Skip to main content

Table 1 Orthologs of WSSV genes identified on the three viral scaffolds of Metopaulias depressus

From: Characterization of fossilized relatives of the White Spot Syndrome Virus in genomes of decapod crustaceans

Scaffold

Position, bp

Strand

Length, bp

Predicted protein length, aa

ORF number in WSSV b

Protein in WSSV

 

Truncated ends

Frameshifts g

MAFFT alignment

     

CN

TH

TW

Family c

Protein length

Function d

   

Pairwise identity, %

Alignment length, aa

I

2,517-3,356

-

840

279

299

147

355

 

309

    

21.1

341

I

3,524-5,980

+

2,457

818

303

149

359

 

891

TATA box binding protein (TBP)

   

48.3

894

I

8,084-12,361

-

4,278

1,425

151

89

207

 

1,436

Latency-related

   

26.8

1,538

I

13,933-17,373

+

3,441

1,145

11

36

67

 

1,301

VP53A, VP150

E

3’

 

41.2

1,326

I

19,141-21,198

+

2,058

685

220

112

275

 

674

VP674, VP76, class I cytokine receptor

C

  

37.6

703

I

22,400-24,835

-

2,436

811

172

92

228

 

848

Ribonucleotide reductase large subunit (RR1)

   

55.4

850

I

24,958-28,317

+

3,360

1,119

166

91

222

(NA)

1,072

    

35.0

1,166

I

29,688-35,294

+

5,607

1,868

447

9

507

 

1,936

Helicase

   

43.5

1,986

I

36,408-43,088

+

6,681

2,227 a

143

84

198

 

2,314

   

Poly

22.9

2,509

I

43,108-44,328

+

1,221

406

188

98

243

 

413

Ribonucleotide reductase small subunit (RR2)

   

47.3

442

I

45,135-45,998

+

864

288

(112)

(71)

(168)

 

462

dUTPase

   

22.8

468

I

46,200-47,384

-

1,185

394

446

7 + 8

506

 

526

    

19.4

563

I

47,874-52,274

+

4,401

1,466

465

16

524

 

1,243

VP136B

   

19.3

1,546

I

52,821-55,352

-

2,532

843

45

43

102

 

981

    

35.1

1,020

I

55,376-58,807

-

3,432

1,143

37

42

94

 

1,279

VP160B

C

  

49.2

1,309

I

59,002-61,614

+

2,613

870

119

73

175

 

1,044

    

32.8

1,084

I

61,759-62,034

+

276

91

35

41

92

 

972

VP110

E

5’, fragment e

 

50.0 i

973 i

II

898-18,972

-

18,075

6,024

360

167

419

 

6,077

VP664

C

  

50.6

6,221

II

19,204-31,302

+

12,099

4,031

343

165 + 166

399 + 412

 

4,180

    

38.0

4,331

II

31,716-34,289

+

2,574

857

423

2

482

 

730

Protein kinase 1 (PK1)

   

35.0

888

II

34,316-34,906

-

591

196

421

1

480

 

204

VP28

E

  

25.5

204

II

35,421-38,787

+

3,367

1,120 a

139

82

194

 

1,208

   

STR

39.8

1,247

II

38,756-39,691

+

936

311

137

81

192

 

337

VP337

   

25.4

351

II

40,142-41,488

-

1,347

448 a

131

77

186

 

484

   

Poly

33.4

495

II

41,511-42,371

+

861

286

133

78

188

 

271

    

33.4

302

III

561-848

-

288

95

21

37

77

 

200

hr-binding protein

 

5’; 3’ e

 

15.7

204

III

927-1,754

-

828

275

23

38

79

 

286

    

37.2

289

III

1,820-2,215

-

396

131

25

39

81

 

231

  

5’ e

 

16.2

247

III

2,231-6,865

-

4,635

1,543

26

40

86 + 82

 

1,535

VP507

   

50.2

1,590

III

8,195-11,185

-

2,991

996

226

114

281

 

936

    

27.2

1,074

III

11,727-14,753

-

3,027

1,008

192

100

247

 

1,019

    

44.8

1,051

III

14,831-15,739

+

909

302

191

99

246

 

311

Endonuclease

   

44.9

325

III

17,211-18,929

-

1,719

572

427

3

486

 

623

Latency-related

   

34.2

658

III

19,167-22,964

+

3,798

1,265

433

4

492 + 496

 

1,261

    

51.6

1,323

III

23,005-24,687

+

1,683

560

440

5

500

 

607

    

