Comparative And Evolutionary Genomic Analysis Of Yersinia Pestis

Y. pestis is the causative agent of plague and it caused three human plague pandemics in the history. Comparative and evolutionary genomics of Y. pestis were extensively investigated in our present work. Understanding the genomic variability and the adaptive evolution of Y. pestis from the points of genomic views will contribute greatly to plague detection, identification, control and prevention.Development of Y. pestis whole-genome DNA microarrays for comparative genomic analysisThe non-redundant mixed whole-genome DNA microarrays were developed based on the genomic sequences of Y. pestis CO92 and 91001 and were used as a tool to perform the comparative genomic analysis. A total number of 4005 Y. pestis genes was amplified by PCR and printed in duplicate onto glass slides. Fluorescently labelled probes were prepared by priming of genomic DNAs with random hexamers and extension with Klenow. Labelled DNAs were hybridized to the microarrays by methods of two-fluorescence comparative hybridization. Furthermore, to establish the benchmark metrics of this technique, three sets of two-fluorescence hybridizations were performed to examine the absence/presence of each gene. It was found that the results agree with those derived from the in silico genomic comparison.Parallel microevolution of Y. pestis genomeThe DNA microarray in conjunction with PCR was used as a tool to perform the comparative genomic analysis of a large collection of Y. pestis isolates, using Y. pseudotuberculosis strains as controls. Our microarray and PCR data revealed twenty two genomic regions (termed as Different Regions, DFRs) to be absent in one or more of Y. pestis isolates studied. The DFRs represent the dynamic regions of the Y. pestis genome in natural populations, suggesting their features of acquisition or deletion in the adaptive evolution of Y. pestis. A genomotypmg system was then established to group homologous Chinese isolates of Y. pestis into 14 genomovars based on profiling the acquisition/loss of DFRs in their genomes.Our study revealed that the genome of Y. pestis, a newly emerged pathogen, is at an intermediate stage of genetic flux with evidence of selective genome expansion by horizontal acquisition of plasmids or chromosomal islands and genome reduction by loss of DNA regions. The acquisition of a large number of foreign genes (two plasmids and three chromosomal islands) induce Y. pestis to evolve rapidly from Y. pseudotuberculosis to a newly emerged pathogen that is not only able to parasitize insects in part of its life cycle, but also highly virulent to rodents and humans causing pandemics of a systemic and often fatal disease. It dramatically differs from its ancestor Y. pseudotuberculosis, which only causes non-fatal gastrointestinal disease in similar hosts. Horizontal gene acquisition also plays a key role in dramatic evolutionary segregation of Y. pestis lineages (biovaro and genomovars). Opposing to selective genome expansion by gene acquisition, genome reduction occurs in Y. pestis through the loss of DNA regions (DFRs). The parallel loss of DFRs leads to the discrete segregation between the progenitor and offspring strains. This genome reduction gradually promotes the offspring strains to habitat in a more specific host-niche, without niche-overlapping between its progenitor and counterpart offspring.Links between genome microevolution and niche adaptationThe microevolution of the genomovars is perfectly consistent with the expansion of plague foci. Each of the genomovars is found to be confined in a specific geographic region, namely a plague focus or part of a focus with a unique set of natural environment, reservoirs and vectors. Hence, we presented a paradigm of transmission, colonization, expansion of Y pestis in China. Y. pestis strains from Central Asia and Far East of Russia may have migrated into the Xinjiang-Tibet region and Northeast China respectively, and then separated into three branches with the expansion of plague foci.The revealed genome dynamics in natural populations of Y. pestis off...