Skip to main content

Table 2 Identity and probable function of genes showing highest observed values of three statistics (θw, Tajima’s D, and Fu & Li’s D*) in the genome-wide analysis of RSSC phylotypes

From: A genome-wide scan for genes under balancing selection in the plant pathogen Ralstonia solanacearum

Phylotype/replicon

Gene IDa

Gene name

Number of significant hitsb

Summary statisticsc

Gene description/function

θw

Tajima’s D

Fu & Li’s D*

I/chromosome

RSc2735

phcB

5

0.0661**

1.6873**

1.7108**

Class I SAM-dependent methyltransferase

I/chromosome

RSc2736

phcS

2

0.0729**

1.6139**

1.7266**

Two-component sensor histidine kinase

I/chromosome

RSc0688

–

1

0.0482**

2.9588**

1.6747**

Glycosyl transferase

I/chromosome

RSc2066

–

4

0.0595**

3.4633**

1.7026**

Haloacid dehalogenase-like hydrolase

I/chromosome

RSc2670

lrgB

1

0.0154**

2.2028**

1.4372**

Effector of murein hydrolase transmembrane protein

I/chromosome

RSc2669

lrgA

1

0.0210**

2.4378**

1.1771*

Effector of murein hydrolase

I/megaplasmid

RSp0832

uxuL

1

0.0155**

1.6730**

1.4372**

Glucuronolactone/galactarolactone lactonase

I/megaplasmid

RSp0304

ripD

2

0.0352**

1.5729**

1.4062**

Type III effector protein, avrPphD family

I/megaplasmid

RSp0487

ripA4

1

0.0183**

2.5310**

1.4823**

Type III effector protein (formerly AWR4)

I/megaplasmid

RSp1212

ripU

2

0.1156**

1.4848**

1.4752**

Type III effector protein

I/megaplasmid

RSp0238

glgX

1

0.0296**

2.3832**

1.3369**

Probable pulA pullulanase related glycosidase protein, glycogen debranching enzyme

I/megaplasmid

RSp1530

–

1

0.0944**

1.5829**

1.6620**

Polyphenol oxidase (laccase) oxidoreductase

I/megaplasmid

RSp1100

–

1

0.0493**

2.1856**

1.3555**

Putative signal sensing transmembrane protein, phosphorelay sensor kinase activity

IIA/chromosome

RCFBP_11371

paaH2

1

0.0298**

2.0233**

1.5364**

Putative 3-hydroxybutyryl-coA dehydrogenase oxidoreductase

IIA/chromosome

RCFBP_11349

–

1

0.0364**

2.1164**

1.5632**

Putative high-affinity branched-chain amino acid transport system permease (liv operon)

IIA/chromosome

RCFBP_20503

parC

1

0.0381**

1.8461**

1.5686**

DNA topoisomerase IV, subunit A

IIA/chromosome

RCFBP_11056

spec

1

0.0248**

2.1501**

1.5085**

Ornithine decarboxylase

IIA/chromosome

RCFBP_10967

ileS

1

0.0248**

2.0846**

1.5085**

Isoleucine--tRNA ligase

IIA/chromosome

RCFBP_21311

argC

1

0.0232**

1.9107**

1.4970**

N-acetyl-gamma-glutamyl-phosphate reductase

IIA/chromosome

RCFBP_10305

 

