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Table 5 Genes with evidence for positive selection

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

Gene annotation no. for S.Typhimurium LT2

Gene name

Protein namea

Alignment length (bp)

Positive selection (q- value)b

BEB (P>95%)c

Genes in JCVI role category d "Cell Envelope"

STM1441

-

Membrane protein, putative

1995

Ch# (0.0043)

-

STM2267

ompC

Outer membrane protein C precursor

1134

Ch# (0.0986)

274

STM0743

-

Putative lipoprotein

273

Ch# (0.1830)

-

STM2801

ygaC

Conserved hypothetical protein

300

Pty# (0.020)

-

STM0301

safC

Outer membrane usher, Salmonella atypical fimbria

2508

TO (0.0104)

85, 111, 405, 692

Genes in JCVI role category "Cellular processes"

STM4106

katG

Catalase hydroperoxidase HPI(I)

2178

TO (0.0035)

-

STM1425

ydhE

Hypothetical integral membrane protein

1371

Tym# (0.0145)

-

Genes in JCVI role category "Energy metabolism"

STM4023

-

Putative 3-hydroxyisobutyrate dehydrogenase

840

Ch# (0.0138)

-

STM3680

aldB

Aldehyde dehydrogenase B

1536

Pty# (0.020)

-

STM0698

pgm

Phosphoglucomutase, alpha-D-glucose phosphate-specific

1638

Ty# (0.0157)

-

STM3515

malt

MalT regulatory protein

2703

Ty# (0.0198)

801

STM4187

iclR

Acetate operon repressor

819

Ty# (0.0693)

-

STM0401

malZ

Glycosyl hydrolase, family 13

1815

Tym# (0.1005)

-

Genes in JCVI role category "Hypothetical proteins"

STM3329

-

Conserved hypothetical protein TIGR01212

927

Ch# (0.1471)

-

STM1854

-

Hypothetical protein

162

Pty# (0.1973)

32, 40, 44, 45

STM0861

-

Conserved hypothetical protein

471

Tym# (0.1149)

-

STM1515

-

Conserved hypothetical protein TIGR00156 domain protein

384

Ty# (0.0167)

-

STM4015

-

Hypothetical protein

846

Ty# (0.0693)

-

STM4258

-

Conserved hypothetical protein

1386

Ty# (0.0884)

-

STM1532

-

Hypothetical protein

678

Ty# (0.1614)

-

STM1280

-

Conserved hypothetical protein

396

Tym# (0.0145)

-

STM3463

-

Conserved hypothetical protein

201

Tym# (0.1005)

-

Genes in JCVI role category "Purines, pyrimidines, nucleosides, and nucleotides"

STM0534

purE

Phosphoribosylaminoimidazole carboxylase, catalytic subunit

507

Ty# (0.0194)

-

STM2806

nrdI

NrdI protein

408

Ty# (0.0693)

-

STM2107

wcaH

GDP-mannose mannosyl hydrolase

435

Tym# (0.1081)

-

Genes in JCVI role category "Transport and binding proteins"

STM1679

oppA

Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein

1605

Ch# (0.0121)

-

STM3685

mtlA

PTS system, mannitol-specific IIC component subfamily, putative PTS system IIA component, putative

1914

TO (0.0035)

-

STM3258

-

 

462

Ty# (0.0157)

124, 139, 143, 144, 147

STM3626

oppF

Oligopeptide ABC transporter, ATP-binding protein

1011

Ty# (0.0157)

-

Genes in JCVI role category "Unclassified and unknown function"

STM3592

-

Proton/peptide symporter family protein

1470

TO (0.0104)

-

STM1088

pipB

Pathogenicity island encoded protein: SPI5, PipB

873

TO (0.0688)

173

STM0248

-

Histidinol phosphatase-related protein

573

Ch# (< 0.0001)

175, 184, 185, 191

STM3565

-

Acetyltransferase, GNAT family

381

Pty# (0.0391)

-

STM3955

rarD

RarD protein

879

Ty# (0.0194)

-

Genes in JCVI role category "Biosynthesis of cofactors, prosthetic groups, and carriers"

STM1450

-

Pyridoxal kinase

666

Ty# (0.0147)

-

STM3057

ubiH

2-octaprenyl-6-methoxyphenol hydroxylase, UbiH

1176

Tym# (0.1149)

-

Genes in JCVI role category "Viral functions"

STM2678

b2611

Putative membrane protein, CorE

750

Ch# (0.1411)

-

STM4242

-

99% identical to TraF of plasmid R64

1284

Pty# (0.0329)

-

Genes in other JCVI role categories e

STM3655

glyS

Glycyl-tRNA synthetase, beta subunit

2067

Ty# (0.0393)

313

STM0603

araT

Aminotransferase, class I

1158

Ty# (0.1976)

-

STM0395

-

Exonuclease SbcC, putative

3096

Ty# (0.1041)

-

  1. aProtein designations were taken from the Typhi CT18 annotation; where limited annotation information was available, additional information was extracted from JCVI primary annotations and Typhimurium LT2 and Paratyphi A annotations
  2. btests that were significant for positive selection (FDR <20%) are shown; TO = overall test; Ch# = Choleraesuis branch specific test; Pty# = Paratyphi A branch specific test; Ty# = Typhi branch specific test; Tym# = Typhimurium branch specific test; numbers in brackets indicate q-values
  3. caa sites identified by Bayes Empirical Bayes (BEB) as having probability > 95% of being under positive selection are shown; aa sites are based on site location in the alignment (alignments for genes under positive selection are provided as Additional file 6)
  4. dRole categories were assigned based on annotations for S. Typhi CT18; JCVI locus names for Typhi CT18 for these genes are listed in Additional file 5.
  5. eOther role categories include Protein synthesis (STM3655), Central intermediary metabolism (STM0603), DNA metabolism (STM0395)
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BMC Ecology and Evolution

ISSN: 2730-7182

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