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Table 4 Genes under positive selection.

From: Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes

Gene locus

Gene description (gene symbol)

COG(1)

Recombination(2)

Branch under pos. selection

Q-value

ω(3)

p(4)

BEB (P> 95%)(5)

Lmo0098

PTS system, mannose/fructose/sorbose family, IID component (mptD)

NCOG

GCV; MAX

LI/LM

0.170

472.58

0.004

-

Lmo0099

conserved hypothetical protein

NCOG

-

LI/LM

0.170

0.009

-

Lmo0139

conserved hypothetical protein

NCOG

-

LM2A

0.160

56.74

0.054

95

Lmo0297

PRD/PTS system IIA 2 domain protein

K; G; T

GCV; MAX; NSS; PHI

LM2A

0.164

0.012

499

Lmo0397

conserved hypothetical protein

S

GCV; MAX

LM2A

0.1264

0.043

-

Lmo0429

glycosyl hydrolase, family 38

G

GCV; MAX; NSS; PHI

LM2A

0.0325

977.51

0.008

667

Lmo0455

conserved hypothetical protein

T; Q

GCV; MAX; NSS; PHI

LM2A

0.1214

0.004

-

Lmo0653

conserved hypothetical protein

S

MAX

LM2A

0.033

0.012

306

Lmo0658

endonuclease III domain protein

L

MAX; NSS

LM2A

0.108

0.023

209

Lmo0692

chemotaxis protein CheA (cheA)

T; N

GCV; MAX; NSS; PHI

LM1A

0.156

0.002

-

Lmo0693

flagellar motor switch domain protein

N; U

-

LM2A

0.007

0.022

-

Lmo0695

conserved hypothetical protein

NCOG

MAX; NSS; PHI

LM1A

0.175

0.014

-

Lmo0732

cell wall surface anchor family protein

NCOG

GCV

LM1A

0.185

6.92

0.076

-

Lmo0782

PTS system, mannose/fructose/sorbose family, IIC component (mpoD)

NCOG

GCV; MAX

Overall;

0.146;

88.23;

0.008;

-

    

LM1A;

0.052;

∞;

0.0001;

-

    

LM2A

0.098

0.004

-

Lmo0785

sigma-54 dependent Kal regulator (manR)

K; T

GCV; MAX

LM2A

0.129

1.00

0.000

-

Lmo0872

major facilitator family transporter

G

GCV; MAX; NSS

LM2A

0.137

0.008

-

Lmo0910

putative membrane protein

R

MAX; NSS

LM1A

0.019

0.012

-

Lmo1146

conserved hypothetical protein

NCOG

GCV; MAX

LI/LM

0.046

223.37

0.023

169

Lmo1164

PduO protein (pduO)

S; R

GCV

LI/LM

0.170

195.87

0.038

-

Lmo1412

DNA topology modulation protein FlaR (flaR)

F

-

LM2A

0.160

8.56

0.139

12; 37; 68

Lmo1424

transporter, NRAMP family (mntH)

P

GCV

LM1A

0.185

1.00

0.000

-

Lmo1523

GTP pyrophosphokinase (relA)

K; T

-

LM2A

0.033

1.00

0.000

-

Lmo1529

preprotein translocase, YajC subunit

U

-

LI/LM

0.170

0.011

-

Lmo2102

glutamine amidotransferase, SNO family (pdxT)

H

GCV; MAX; NSS; PHI

LM1A

0.185

0.017

66

Lmo2121

glycosyl transferase, family 65

G

GCV; MAX; NSS

LM1A

7.6E-06

35.31

0.031

722; 723; 725; 729; 730; 744; 752;

Lmo2178

cell wall surface anchor family protein

M

GCV; MAX; NSS; PHI

LI/LM;

0.193;

15.92;

0.001;

-

    

LM2A

0.137

5.34

0.025

1769

Lmo2215

ABC transporter, ATP-binding protein

V

MAX; NSS

Overall

0.188

14.23

0.008

-

Lmo2222

Ser/Thr protein phosphatase family protein

L

GCV; MAX

LM2A

0.160

0.021

253

Lmo2446

glycosyl hydrolase, family 31

G

GCV; MAX; NSS; PHI

LM2A

0.003

0.0001

-

Lmo2596

ribosomal protein S9 (rpsI)

NCOG

-

LM2A

0.021

0.010

-

Lmo2611

adenylate kinase (adk)

F

GCV; MAX

LM2A

0.120

24.80

0.013

-

Lmo2724

conserved hypothetical protein

S

NSS

LI/LM

0.170

0.008

-

Lmo2802

glucose-inhibited division protein B (girB)

M

GCV; MAX; NSS; PHI

LM1A

0.046

0.013

-

Lmo2804

conserved hypothetical protein

NCOG

GCV; MAX; NSS; PHI

Overall

6.5E-17

16.53

0.044

-

Lmo2824

D-isomer specific 2- hydroxyacid dehydrogenase family protein

E; H

GCV; MAX; NSS

LM2A

0.160

229.62

0.003

-

  1. (1) NCOG: Not in COGs; K: Transcription; G: Carbohydrate transport and metabolism; T: Signal transduction mechanisms; S: Function unknown; Q: Secondary metabolites biosynthesis, transport and catabolism; L: Replication, recombination and repair; N: Cell motility; U: Intracellular trafficking and secretion; R: General function prediction only; F: Nucleotide transport and metabolism; P: Inorganic ion transport and metabolism; E: Amino acid transport and metabolism; H: Coenzyme transport and metabolism; M: Cell wall/membrane biogenesis; V: Defense mechanisms
  2. (2) GCV: GENECONV; MAX: Maximum χ2; NSS: Neighbour Similarity Score; PHI: Pairwise Homoplasy Test
  3. (3) ω = dN/dS (Number of nonsynonymous changes per nonsynonymous sites/Number of synonymous changes per synonymous sites); infinite values of ω (∞) indicate that the model did not find synonymous changes for the branches tested (dS = 0; ω ~ ∞). However, this (i.e., ω ~ ∞) does not affect the validity of the Likelihood Ratio Test, which was used to identify the genes under positive selection (Z. Yang, pers. Communication; see http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2079&sid=c4a82e1ca334ca84a00a8b85e0f33c9d and http://gsf.gc.ucdavis.edu/viewtopic.php?f=1&t=2329&sid=c4a82e1ca334ca84a00a8b85e0f33c9d;
  4. (4) Proportion of sites under positive selection
  5. (5) This column lists sites identified using Bayes Empirical Bayes (BEB) as being under positive selection; numbers identify the amino acid sites (in alignments) that are under positive selection