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Table 2 Duplicate gene-pairs in R. sphaeroides with selective constraint (ω) < 1 (ordered by ω)

From: Evolutionary constraints and expression analysis of gene duplications in Rhodobacter sphaeroides 2.4.1

aGene 1

aGene 2

Function

bLocation

cLength

dDivergence

e Ka

e Ks

eω

fCorrelation

gCosine

RSP_1647

RSP_3650

Protease

CI/CII

312

13

0.0207

0.7894

0.0262

0.7507

0.9805

RSP_6194

RSP_6200

Hypothetical

CII/CII

140

4

0.0174

0.4721

0.0369

N/A

N/A

RSP_3624

RSP_3792

Hypothetical

CII/CII

238

8

0.0318

0.8434

0.0377

0.7706

0.9452

RSP_2482

RSP_4189

Receptor

PC/PD

294

6

0.0270

0.5608

0.0481

0.9162

0.9250

RSP_2064

RSP_6012

Hypothetical

CI/CI

126

11

0.0485

0.9247

0.0525

N/A

N/A

RSP_4252

RSP_3907

Hypothetical

PD/PA

163

2

0.0050

0.0757

0.0658

N/A

N/A

RSP_1653

RSP_6190

Hypothetical

CI/CII

208

18

0.0821

1.0949

0.0750

N/A

N/A

RSP_3908

RSP_4251

Hypothetical

PA/PD

185

1

0.0023

0.0279

0.0811

N/A

N/A

RSP_1638

RSP_2062

Hypothetical

CI/CI

126

5

0.0406

0.4615

0.0881

0.7369

0.7604

RSP_1645

RSP_3652

Phage‐related

CI/CII

419

4

0.0565

0.5853

0.0965

0.9933

0.9694

RSP_2063

RSP_1639

Hypothetical

CI/CI

147

9

0.0317

0.3017

0.1051

0.9995

0.9700

RSP_3627

RSP_3784

Protease

CII/CII

448

5

0.0180

0.1697

0.1061

N/A

N/A

RSP_7390

RSP_3896

Transposase

PD/PA

413

15

0.0759

0.6951

0.1091

N/A

N/A

RSP_1956

RSP_6196

Hypothetical

CI/CII

124

8

0.0396

0.2751

0.1439

N/A

N/A

RSP_4138

RSP_3902

Hypothetical

PD/PA

265

4

0.0156

0.1028

0.1513

N/A

N/A

RSP_1951

RSP_3622

Hypothetical

CI/CII

116

4

0.0242

0.1428

0.1692

0.2186

0.7307

RSP_4178

RSP_3012

Transposase

PD/CII

119

26

0.1629

0.7886

0.2066

0.5797

0.9629

RSP_2061

RSP_1637

Hypothetical

CI/CI

70

15

0.0548

0.2219

0.2467

0.1230

0.1230

RSP_6035

RSP_3772

Hypothetical

CI/CII

113

36

0.2654

0.9499

0.2794

N/A

N/A

RSP_3904

RSP_7352

Conjugation

PA/PE

638

2

0.3479

1.0456

0.3327

N/A

N/A

RSP_3628

RSP_3786

Hypothetical

CII/CII

106

16

0.1400

0.3513

0.3985

0.1197

0.8483

RSP_1966

RSP_3007

Transposase

CI/CII

242

1

0.0279

0.0577

0.4842

0.9688

0.9963

RSP_3894

RSP_3978

Transport

PA/PB

276

4

0.0620

0.1005

0.6171

0.0315

0.9396

RSP_1955

RSP_3647

Hypothetical

CI/CII

219

28

0.2077

0.2090

0.9937

0.7644

0.8779

  1. agene name as shown in R. sphaeroides 2.4.1 annotation at NCBI.
  2. blocation: chromosome I (CI), chromosome II (CII), or plasmids (PA,PB, PC, PD, or PE).
  3. caverage length of the duplicate genes.
  4. dpercentage of amino acid divergence between protein homologs.
  5. eevolutionary constraint parameters: nonsynonymous substitution rate (K a ), synonymous substitution rate (K s ), and K a / K s (ω).
  6. fPearson’s correlation.
  7. gcosine similarity.
  8. Note that “N/A” is given for the pair, whose corresponding gene expression does not exist in the microarray.
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BMC Research Notes

ISSN: 1756-0500

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