PMID:
     16740952
Authors:
     Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM,
     Worsham P, Chu MC, Andersen GL.
Title:
     Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516:
     evidence of gene reduction in an emerging pathogen.
Journal:
     J Bacteriol. 2006 Jun;188(12):4453-63.
Abstract:
     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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