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The Salmonella enterica Pan-genome

Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 compl...

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Autores principales: Jacobsen, Annika, Hendriksen, Rene S., Aaresturp, Frank M., Ussery, David W., Friis, Carsten
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer-Verlag 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175032/
https://www.ncbi.nlm.nih.gov/pubmed/21643699
http://dx.doi.org/10.1007/s00248-011-9880-1
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author Jacobsen, Annika
Hendriksen, Rene S.
Aaresturp, Frank M.
Ussery, David W.
Friis, Carsten
author_facet Jacobsen, Annika
Hendriksen, Rene S.
Aaresturp, Frank M.
Ussery, David W.
Friis, Carsten
author_sort Jacobsen, Annika
collection PubMed
description Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences). Of these, 35 were found to be of sufficiently good quality to allow a detailed analysis, along with two Escherichia coli strains (K-12 substr. DH10B and the avian pathogenic E. coli (APEC O1) strain). All genomes were subjected to standardized gene finding, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection of variable genomic regions or islands. These include the SPIs but also encompass phage insertion sites and transposable elements. The islands were typically well conserved in several, but not all, isolates—a difference which may have implications in, e.g., host specificity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00248-011-9880-1) contains supplementary material, which is available to authorized users.
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spelling pubmed-31750322011-09-26 The Salmonella enterica Pan-genome Jacobsen, Annika Hendriksen, Rene S. Aaresturp, Frank M. Ussery, David W. Friis, Carsten Microb Ecol Minireviews Salmonella enterica is divided into four subspecies containing a large number of different serovars, several of which are important zoonotic pathogens and some show a high degree of host specificity or host preference. We compare 45 sequenced S. enterica genomes that are publicly available (22 complete and 23 draft genome sequences). Of these, 35 were found to be of sufficiently good quality to allow a detailed analysis, along with two Escherichia coli strains (K-12 substr. DH10B and the avian pathogenic E. coli (APEC O1) strain). All genomes were subjected to standardized gene finding, and the core and pan-genome of Salmonella were estimated to be around 2,800 and 10,000 gene families, respectively. The constructed pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype. Any given Salmonella strain has a large stable core, whilst there is an abundance of accessory genes, including the Salmonella pathogenicity islands (SPIs), transposable elements, phages, and plasmid DNA. We visualize conservation in the genomes in relation to chromosomal location and DNA structural features and find that variation in gene content is localized in a selection of variable genomic regions or islands. These include the SPIs but also encompass phage insertion sites and transposable elements. The islands were typically well conserved in several, but not all, isolates—a difference which may have implications in, e.g., host specificity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00248-011-9880-1) contains supplementary material, which is available to authorized users. Springer-Verlag 2011-06-04 2011 /pmc/articles/PMC3175032/ /pubmed/21643699 http://dx.doi.org/10.1007/s00248-011-9880-1 Text en © The Author(s) 2011 https://creativecommons.org/licenses/by-nc/4.0/ This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
spellingShingle Minireviews
Jacobsen, Annika
Hendriksen, Rene S.
Aaresturp, Frank M.
Ussery, David W.
Friis, Carsten
The Salmonella enterica Pan-genome
title The Salmonella enterica Pan-genome
title_full The Salmonella enterica Pan-genome
title_fullStr The Salmonella enterica Pan-genome
title_full_unstemmed The Salmonella enterica Pan-genome
title_short The Salmonella enterica Pan-genome
title_sort salmonella enterica pan-genome
topic Minireviews
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175032/
https://www.ncbi.nlm.nih.gov/pubmed/21643699
http://dx.doi.org/10.1007/s00248-011-9880-1
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