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

Abstract

Background: The 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.

Results: Overall, 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.

Conclusion: Our 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.

Figure 1

Example of neighbor joining tree used for positive selection analysis. Gene specific trees were used for all positive selection analysis. The tree showed here represented the phylogeny of 849 genes. Branches used for branch specific analyses are indicated; Ch# = Choleraesuis branch specific test; Ty# = Typhi branch specific test; Tym# = Typhimurium branch specific test; Pty# = Paratyphi A branch specific test.

Figure 2

Proportions of genes with evidence of recombination among individual JCVI role categories. Genes with evidence for recombination (Q < 0.1) in at least one of the four tests were included. Bars indicate estimated standard error for the proportion of genes with evidence of recombination in each role category; standard errors were calculated as square root of p (1-p)/n, where p is the proportion of genes with evidence of positive selection in a given role category, and n is the total number of genes in a given role category. Among the 20 JCVI role categories, two did not include genes with evidence of recombination (i.e., "Signal Transduction" and "Viral functions") and are thus not included in this figure.

Figure 3

Proportions of genes with evidence of positive selection among individual JCVI role categories. Only genes that showed no evidence for recombination were used to generate the data showed here. Bars indicate estimated standard error for the proportion of genes with evidence of positive selection in each role category; standard errors were calculated as the square root of p (1-p)/n, where p is the frequency of genes with evidence of positive selection in a given role category, and n is the total number of genes in a given role category. Among the 20 JCVI role categories, seven did not include genes with evidence of positive selection and are thus not included in this figure. For each role category, proportion of genes with evidence of positive selection in the overall test (TO) and each of the four branch specific tests (Ch# = Choleraesuis branch specific test; Ty# = Typhi branch specific test; Tym# = Typhimurium branch specific test; Pty# = Paratyphi A branch specific test) are shown.