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Braving the attitude of altitude: Caragana jubata at work in cold desert of Himalaya. Authors


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aPercent of the fraction assembled in the contigs/total no. of ESTs

Supplementary Table S2: Expressed sequence tags (ESTs) obtained in the forward suppression subtractive hybridization cDNA library (CjSF), their homology, score/ E-value and length. Plasmids were sequenced, the sequences were analysed using BLASTX programme (default) at NCBI database and categorised into: (1), proteins with known function; (2), proteins with unknown function; and (3), proteins with no match in the database. All the redundant EST sequences were clustered into singletons (i.e. unique clones) and contigs (i.e. 2 or more clones). Both of these together formed a non-redundant independent sequence termed as unigenes. All the unigenes sequences were submitted to NCBI dbEST database. ESTs were functionally annotated by BLAST analysis against the GenBank non-redundant protein database and subsequently classified manually into functional categories according to their putative functions3. ESTs obtained in CjSF were expected to be up-regulated during exposure to low temperature (4°C).


Clone ID

GenBank accession no.

Homology

Clones with similar homology§

Redundancy#

cDNA insert

size (bp)

Score/E-value

DNA/RNA binding (transcription factors)

CjSF2

FE968694

MYB transcription factor MYB133

2

1

438

37.0 bits/ 0.42

CjSF72

FE968738

MYB transcription factor MYB177

6, 72

2

560

58.9 bits/ 2e-07


CjSF76

FE968740

Homeobox-leucine zipper protein HAT22

76

1

381

78.6 bits/ 1e-13

CjSF120

FE968766

WRKY DNA-binding protein 6

120

1

726

40.4 bits/ 0.11

CjSF235

FE968828

Ethylene-responsive transcription factor 3

235

1

364

88.2 bits/2e-16


CjSF324

FE968873

KOW domain-containing transcription factor family protein

324

1

1118

48.5 bits/9e-04

CjSF370

FE968893

Auxin response factor 7

370

1

537

260 bits/3e-68

CjSF454

FE968942

WUS-Interacting Protein

454

1

773

196 bits/1e-48

CjSF338

FE968880

MYB transcription factor MYB129

338

1

666

160 bits/6e-38

CjSF18

FE968701

P72 DEAD box protein

18

1

678

52.4 bits/ 5e-08

CjSF183

FE968798

RNA polymerase sigma subunit E

183,260,290,361,556

5

560

198 bits/2e-49


CjSF443

FE968936

Resolvase, N-terminal domain

443

1

452

37.0 bits/0.44


CjSF138

FE968775

RNA binding domain protein

138,411,430

3

326

29.3 bits/ 0.80

CjSF388

FE968904

HAT22 (homeobox-leucine zipper protein 22); transcription factor

388

1

660

160 bits/6e-38

CjSF397

FE968913

RNA polymerase beta' subunit

397

1

965

501 bits/2e-140


CjSF383

FE968899

Putative small nuclear ribonucleoparticle-associated protein

383

1

1137

40.0 bits/0.31

Defense




CjSF206

FE968810

Putative Mce family protein

206

1

283

33.1 bits/6.5

CjSF428

FE968929

Possible internalin protein

428

1

418

43.9 bits/0.004

CjSF519

FE968973

Putative uromodulin

21

1

574

33.5 bits/8.1

CjSF33

FE968712

Cold acclimation responsive protein CAR2

33

1

828

57.8 bits/8e-07

CjSF62

FE968732

Low temperature and salt responsive protein LTI6A

62

1

435

77.4 bits/ 3e-13


CjSF95

FE968752

RCI2A (RARE-COLD-INDUCIBLE 2A)