46.2

623

III

24,642-27,239

+

2,598

865

442

6

502

 

800

VP800, VP95

T

  

30.4

895

III

30,327-33,310

-

2,984

994 a

64 + 63

53

121 + 120

 

843

   

Poly

16.4

1,099

III

38,213-40,172

-

1,960

653

277

135

332

 

791

    

31.6

807

III

40,595-44,461

-

3,867

1,289

271

134

326

 

1,219

VP136A

C

 

Poly

36.1

1,348

III

44,426-44,971

+

546

181

270

133

325

 

170

    

34.2

190

III

44,938-46,377

+

1440

479

269

132

324

 

489

VP53c

   

53.9

505

III

46,469-47,209

+

741

246

267

131

321

 

281

    

28.1

281

III

47,325-49,637

+

2,313

770

260

130

315

 

922

VP387

   

25.3

965

III

50,920-52,581

-

1,662

553

1

30

52

 

1,684

VP1684, collagen

E

  

23.5 i

613 i

III

52,725-55,115

-

2,391

796

332

160

388

 

786

VP75

   

38.2

824

III

55,224-57,680

+

2,457

818

327

159

383

 

856

VP90

E

  

40.1

872

III

58,441-59,865

+

1,425

473

147

85

202

 

459

    

19.8

515

III

62,523-63,143

-

621

206

419

(NA)

478

 

193

    

31.9

210

III

62,963-64,516

-

1,554

517

415

183

474

 

544

VP544, VP60 §

C

  

43.0

547

III

64,652-65,005

+

354

117

414

182

473

 

121

VP19

E

  

39.3

122

III

65,332-65,604

+

273

90

324

157

380

 

82

    

31.3

98

III

65,906-66,142

-

237

78

322

156

378

 

227

  

5’, 3’; fragment

 

16.1 i

227 i

III

66,363-66,752

-

390

129

321

155

377

 

117

VP13B, VP16

E

  

39.5

129

III

66,908-69,883

+

2,976

991

313

154

369

 

1,179

    

29.9

1,224

III

69,974-70,567

+

594

197

311

153

367

 

204

VP26

T

  

28.2

206

III

70,645-71,418

-

774

257

310

152

366

 

272

    

33.0

277

III

71,415-72,818

-

1,404

467

308

151

364

 

466

VP466, VP51

C

  

44.4

480

III

72,809-73,111

-

303

100

306

150

362

 

419

VP39A

T

5’ e

 

10.8

435

III

73,422-75,302

+

1,881

626

282

140

337

 

634

    

54.1

658

III

75,443-77,426

+

1,984

660 a

161

90

217

 

759

   

Poly

29.8

786

III

77,503-84,399

+

6,897

2,298

514

27

39

 

2,351

DNA polymerase

   

55.0

2,409

III

84,915-86,372

+

1,458

485

no homology

  

Inhibitor of apoptosis protein

     

III

86,662-87,348

-

687

228

295

146

351

 

209

    

23.6

267

III

87,428-87,922

-

495

164

294

145

350

 

206

    

17.6

216

III

88,010-88,258

+

249

82

293a

144

349

 

97

VP14

 

5’ ef

 

55.3

97

III

88,215-92,825

+

4,611

1,536

289

143

344

 

1,564

VP160A, VP190

C

  

38.1

1,627

III

93,236-96,400

-

3,165

1,054

285

142

340

 

1,100

    

36.9

1,116

III

96,852-98,046

-

1,195

398 a

78

59

135

 

398

hr-binding protein

  

Poly

20.9

460

  1. abased on protein sequences after “correction” of the frameshifts
  2. bAccession numbers for the three reference genomes see in text. ORF identification numbers are taken either from original publications or from GenBank annotations. Cases of frameshifts in the WSSV genomes are marked with “+” connecting two parts of the original ORF. “(NA)” marks an ORF present in WSSV-TH genome, but not annotated
  3. cfamilies of paralogs according to [8]. “(NA)” marks one family not reported in that study
  4. dbased largely on the summary presented by [1]. Structural proteins are prefixed with “VP”, their location (when known) is marked with letters: C – nucleocapsid; T – tegument; E – envelope
  5. ecases of truncations confirmed with Sanger-sequencing
  6. fadditionally: predicted start codon is non-canonical (ACG)
  7. gcauses of frameshifts (when present, presumably sequencing artefacts): Poly – homopolymer regions; STR – short tandem repeats
  8. hall alignments were performed with the G-INS-i mode. If not noted otherwise, identities are reported for the whole alignments
  9. ibased on truncated alignments