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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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Neighbor-Joining Dendrogram of the 32 genomovars based on DFR profiles.The black and grey squares indicated the presence and absence of the corresponding DFRs, respectively. There are three clusters (A, B and C) for most of the genomovars.
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pone-0002166-g001: Neighbor-Joining Dendrogram of the 32 genomovars based on DFR profiles.The black and grey squares indicated the presence and absence of the corresponding DFRs, respectively. There are three clusters (A, B and C) for most of the genomovars.

Mentions: The 909 strains were grouped into 32 genomovars. The DFR profiles and Neighbor-Joining dendrogram of the 32 genomovars were shown in Figure 1. Most of the genomovars were clustered into 3 clusters, namely A, B and C, except for genomovar01b and genomovar04. All Orientalis strains (205 strains in 3 genomovars) were grouped together in cluster A, all Medievalis strains (122 strains in 8 genomovars) in cluster B and Microtus strains (66 strains in 3 genomovars) in cluster C. This clearly illustrated the close relationship of strains of the same biovar in China. However, Antiqua strains (516 strains in 18 genomovars) were distributed in different branches of all 3 clusters, revealing considerable genome diversities of Antiqua strains. This is not the first time to find this fact. SNPs(Single nucleotide polymorphisms) analysis has identified 2 different molecular groups of Antiqua strains on 2 evolutionary lineages of Y. pestis (1.ANT and 2.ANT), which fitted into Orientalis and Medievalis branches, respectively [3]. CRIPSR analysis also identified 2 clusters of Antiqua strains (Asian and African)[22]


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)

Neighbor-Joining Dendrogram of the 32 genomovars based on DFR profiles.The black and grey squares indicated the presence and absence of the corresponding DFRs, respectively. There are three clusters (A, B and C) for most of the genomovars.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0002166-g001: Neighbor-Joining Dendrogram of the 32 genomovars based on DFR profiles.The black and grey squares indicated the presence and absence of the corresponding DFRs, respectively. There are three clusters (A, B and C) for most of the genomovars.
Mentions: The 909 strains were grouped into 32 genomovars. The DFR profiles and Neighbor-Joining dendrogram of the 32 genomovars were shown in Figure 1. Most of the genomovars were clustered into 3 clusters, namely A, B and C, except for genomovar01b and genomovar04. All Orientalis strains (205 strains in 3 genomovars) were grouped together in cluster A, all Medievalis strains (122 strains in 8 genomovars) in cluster B and Microtus strains (66 strains in 3 genomovars) in cluster C. This clearly illustrated the close relationship of strains of the same biovar in China. However, Antiqua strains (516 strains in 18 genomovars) were distributed in different branches of all 3 clusters, revealing considerable genome diversities of Antiqua strains. This is not the first time to find this fact. SNPs(Single nucleotide polymorphisms) analysis has identified 2 different molecular groups of Antiqua strains on 2 evolutionary lineages of Y. pestis (1.ANT and 2.ANT), which fitted into Orientalis and Medievalis branches, respectively [3]. CRIPSR analysis also identified 2 clusters of Antiqua strains (Asian and African)[22]

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