1

0.0282**

1.9675**

1.5280**

Putative transcription regulator protein

IIA/chromosome

RCFBP_10218

soxF

1

0.0248**

2.0192**

1.5085**

Sulfide dehydrogenase [flavocytochrome c] flavoprotein chain precursor

IIA/chromosome

RCFBP_11858

bioA

1

0.0265**

1.9424**

1.5188**

Adenosylmethionine--8-amino-7-oxononanoate transaminase, PLP-dependent

IIA/chromosome

RCFBP_10092

–

1

0.0381**

1.9520**

1.5686**

Putative transporter, with ABC transmembrane type-1 domain

IIA/chromosome

RCFBP_10712

phcQ

1

0.0282**

1.9908**

1.5280**

Response regulator receiver

IIA/chromosome

RCFBP_10711

–

2

0.0450**

2.0770**

1.5866**

Putative methyltransferase

IIA/chromosome

RCFBP_21242

–

1

0.0414**

2.5492**

1.5782**

Putative isomerase, with PhzC/PhzF domain

IIA/chromosome

RCFBP_20936

srkA

1

0.0298**

2.0897**

1.5364**

Stress response kinase A

IIA/chromosome

RCFBP_10686

ripW

2

0.0911**

2.0865**

1.5603**

Type III effector protein

IIA/chromosome

RCFBP_11806

ripG4

2

0.0381**

2.0578**

1.5686**

Type III effector protein

IIA/chromosome

RCFBP_11870

ripM

1

0.0298**

2.1673**

1.5364**

Type III effector protein

IIA/chromosome

RCFBP_20594

ripS5

1

0.0265**

1.9424**

1.5188**

Type III effector protein

IIA/megaplasmid

RCFBP_mp10317

cyaB

1

0.0939**

0.9326

1.5961**

ABC transporter (cyclolysin-type)

IIA/megaplasmid

RCFBP_mp10609

–

1

0.0776**

1.4690*

1.1125

Putative adhesin/hemolysin

IIA/megaplasmid

RCFBP_mp30035

cls

1

0.2490**

1.7362**

1.6971**

Cardiolipin synthase A

IIA/megaplasmid

RCFBP_mp30119

–

1

0.0653**

1.2030*

1.4386**

Putative type IV fimbrial biogenesis protein pilY1 with A-like domain

IIA/megaplasmid

RCFBP_mp30438

ripF1

1

0.1**

1.0458

1.5313**

Type III effector protein (formerly PopF1)

IIA/megaplasmid

RCFBP_mp20003

–

1

0.0551**

1.6353**

1.0059

Bacteriophage-related protein of unknown function

IIB/chromosome

RSPO_c00124

atpH

1

0.0226**

2.1129**

1.5336**

ATP synthase, f1 sector subunit delta

IIB/chromosome

RSPO_c00113

livK

1

0.0211**

2.0978**

1.5182**

Leucine-specific binding precursor transmembrane protein

IIB/chromosome

RSPO_c00179

gcl

1

0.0240**

2.1552**

1.5475**

Tartronate-semialdehyde synthase (glyoxylate carboligase)

IIB/chromosome

RSPO_c00415 RSPO_c00416

–

1

0.0352**

2.0846**

1.4063**

b-ketoadipate enol-lactone hydrolase protein and 3-ketoacyl-(acyl-carrier-protein) reductase

IIB/chromosome

RSPO_c00497

secY

1

0.0282**

1.9898**

1.5826**

Preprotein translocase (membrane subunit)

IIB/chromosome

RSPO_c00765

phcB

1

0.0240**

2.1264**

1.5475**

Regulatory protein

IIB/chromosome

RSPO_c02646

pilX

1

0.0211**

2.0335**

1.5182**

Putative type IV pili assembly protein

IIB/chromosome

RSPO_c01209

–

1

0.0282**

2.7986**

1.5826**

1-deoxy-d-xylulose-5-phosphate synthase protein

IIB/chromosome

RSPO_c01332

ripAJ

2

0.0226**

2.2473**

1.5336**

Type III effector protein

IIB/chromosome

RSPO_c02391

lldP

1

0.0183**

1.9736**

1.4823**

l-lactate permease protein

IIB/chromosome

RSPO_c02306

lepA

1

0.0268**

2.0272**

1.5718**

GTP-binding elongation factor

IIB/chromosome

RSPO_c01998

ripG7

3

0.0804**

2.0276**

1.4278**

Type III effector protein (formerly GALA7)

IIB/chromosome

RSPO_c01999

ripG6

1

0.0268**

2.6851**

1.5718**

Type III effector protein (formerly GALA6)

