Results: 3

1.
Figure 1

Figure 1. Dendrogram based on the 25 VNTR loci.. From: Genotyping and Phylogenetic Analysis of Yersinia pestis by MLVA: Insights into the Worldwide Expansion of Central Asia Plague Foci.

Clustering analysis was done using the categorical distance coefficient and the Neighbor-Joining clustering method. The Y. pseudotuberculosis representative (blue dot) was chosen as outgroup to root the tree. Red dot, Angola isolate. Red arrows, Y. pestis subsp. pestis isolates with exceptional genotypes. The branches color code is as indicated in legends from Figure 2 and Figures S1, S2, S3.

Yanjun Li, et al. PLoS One. 2009;4(6):e6000.
2.
Figure 3

Figure 3. The close relationship among the foci in China and Central Asia.. From: Genotyping and Phylogenetic Analysis of Yersinia pestis by MLVA: Insights into the Worldwide Expansion of Central Asia Plague Foci.

The color code reflects some significant genetic relationships as indicated by MLVA clustering. Orange, the bv. Microtus investigated here, including subspecies caucasica (4), ulegeica (BP), and the most closely related hissarica (34) altaica (36), xilingolensis (L) and qinghaiensis (M). Red foci, Y. pestis subsp. pestis biovar Medievalis. Purple foci, bv. Orientalis foci. Other colors, different varieties of Y. pestis subsp. pestis bv. Intermedium and Antiqua strains. The more detailed composition of each focus is presented in Figures 2 and Figures S1, S2, S3.

Yanjun Li, et al. PLoS One. 2009;4(6):e6000.
3.
Figure 2

Figure 2. The Y. pestis bv. Microtus isolates, dendrogram based on the 25 VNTR loci.. From: Genotyping and Phylogenetic Analysis of Yersinia pestis by MLVA: Insights into the Worldwide Expansion of Central Asia Plague Foci.

From left to right, the columns designate the strain Id, focus of origin, biovar (bv.), subspecies (subsp.), geographic origin (location), host or vector, genomovar based on DFR analysis [28]. The biovar or subspecies designation follows current usage, with inconsistencies in terms of a future nomenclature since “biovar Microtus” contains a number of “subspecies”. The ‘genomovar+DFRX’ and ‘genomovar-DFRX’ respectively indicates that the strain is similar to this genomovar except for DFRX which was present or absent. The branches color code reflects the focus of origin. Five atypical isolates corresponding to essentially two strains fall into two very long and loosely connected branches (red rectangles). At least three were derived from patients.

Yanjun Li, et al. PLoS One. 2009;4(6):e6000.

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