Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

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 genom...

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Main Authors: Chain, Patrick S. G., Hu, Ping, Malfatti, Stephanie A., Radnedge, Lyndsay, Larimer, Frank, Vergez, Lisa M., Worsham, Patricia, Chu, May C., Andersen, Gary L.
Formato: Artigo
Idioma:English
Publicado em: American Society for Microbiology 2006
Assuntos:
Genomics and Proteomics
Acesso em linha:https://ncbi.nlm.nih.gov/pmc/articles/PMC1482938/
https://ncbi.nlm.nih.gov/pubmed/16740952
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1128/JB.00124-06
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spelling pubmed-14829382006-10-01 Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen Chain, Patrick S. G. Hu, Ping Malfatti, Stephanie A. Radnedge, Lyndsay Larimer, Frank Vergez, Lisa M. Worsham, Patricia Chu, May C. Andersen, Gary L. J Bacteriol Genomics and Proteomics 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. American Society for Microbiology 2006-06 /pmc/articles/PMC1482938/ /pubmed/16740952 http://dx.doi.org/10.1128/JB.00124-06 Text en
institution US National Library of Medicine
collection PubMed Central
language English
format Article
topic Genomics and Proteomics
spellingShingle Genomics and Proteomics
Chain, Patrick S. G.
Hu, Ping
Malfatti, Stephanie A.
Radnedge, Lyndsay
Larimer, Frank
Vergez, Lisa M.
Worsham, Patricia
Chu, May C.
Andersen, Gary L.
Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen
description 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.
author Chain, Patrick S. G.
Hu, Ping
Malfatti, Stephanie A.
Radnedge, Lyndsay
Larimer, Frank
Vergez, Lisa M.
Worsham, Patricia
Chu, May C.
Andersen, Gary L.
author_facet Chain, Patrick S. G.
Hu, Ping
Malfatti, Stephanie A.
Radnedge, Lyndsay
Larimer, Frank
Vergez, Lisa M.
Worsham, Patricia
Chu, May C.
Andersen, Gary L.
author_sort Chain, Patrick S. G.
title Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen
title_short Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen
title_full Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen
title_fullStr Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen
title_full_unstemmed Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen
title_sort complete genome sequence of yersinia pestis strains antiqua and nepal516: evidence of gene reduction in an emerging pathogen
publisher American Society for Microbiology
publisher_facet American Society for Microbiology
publishDate 2006
url https://ncbi.nlm.nih.gov/pmc/articles/PMC1482938/
https://ncbi.nlm.nih.gov/pubmed/16740952
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1128/JB.00124-06
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