Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM,
Worsham P, Chu MC, Andersen GL.
Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516:
evidence of gene reduction in an emerging pathogen.
J Bacteriol. 2006 Jun;188(12):4453-63.
Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has
undergone detailed study at the molecular level. To further investigate the
genomic diversity among this group and to help characterize lineages of the
plague organism that have no sequenced members, we present here the genomes of
two isolates of the "classical" antiqua biovar, strains Antiqua and Nepal516. The
genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956
open reading frames, respectively. Though both strains belong to one of the three
classical biovars, they represent separate lineages defined by recent
phylogenetic studies. We compare all five currently sequenced Y. pestis genomes
and the corresponding features in Yersinia pseudotuberculosis. There are
strain-specific rearrangements, insertions, deletions, single nucleotide
polymorphisms, and a unique distribution of insertion sequences. We found 453
single nucleotide polymorphisms in protein-coding regions, which were used to
assess the evolutionary relationships of these Y. pestis strains. Gene reduction
analysis revealed that the gene deletion processes are under selective pressure,
and many of the inactivations are probably related to the organism's interaction
with its host environment. The results presented here clearly demonstrate the
differences between the two biovar antiqua lineages and support the notion that
grouping Y. pestis strains based strictly on the classical definition of biovars
(predicated upon two biochemical assays) does not accurately reflect the
phylogenetic relationships within this species. A comparison of four virulent Y.
pestis strains with the human-avirulent strain 91001 provides further insight
into the genetic basis of virulence to humans.
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