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Citation for Study 14912

Citation title: "Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.".

Study name: "Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.".

This study is part of submission 14912 (Status: Published).

Citation

Timme R.E., Pettengill J.B., Allard M., Strain E., Barrangou R., Wehnes C., Van kessel J., Karns J., Musser S., & Brown E. 2013. Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters. Genome Biology and Evolution, .

Authors

• Timme R.E. (submitter) 202 506-0221
• Pettengill J.B.
• Allard M.
• Strain E.
• Barrangou R.
• Wehnes C.
• Van kessel J.
• Karns J.
• Musser S.
• Brown E.

Abstract

The enteric pathogen, Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing over 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles - some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of CRISPR loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large scale Salmonella enterica subsp. enterica phylogeny inferred from new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (107 were newly-sequenced) reveals two major lineages, each with many strongly supported sub-lineages. One of these lineages is the Salmonella Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) loci reveal different evolutionary patterns than that of the phylogeny, suggesting horizontal gene transfer might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes, and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.

Keywords

H antigens; serovar O antigens; CRISPR; lineage through time plot; comparative method

External links

• DOI: 10.1093/gbe/evt159
• Other URL: http://gbe.oxfordjournals.org/content/early/2013/10/23/gbe.evt159.abstract

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S14912
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref22547,
  	 author = {Ruth Evangeline Timme and James B Pettengill and Marc  Allard and Errol  Strain and Rodolphe  Barrangou and Chris  Wehnes and JoAnn  Van Kessel and Jeffrey  Karns and Steven  Musser and Eric  Brown},
  	 title = {Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.},
  	 year = {2013},
  	 keywords = {H antigens; serovar O antigens; CRISPR; lineage through time plot; comparative method},
  	 doi = {10.1093/gbe/evt159},
  	 url = {http://gbe.oxfordjournals.org/content/early/2013/10/23/gbe.evt159.abstract},
  	 pmid = {},
  	 journal = {Genome Biology and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {The enteric pathogen, Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing over 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles - some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of CRISPR loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large scale Salmonella enterica subsp. enterica phylogeny inferred from new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (107 were newly-sequenced) reveals two major lineages, each with many strongly supported sub-lineages. One of these lineages is the Salmonella Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) loci reveal different evolutionary patterns than that of the phylogeny, suggesting horizontal gene transfer might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes, and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 22547
  AU  - Timme,Ruth Evangeline
  AU  - Pettengill,James B
  AU  - Allard,Marc 
  AU  - Strain,Errol 
  AU  - Barrangou,Rodolphe 
  AU  - Wehnes,Chris 
  AU  - Van Kessel,JoAnn 
  AU  - Karns,Jeffrey 
  AU  - Musser,Steven 
  AU  - Brown,Eric 
  T1  - Phylogenetic diversity of the enteric pathogen Salmonella enterica subsp. enterica inferred from genome-wide reference-free SNP characters.
  PY  - 2013
  KW  - H antigens; serovar O antigens; CRISPR; lineage through time plot; comparative method
  UR  - http://gbe.oxfordjournals.org/content/early/2013/10/23/gbe.evt159.abstract
  N2  - The enteric pathogen, Salmonella enterica is one of the leading causes of foodborne illness in the world. The species is extremely diverse, containing over 2,500 named serovars that are designated for their unique antigen characters and pathogenicity profiles - some are known to be virulent pathogens, while others are not. Questions regarding the evolution of pathogenicity, significance of antigen characters, diversity of CRISPR loci, among others, will remain elusive until a strong evolutionary framework is established. We present the first large scale Salmonella enterica subsp. enterica phylogeny inferred from new reference-free k-mer approach of gathering single nucleotide polymorphisms (SNPs) from whole genomes. The phylogeny of 156 isolates representing 78 serovars (107 were newly-sequenced) reveals two major lineages, each with many strongly supported sub-lineages. One of these lineages is the Salmonella Typhi group; well nested within the phylogeny. Lineage-through-time analyses suggest there have been two instances of accelerated rates of diversification within the subspecies. We also found that antigen characters and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) loci reveal different evolutionary patterns than that of the phylogeny, suggesting horizontal gene transfer might have influenced the present character distribution. Our study also shows the ability to extract reference-free SNPs from a large set of genomes, and then to use these SNPs for phylogenetic reconstruction. This automated, annotation-free approach is an important step forward for bacterial disease tracking and in efficiently elucidating the evolutionary history of highly clonal organisms.
  L3  - 10.1093/gbe/evt159
  JF  - Genome Biology and Evolution
  VL  - 
  IS  - 
  ER  -