Application of DNA microarrays to study the evolutionary genomics of Yersinia pestis and Yersinia pseudotuberculosis

Abstract

Yersinia pestis, the causative agent of plague, diverged from Yersinia pseudotuberculosis, an enteric pathogen, an estimated 1500-20,000 years ago. Genetic characterization of these closely related organisms represents a useful model to study the rapid emergence of bacterial pathogens that threaten mankind. To this end, we undertook genome-wide DNA microarray analysis of 22 strains of Y. pestis and 10 strains of Y. pseudotuberculosis of diverse origin. Eleven Y. pestis DNA loci were deemed absent or highly divergent in all strains of Y. pseudotuberculosis. Four were regions of phage origin, whereas the other seven included genes encoding a vitamin B12 receptor and the insect toxin sepC. Sixteen differences were identified between Y. pestis strains, with biovar Antiqua and Mediaevalis strains showing most divergence from the arrayed CO92 Orientalis strain. Fifty-eight Y. pestis regions were specific to a limited number of Y. pseudotuberculosis strains, including the high pathogenicity island, three putative autotransporters, and several possible insecticidal toxins and hemolysins. The O-antigen gene cluster and one of two possible flagellar operons had high levels of divergence between Y. pseudotuberculosis strains. This study reports chromosomal differences between species, biovars, serotypes, and strains of Y. pestis and Y. pseudotuberculosis that may relate to the evolution of these species in their respective niches.

Figure 1

Chromosomal comparison of 22 strains of Y. pestis and 10 strains of Y. pseudotuberculosis to the sequenced CO-92 strain. This data was generated by Genespring software. Y. pestis strains are grouped according to biovar, whereas Y. pseudotuberculosis strains are grouped according to serotype. Gene status is color coded according to the Genespring software default colors with reference to the control strain (CO-92). Thus, in this comparison, yellow indicates presence, blue indicates absence or high divergence, and orange/red indicates a duplication.

Figure 2

Schematic of chromosomal comparison of 22 strains of Y. pestis detailing all of the regions of divergence from CO-92. Strains are grouped by biovar. The 102-kb unstable region (YPO1902–YPO1967) has not been included in this comparison. Gene status is color coded as in Figure 1 for ease of comparison, with yellow indicating presence, blue indicating absence, and red indicating a duplication.

Figure 3

Parsimony analysis of Y. pestis strain microarray data. Bootstrap 50% majority-rule consensus tree with bootstrap values (1000 replicates) overlying branch points. A total of 22 characters were used, of which 8 were parsimony informative and given equal weight. Six equally parsimonious trees were found (see Supplemental Data, available at www.genome.org). Strain names are followed by their biovar in parentheses.

Figure 4

Parsimony analysis of Y. pseudotuberculosis and representative Y. pestis strain microarray data. The two most parsimonious trees are shown. Of 87 variable characters, 63 were parsimony informative and equally weighted. Y. pseudotuberculosis strain names are followed by their serotype in parentheses. Three Y. pestis strains are shown, one from each of the main clades in Fig. 3 and are followed by their biovar in parentheses. Horizontal scale bar indicates number of character changes (Reanalysis omitting all characters pertaining to the O-antigen locus gives a similar result, see Supplemental Data).