IIB/chromosome

RSPO_c01798

aidB

1

0.0536**

2.2941**

1.3902**

Isovaleryl CoA dehydrogenase

IIB/chromosome

RSPO_c01795

fadB

1

0,0338**

2.0162**

1.6180**

Fused 3-hydroxybutyryl-CoA epimerase

IIB/chromosome

RSPO_c00909

–

1

0.0620**

3.0207**

1.5774**

Lipoprotein

IIB/chromosome

RSPO_c01066

metG1

1

0.0254**

2.2792**

1.5602**

Methionyl-tRNA synthetase

IIB/chromosome

RSPO_c01082

spec

1

0.0338**

2.5566**

1.3908**

Biodegradative ornithine decarboxylase protein

IIB/chromosome

RSPO_c03170

–

1

0.0354**

2.0256**

1.5602**

Chromate transport protein

IIB/chromosome

RSPO_c03029

–

1

0.0312**

1.9276**

1.3562**

Sensory box/GGDEF family protein

IIB/megaplasmid

RSPO_m01227

fabI

1

0.0466**

2.2681**

1.6703**

Enoyl-[acyl-carrier-protein] reductase (NADH)

IIB/megaplasmid

RSPO_m01150 RSPO_m01151

pehC

1

0.0409**

2.3366**

1.4587**

Gluconolactonase and polygalacturonase proteins

IIB/megaplasmid

RSPO_m00202

ripH2

9

0.0776**

2.2152**

1.7322**

Type III effector protein

IIB/megaplasmid

RSPO_m00035

ripG3

1

0.0676**

2.3026**

1.4768**

Type III effector protein (formerly GALA3)

IIB/megaplasmid

RSPO_m01206

ripAO

1

0.0494**

2.1286**

1.6788**

Type III effector protein

IIB/megaplasmid

RSPO_m01229

ripS3

3

0.0409**

1.9967**

1.6505**

Type III effector protein (formerly SKWP3)

IIB/megaplasmid

RSPO_m01312

ripZ

1

0.0747**

2.9580**

1.7286**

Type III effector protein

IIB/megaplasmid

RSPO_m01371

ripC1

1

0.0338**

2.5836**

1.3908**

Type III effector protein

IIB/megaplasmid

RSPO_m00869

ripN

1

0.0620**

2.0883**

1.5774**

Type III effector protein

IIB/megaplasmid

RSPO_m00770

ripAR

2

0.0380**

2.2529**

1.6388**

Type III effector protein

IIB/megaplasmid

RSPO_m01600

ripBH

3

0.0620**

2.7880**

1.7082**

Type III effector protein

IIB/megaplasmid

RSPO_m01541

ripF1

2

0.0366**

2.1843**

1.6322**

Type III effector protein (formerly PopF1)

IV/chromosome

RPSI07_1784

–

2

0.0312**

1.5828**

1.5828**

Putative ABC-type transporter, periplasmic component

IV/chromosome

RPSI07_2871

tyrS

2

0.0312**

1.5828**

1.5828**

Tyrosyl-tRNA synthetase

IV/chromosome

RPSI07_1208

rpoD

3

0.0768**

1.8719**

1.8719**

RNA polymerase sigma70 factor

IV/chromosome

RPSI07_1185

galU

2

0.048**

1.6941**

1.6941**

Glucose-1-phosphate uridylyltransferase

IV/chromosome

RPSI07_0660

mraY

1

0.384**

1.6419**

16419**

Phospho-N-acetylmuramoyl-pentapeptide transferase

IV/chromosome

RPSI07_0072

ripE1_1

2

0,1056**

1.6690**

1.6690**

Type III effector protein

IV/chromosome

RPSI07_0735

ripW

3

0.1056**

1.9186**

1.6690**

Type III effector protein

IV/megaplasmid

RPSI07_mp0105

–

1

0.1464**

1.7880**

1.7880**

Putative acetyltransferase

IV/megaplasmid

RPSI07_mp0022

clcB

1

0.0624**

1.6238**

1.6238**

Chloride channel clcB-like protein

  1. a Systematic gene identifier according to GMI1000, CFBP2957, Po82 or PSI07 strain nomenclature for phylotype I, IIA, IIB or IV respectively
  2. b Number of significant windows overlapping described gene
  3. c Observed values of statistics for each gene and significance of coalescent simulations using standard neutral model: * p < 0.1 and ** p < 0.05