. A virtual genomovarX was proposed to illustrate the step-by-step reductionism evolution.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2367435&req=5

pone-0002166-g003: The microevolution scenario of Orientalis strains based on the gain-and-loss of DFRs.Orientalis strains evolved from genomovar07 Antiqua strains of Focus E, by acquiring DFR13, and then evolved as different genomovars by losing certain DFRs. A virtual genomovarX was proposed to illustrate the step-by-step reductionism evolution.
Mentions: By Comparing DFR profiles of the 6 sequenced Orientalis strains and the tested Orientalis strains in China, we deduced the microevolutionary pattern of Orientalis strains based reductionism (Figure 3). We also proposed a virtual genomovarX as the missing link of genomovar09 to MG05-1020 and IP275. Interestingly, MG05-1020 and IP275 were both isolated in Madagascar. It is hopeful that we can find this genomovar in Madagascar or elsewhere, which will be of great help for better understanding the spreading of the third plague pandemics.

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