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

Table 2 Genes used to confirm positive selection and recombination patterns identified in genome wide analyses

Gene Name	Protein name	JCVI Role Category	Gene length (bp)	Genome analyses results for		Sequence analyses results for^c
				Positive Selection^a	Recombination^b	Positive Selection^d	Recombination^e
folK-2	2-amino-4-hydroxy-6-hydroxymethyldihydro pteridine pyrophosphokinase	Biosynthesis of cofactors, prosthetic groups, and carriers	480	(TO, Ty#)	GEN, MAX	(Ty#)	GEN, MAX, NSS
STM3258	Putative PTS system IIA component	Transport and binding proteins	465	Ty#	-	Ty#	-
sseC	Probable pathogenicity island effector protein	Unclassified	1455	(Ch#)	GEN, MAX	(TO, Ch#)	GEN, MAX, NSS, PHI
purE	Phosphoribosylamino-imidazole carboxylase, catalytic subunit	Purines, pyrimidines, nucleosides, and nucleotides	510	Ty#	-	Ty#	NSS

^apositive selection tests that were significant (Q < 0.2) are listed; TO = overall test; Ch# = Choleraesuis branch specific test; Ty# = Typhi branch specific test; for genes that showed evidence of recombination, results are shown in a parenthesis as recombination may affect the positive selection analyses.
^brecombination tests that were significant (Q < 0.1) are listed; GEN = GENECONV; MAX = Maximum χ²; PHI = pairwise homoplasy; NSS = neighbor similarity score
^cResults of positive selection and recombination analyses were based on gene sequence data for the 5 genomes and 42 additional Salmonella isolates (see Additional file 2); for folK-2 and sseC sequences were only obtained for 36 additional isolates; for STM3258 sequences were only obtained for 37 additional isolates.
^dpositive selection tests that were significant (P < 0.05); for genes that showed evidence of recombination with multiple tests, results are shown in a parenthesis as recombination may affect the positive selection analyses.
^erecombination tests that were significant (P < 0.05)

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