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To gain insights into the evolutionary origin, emergence, and pathogenicity of the etiologic agent of plague, we have sequenced the genomes of four Yersinia pestis strains isolated from the zoonotic rodent reservoir in foci of endemic plague in China. These resources enable in-depth studies of Y. pestis sequence variations and detailed whole-genome comparisons of very closely related genomes from the supposed site of the origin and the emergence of global pandemics of plague.
Here we report on the genomes of Yersinia pestis strains B42003004, K1973002, E1979001, and F1991016, which represent a sample of the genetic diversity found in four foci of endemic plague in China (24). Y. pestis bv. orientalis strain F1991016 was isolated in 1991 from Cangyuan County, China, from a rat (Rattus flavipectus), and Y. pestis bv. antiqua strain E1979001 was isolated in 1979 from Jianchuan, China, from a vole (Eothenomys miletus). Both Y. pestis strains K1973002 and B42003004 of biovars medievalis and antiqua, respectively, originate from marmota species (Marmota himalayana Hetian 1973; Marmota baibacina Wenquan 2003) (24). Genome analyses of these key isolates outline the details of microevolution of the plague bacterium, as these isolates represent important evolutionary milestones of the species, which is thought to have originated in Central Asia as a clonal descendant of Yersinia pseudotuberculosis (1). Genomic DNA was subjected to whole-genome shotgun sequencing and closure strategies as previously described (15). Plasmid (pHOS2) and fosmid (pCC1fos) libraries were constructed, with insert sizes of 4 to 6 kb and 30 to 40 kb, respectively. An average of 67,000 high-quality Sanger reads (total, 268,160) was obtained with an 860-bp average read length. The genomes with an average 12-fold read coverage depth were assembled using a Celera Assembler (11) and manually annotated using Manatee (http://manatee.sourceforge.net/). Genomic architectures were compared using Mauve (5, 18), and proteomes were analyzed with the BLAST score ratio tool (17).
The young evolutionary history of the species and resulting homogenous population structure is reflected in a high degree of proteome conservation between the sequenced isolates and the modern strain CO92 (16). Y. pestis pathogenicity is anchored in its mobile inventory, and typically, isolates harbor three virulence plasmids, the species-specific plasminogen activator and murine toxin plasmids and the low-calcium-response plasmid pCD (23). Their pCD-borne lcrV antigen shows a genetic makeup identical to that of CO92 (2, 16). The insertion sequence element expansion clearly distinguishes these Central Asian isolates from the progenitor Y. pseudotuberculosis (3, 8). Comprehensive analyses reveal a lack of genome-wide synteny and suggest massive intrachromosomal rearrangements, a characteristic feature of Y. pestis genome evolution (6, 8). Besides insertion sequence element abundance, we observed isolate-specific propagation patterns that not only shaped the reorganization of the genomic architecture but also are known to drive microevolutionary adaptation in Y. pestis (4, 9, 14, 21, 24). Based upon the phenotypic and genotypic features that differentiate these isolates (13, 20, 24), B42003004 belongs to the most ancient Y. pestis lineage known to exist in China; hence, it is phylogenetically thought to be closest to the species progenitor Y. pseudotuberculosis (22). We studied metabolic genes that determine their biovar classification and investigated the underlying genetic determinants (24). Isolate K1973002 is defective in the nitrate reductase napA gene, similar to strain KIM (7), and represents the results of the evolutionary processes implicated in the biovar conversion from antiqua to medievalis. Isolate F1991016 carries an in-frame deletion in the glycerol-3-phosphate dehydrogenase glpD gene (19), similar to strain CO92 (16), and characteristic of the antiqua-to-orientalis conversion. The observed genetic traits strengthen the hypothesis that biovars medievalis and orientalis arose through parallel evolution from a glycerol- and nitrate-positive antiqua progenitor due to the acquisition of independent mutations (1, 10, 14). Variable-number tandem-nucleotide-repeat alleles (12) (allele K, K1973002; allele K, B42003004; allele P, E1979001; allele G, F1991016) are not biovar specific and are not discriminative enough to differentiate these isolates, which clearly supports a population-based phylogeny, as introduced by Achtman et al. (1).
The whole-genome draft sequences of these evolutionary key isolates of Y. pestis will facilitate additional bioinformatic and phylogenetic analyses. The availability of high-quality Sanger sequences is crucial to resolve the genetically homogenous population structure and to shed light on Y. pestis speciation. Understanding the plasticity and genome dynamics further aids in forensic and epidemiological analyses by setting up the basis for an accurate and robust typing system for plague surveillance and promotes diagnostics development and control measures.
The genome sequences were deposited in GenBank under accession numbers AAYU01000000 (for strain B42003004), AAYT01000000 (for strain K1973002), AAYV01000000 (for strain E1979001), and ABAT01000000 (for strain F1991016). Genome assemblies were deposited in the NCBI Assembly Archive under Assembly IDs 2707, 2618, 2607, and 2774, and the electropherogram data of sequencing traces are available from the NCBI Trace Archive.
The genome projects were supported with federal funds as a joint collaborative effort of the National Institute of Allergy and Infectious Diseases, the National Institutes of Health, and the Department of Homeland Security through Interagency Agreement RSRD-04-00142 under NIAID contract N01-AI-30071. The genome sequencing was partly supported by the National Science Fund of China for Distinguished Young Scholars (contract 30525025).
Published ahead of print on 9 October 2009.