Genome rearrangements of completely sequenced strains of Yersinia pestis

Abstract

Yersinia pestis has caused three worldwide plagues in human history that have led to innumerable deaths. We have completely sequenced the genomes of two strains (D106004 and D182038) of Y. pestis isolated from Yunnan Province of China. The most striking finding of our study is that large amounts of genome rearrangement events exist between the genomes of two Yunnan strains despite being isolated from two foci only 50 kilometers apart. When we compared the genome sequences of the Yunnan strains with six strains (CO92, KIM, 91001, Antiqua, Nepal516, and Pestoides F) of Y. pestis sequenced previously, we found that the genomes of Y. pestis were divided into 61 relatively independent segments. Pairwise comparisons of all 61 segments among eight strains showed that the Yunnan strains were most closely related to strain CO92. We concluded that Y. pestis genomes consist of segments that can change their positions and directions within the genomes caused by genome rearrangements, and our study confirmed the inference that the third plague pandemic originated in Yunnan since the genome sequences of Yunnan strains were closest to the strain CO92 isolated from the United States.

FIG. 1.

Method used for gap sequences assignment. Rectangle indicates the genome plate, and double black line indicates the gap sequence. The number in rectangle indicates the serial number of genome plate and the name of Y. pestis strains are placed forward. Two genome plates that have a high degree of similarity are shown by rectangles with the same color. Straight arrow indicates the direction of genome plate. Gap sequences linked by the dotted line are 100% identity between CO92 and KIM. The overlapped region is marked by a cross-slash.

FIG. 2.

Phylogenetic relationships between eight Y. pestis genomes inferred by UPGMA using BioNumerics v4.0 software based on the average sequence identity of the genome plates that was listed in Table 2.

FIG. 3.

Arrangement patterns of genome plates of each chromosome from eight completely sequenced Y. pestis strains. Each chromosome has been laid out horizontally, and the origin of replication is located in the left-most. Each rectangle indicates a plate (scale is not shown), and the number in the rectangle indicates the serial number of plate of strain CO92, which acts as reference strain. For example, the number “1” in the rectangle represents the plate 1 of CO92. Plates that are inverted relative to strain CO92 are shifted below a genome's center axis shown by a strikethrough line.

FIG. 4.

Phylogenetic relationships among eight Y. pestis genomes inferred from the breakpoint distance matrix using BioNumerics v4.0 software.