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Title: Genomic comparison of the closely-related Salmonella enterica serovars enteritidis, dublin and gallinarum

Abstract

The Salmonella enterica serovars Enteritidis, Dublin, and Gallinarum are closely related but differ in virulence and host range. To identify the genetic elements responsible for these differences and to better understand how these serovars are evolving, we sequenced the genomes of Enteritidis strain LK5 and Dublin strain SARB12 and compared these genomes to the publicly available Enteritidis P125109, Dublin CT 02021853 and Dublin SD3246 genome sequences. We also compared the publicly available Gallinarum genome sequences from biotype Gallinarum 287/91 and Pullorum RKS5078. Using bioinformatic approaches, we identified single nucleotide polymorphisms, insertions, deletions, and differences in prophage and pseudogene content between strains belonging to the same serovar. Through our analysis we also identified several prophage cargo genes and pseudogenes that affect virulence and may contribute to a host-specific, systemic lifestyle. These results strongly argue that the Enteritidis, Dublin and Gallinarum serovars of Salmonella enterica evolve by acquiring new genes through horizontal gene transfer, followed by the formation of pseudogenes. As a result, the loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars.

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Science Foundation (NSF)
OSTI Identifier:
1212416
Alternate Identifier(s):
OSTI ID: 1225016
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 6; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; pseudogenes; genome evolution; comparative genomics; genome annotation; salmonella; animal genomics; bird genomics; operons; genome analysis; bacteriophages

Citation Formats

Matthews, T. David, Schmieder, Robert, Silva, Genivaldo G. Z., Busch, Julia, Cassman, Noriko, Dutilh, Bas E., Green, Dawn, Matlock, Brian, Heffernan, Brian, Olsen, Gary J., Hanna, Leigh Farris, Schifferli, Dieter M., Maloy, Stanley, Dinsdale, Elizabeth A., Edwards, Robert A., and Cloeckaert, Axel. Genomic comparison of the closely-related Salmonella enterica serovars enteritidis, dublin and gallinarum. United States: N. p., 2015. Web. doi:10.1371/journal.pone.0126883.
Matthews, T. David, Schmieder, Robert, Silva, Genivaldo G. Z., Busch, Julia, Cassman, Noriko, Dutilh, Bas E., Green, Dawn, Matlock, Brian, Heffernan, Brian, Olsen, Gary J., Hanna, Leigh Farris, Schifferli, Dieter M., Maloy, Stanley, Dinsdale, Elizabeth A., Edwards, Robert A., & Cloeckaert, Axel. Genomic comparison of the closely-related Salmonella enterica serovars enteritidis, dublin and gallinarum. United States. doi:10.1371/journal.pone.0126883.
Matthews, T. David, Schmieder, Robert, Silva, Genivaldo G. Z., Busch, Julia, Cassman, Noriko, Dutilh, Bas E., Green, Dawn, Matlock, Brian, Heffernan, Brian, Olsen, Gary J., Hanna, Leigh Farris, Schifferli, Dieter M., Maloy, Stanley, Dinsdale, Elizabeth A., Edwards, Robert A., and Cloeckaert, Axel. Wed . "Genomic comparison of the closely-related Salmonella enterica serovars enteritidis, dublin and gallinarum". United States. doi:10.1371/journal.pone.0126883. https://www.osti.gov/servlets/purl/1212416.
@article{osti_1212416,
title = {Genomic comparison of the closely-related Salmonella enterica serovars enteritidis, dublin and gallinarum},
author = {Matthews, T. David and Schmieder, Robert and Silva, Genivaldo G. Z. and Busch, Julia and Cassman, Noriko and Dutilh, Bas E. and Green, Dawn and Matlock, Brian and Heffernan, Brian and Olsen, Gary J. and Hanna, Leigh Farris and Schifferli, Dieter M. and Maloy, Stanley and Dinsdale, Elizabeth A. and Edwards, Robert A. and Cloeckaert, Axel},
abstractNote = {The Salmonella enterica serovars Enteritidis, Dublin, and Gallinarum are closely related but differ in virulence and host range. To identify the genetic elements responsible for these differences and to better understand how these serovars are evolving, we sequenced the genomes of Enteritidis strain LK5 and Dublin strain SARB12 and compared these genomes to the publicly available Enteritidis P125109, Dublin CT 02021853 and Dublin SD3246 genome sequences. We also compared the publicly available Gallinarum genome sequences from biotype Gallinarum 287/91 and Pullorum RKS5078. Using bioinformatic approaches, we identified single nucleotide polymorphisms, insertions, deletions, and differences in prophage and pseudogene content between strains belonging to the same serovar. Through our analysis we also identified several prophage cargo genes and pseudogenes that affect virulence and may contribute to a host-specific, systemic lifestyle. These results strongly argue that the Enteritidis, Dublin and Gallinarum serovars of Salmonella enterica evolve by acquiring new genes through horizontal gene transfer, followed by the formation of pseudogenes. As a result, the loss of genes necessary for a gastrointestinal lifestyle ultimately leads to a systemic lifestyle and niche exclusion in the host-specific serovars.},
doi = {10.1371/journal.pone.0126883},
journal = {PLoS ONE},
number = 6,
volume = 10,
place = {United States},
year = {2015},
month = {6}
}

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