Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes

Abstract

BackgroundThe bacterium Salmonella enterica includes a diversity of serotypes that cause disease in humans and different animal species. Some Salmonella serotypes show a broad host range, some are host restricted and exclusively associated with one particular host, and some are associated with one particular host species, but able to cause disease in other host species and are thus considered "host adapted". Five Salmonella genome sequences, representing a broad host range serotype (Typhimurium), two host restricted serotypes (Typhi [two genomes] and Paratyphi) and one host adapted serotype (Choleraesuis) were used to identify core genome genes that show evidence for recombination and positive selection.ResultsOverall, 3323 orthologous genes were identified in all 5 Salmonella genomes analyzed. Use of four different methods to assess homologous recombination identified 270 genes that showed evidence for recombination with at least one of these methods (false discovery rate [FDR] <10%). After exclusion of genes with evidence for recombination, site and branch specific models identified 41 genes as showing evidence for positive selection (FDR <20%), including a number of genes with confirmed or likely roles in virulence and ompC, a gene encoding an outer membrane protein, which has also been found to be under positive selection in other bacteria. A total of 8, 16, 7, and 5 genes showed evidence for positive selection in Choleraesuis, Typhi, Typhimurium, and Paratyphi branch analyses, respectively. Sequencing and evolutionary analyses of four genes in an additional 42 isolates representing 23 serotypes confirmed branch specific positive selection and recombination patterns.ConclusionOur data show that, among the four serotypes analyzed, (i) less than 10% of Salmonella genes in the core genome show evidence for homologous recombination, (ii) a number of Salmonella genes are under positive selection, including genes that appear to contribute to virulence, and (iii) branch specific positive selection contributes to the evolution of host restricted Salmonella serotypes.

Influence of Molecular Resolution on Sequence-Based Discovery of Ecological Diversity among Synechococcus Populations in an Alkaline Siliceous Hot Spring Microbial Mat

“…The specific percentages are for the loci that we studied, which may not be representative of the entire genome, complicating direct comparison of our results with genomic ANI values. Although clusters of closely related sequences can result from causes other than adaptation (52), our observation of Synechococcus ecotypes is one of a growing number of examples of taxa that exhibit numerous extremely closely related sequence clusters corresponding to ecologically distinct populations (10,12,13,22,25,42,43,50,51,58). These clusters occur at a scale of sequence difference well within that formerly used to classify named species.…”

“…These analyses have revealed extremely closely related ecotypes in free-living prokaryotes, such as soil Bacillus (12,25), marine Vibrio (22), and acid mine Leptospirillum (13) and Procholorococcus (24,29), as well as among pathogens, including Legionella (10), Escherichia (28,50,51), Mycobacterium (42), Salmonella (43), and Yersinia (58). In all these cases, clusters identified by patterns of sequence diversity (in genes not related to ecological divergence) were confirmed to be ecologically distinct.…”

Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park

“…Unique Bacillus sequence clusters were shown to be associated with desert hillsides having distinct solar exposure patterns and soil textures (8,18). Molecular analyses also have shown closely related, ecologically distinct populations in marine Vibrio (14), acid mine Leptospirillum (9), and multiple pathogens, including Legionella (6), Escherichia (21,29,30), Mycobacterium (25), Salmonella (26), and Yersinia (35). Finally, genetically distinct populations of hot spring Synechococcus have been shown to be associated with different temperatures and vertical distributions (12,24,32).…”

Microfluidic PCR Combined with Pyrosequencing for Identification of Allelic Variants with Phenotypic Associations among Targeted Salmonella Genes

“…Comparative genomic analysis has demonstrated that unrelated strains of the same Salmonella serovar are typically more similar to each other than to members of other serovars, suggesting serovar-specific evolution (20). Genomic studies of individual serovars have also uncovered an expanding number of open reading frames with single-nucleotide polymorphisms (SNPs) that give rise to allelic variants that may be involved in the adaptation of individual strains to new environments or hosts (1).…”