title: The Salmonella enterica pan-genome.
abstract: 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.
authors.affiliation: Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, Building 208, 2800 Kongens Lyngby, Denmark.
authors.forename: Annika
authors.initials: A
authors.lastname: Jacobsen
authors.forename: Rene S
authors.initials: RS
authors.lastname: Hendriksen
authors.forename: Frank M
authors.initials: FM
authors.lastname: Aaresturp
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery
authors.forename: Carsten
authors.initials: C
authors.lastname: Friis
mesh_terms: D055028:Comparative Genomic Hybridization; D004251:DNA Transposable Elements; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016680:Genome, Bacterial; D044404:Genomic Islands; D005810:Multigene Family; D010957:Plasmids / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D019779:Salmonella enterica / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S