The Salmonella enterica pan-genome

Microbial Ecology
Annika JacobsenCarsten Friis


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. T...Continue Reading


Nov 20, 2012·Science·Stefania Spanò, Jorge E Galán
Apr 16, 2013·Journal of Bacteriology·Evgeny N GordienkoMikhail S Gelfand
Aug 18, 2012·International Journal of Evolutionary Biology·M Pilar Francino
Mar 14, 2012·BMC Genomics·Pimlapas LeekitcharoenphonDavid W Ussery
May 9, 2013·BMC Genomics·Matteo BrilliMarie-France Sagot
Jul 20, 2013·BMC Genomics·Andrea Isabel Moreno SwittMartin Wiedmann
Feb 8, 2014·PloS One·Pimlapas LeekitcharoenphonFrank M Aarestrup
Jan 7, 2014·BMC Genomics·Matthew N BenedictNathan D Price
Dec 2, 2014·Pathogens·Jason S LehmannDerrick E Fouts
May 9, 2014·Genome Announcements·Daniel A RussellGraham F Hatfull
Sep 2, 2014·Plasmid·Steven P T HootonIan F Connerton
Sep 15, 2012·Biochemical and Biophysical Research Communications·Hiroshi AsakuraShigeki Yamamoto
Oct 7, 2015·New Microbes and New Infections·L RouliD Raoult
May 23, 2013·The New Phytologist·Caroline L MonteilBoris A Vinatzer
Jul 20, 2013·Journal of Evolutionary Biology·R D SchulteH Schulenburg
Dec 11, 2013·Journal of Medical Microbiology·Ana Herrero-FresnoFrank M Aarestrup
Apr 14, 2016·Scientific Reports·Narendrakumar M ChaudhariChitra Dutta
Nov 18, 2014·Biochemical Society Transactions·Shelley D Copley
Nov 16, 2013·Critical Reviews in Microbiology·Chunlei ShiAndrea Isabel Moreno Switt
Jan 30, 2013·Critical Reviews in Microbiology·Mehari Tesfazgi MebrhatuAbram Aertsen
Jun 16, 2015·Frontiers in Cellular and Infection Microbiology·Zhanna A KtsoyanRustam I Aminov
Dec 9, 2014·Current Opinion in Microbiology·George VernikosHervé Tettelin
Mar 20, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Mark AchtmanSteffen Porwollik
Feb 11, 2015·Frontiers in Microbiology·Andrea R McWhorter, Kapil K Chousalkar


Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Sep 1, 1987·Medicine·J I CohenG R Corey
Jul 1, 1993·Nucleic Acids Research·D BensonJ Ostell
Jul 23, 1996·Proceedings of the National Academy of Sciences of the United States of America·H OchmanE A Groisman
Mar 1, 1996·Applied and Environmental Microbiology·E F BoydR K Selander
Jan 28, 1999·Journal of Bacteriology·A B Blanc-PotardE A Groisman
Feb 15, 2000·Research in Microbiology·L J JensenDavid W Ussery
Apr 1, 2000·Microbes and Infection·S L MarcusB Brett Finlay
Jun 1, 2000·Nature·H OchmanE A Groisman
Jun 14, 2000·Journal of Molecular Biology·A G PedersenDavid W Ussery
Feb 24, 2001·Cellular Microbiology·J H BrumellB Brett Finlay
Oct 26, 2001·Nature·Michael McClellandR K Wilson
Jun 20, 2002·Proceedings of the National Academy of Sciences of the United States of America·Steffen PorwollikMichael McClelland
Aug 1, 2002·Journal of Clinical Microbiology·Masao FukushimaRyuji Kawaguchi
Mar 20, 2003·Journal of Bacteriology·Wen DengFrederick R Blattner
Jun 5, 2003·BMC Bioinformatics·Thomas Schou Larsen, Anders Krogh
Oct 21, 2004·International Journal of Medical Microbiology : IJMM·Michael Hensel
Jan 6, 2005·Microbiology·Tim T BinnewiesDavid W Ussery
Sep 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hervé TettelinClaire M Fraser
Oct 27, 2005·Bioinformatics·Pernille Nielsen, Anders Krogh
Nov 9, 2006·Nucleic Acids Research·Sung Ho YoonJihyun F Kim
Feb 10, 2007·Trends in Microbiology·Sophie Abby, Vincent Daubin
Apr 25, 2007·Nucleic Acids Research·Karin LagesenDavid W Ussery
Aug 28, 2007·BMC Genomics·Wei-Qiao LiuShu-Lin Liu
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Nov 21, 2007·Nature Reviews. Microbiology·Andrea HaragaSamuel I Miller
Nov 29, 2007·Current Opinion in Gastroenterology·Guntram A Grassl, B Brett Finlay
Apr 17, 2008·Molecular BioSystems·Peter F HallinDavid W Ussery
Oct 29, 2008·Nature Reviews. Microbiology·Renée M TsolisAndreas J Bäumler
Dec 18, 2008·Current Opinion in Microbiology·Hervé TettelinDuccio Medini

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Alkalescens-Dispar Group
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