95,185

2

435

75.5 bits/ 1e-12


CjSF233

FE968826

Cold-acclimation specific protein 31

233, 352

2

760

47.4 bits/0.001


CjSF250

FE968834

Hydroxyproline-rich glycoprotein family protein

250

1

903

37.0 bits/1.8


CjSF438

FE968933

Proline-rich protein

438

1

836

40.4 bits/0.15

CjSF367

FE968891

Stress protein

367

1

1120

37.4 bits/0.016

Signal transduction




CjSF99

FE968755

Nucleoside diphosphate kinase 2

99,513

2

355

82.0 bits/ 1e-14


CjSF175

FE968793

Serine-threonine kinase

175,204

2

702

287 bits/5e-76

CjSF38

FE968716

HMG-1 like protein gene

38

1

505

82.4 bits/1e-14

CjSF126

FE968770

MtN19-like protein

126

1

553

150 bits/ 5e-35

CjSF280

FE968848

CBL-interacting protein kinase 22

280,470

2

498

143 bits/5e-33


CjSF401

FE968915

Putative signaling protein

401

1

517

36.2 bits/0.94

CjSF483

FE968955

Signal transduction histidine kinase

483

1

249

35.4 bits / 1.3


CjSF29

FE968709

14-3-3-like protein

29

1

406

228 bits/ 1e-58

CjSF107

FE968759

SKP1-like b

107,485

2

744

36.6 bits/ 1.7

CjSF60

FE968730

Indole-3-acetic acid induced protein ARG-2

60, 154

2

270

72.8 bits/ 7e-12

CjSF88

FE968749

ABA-inducible protein-like protein

83,88,106,111,116,168,208,245,273,282,312,339,348,354,357,363,372,382,414,425,431,492,531,533,555

25

607

65.9 bits/ 2e-09


CjSF173

FE968792

Calmodulin-related protein

173,253

2

476

68.6 bits/1e-10

CjSF337

FE968879

Putative calcium dependent protein kinase

337

1

620

192 bits/1e-47


CjSF536

FE968977

Protein phosphatase type 2C

536,550

2

693

242 bits/2e-62

Oxidative stress




CjSF121

FE968767

Manganese superoxide dismutase

121

1

544

33.5 bits/ 6.9

CjSF71

FE968737

Putative NADPH-cytochrome P450 reductase

71,281

2

557

103 bits/ 8e-21

CjSF275

FE968846

Thioredoxin domain 2; Thioredoxin fold

275

1

544

110 bits/6e-23


CjSF390

FE968906

Phospholipid hydroperoxide glutathione peroxidase, chloroplast precursor (PHGPx)

390

1

494

199 bits/5e-50


CjSF391

FE968907

Catalase

391

1

503

59.7 bits/7e-08

Photosynthesis/ energy metabolism




CjSF288

FE968851

Chlorophyll A-B binding family protein

288,551

2

521

232 bits/9e-60

CjSF292

FE968853

NADH-plastoquinone oxidoreductase chain

292

1

398

188 bits/1e-46


CjSF398

FE968914

Photosystem II protein D1

398

1

569

250 bits/4e-65

CjSF444

FE968937

Cytochrome b6

444

1

442

256 bits/5e-67

CjSF46

FE968722

Ribulose-1,5-bisphosphate carboxylase small subunit rbcS1

46,55,64,140,380,403,445,488,543

9

550

254 bits/2e-66

CjSF63

FE968733

Early light inducible protein

40,63,74,105,117,119,123,130,149,153,191,198,201,213,247,259,263,319,373,377,409,432,436,464,472,482

26

700

228 bits/ 3e-58


Metabolism




CjSF171

FE968790

T-protein of the glycine decarboxylase complex

171

1

354

162 bits/9e-39


CjSF234

FE968827

Phytoene synthase

234,508

2

558

299 bits/7e-80

CjSF157

FE968783

Kinesin-like protein

157

1

620

253 bits/ 5e-66

CjSF389

FE968905

Digalactosyldiacylglycerol synthase 1, chloroplast precursor

389

1

1116

323 bits/5e-89


CjSF160

FE968786

DNA primase

160

1

292

33.9 bits/ 3.7

CjSF421

FE968923

Ribulose-5-phosphate-3-epimerase

421,507,512

3

467

221 bits/2e-56


CjSF28

FE968708

Putative acyl-CoA synthetase

28

1

463

54.7 bits/ 2e-06

CjSF36

FE968715

Beta-amylase

36

1

538

234 bits/ 3e-60

CjSF118

FE968765

Isopentenyl-diphosphate delta isomerase

437

1

522

76.3 bits/ 8e-13

CjSF48

FE968723

ATP citrate lyase alpha subunit

48

1

830

279 bits/ 2e-73

CjSF197

FE968806

L-asparaginase

197

1

443

102 bits/7e-21

CjSF311

FE968867

Sin3 histone deacetylase corepressor complex

311

1

241

44.3 bits/ 0.003

CjSF375

FE968818

Putative esterase/lipase/thioesterase family protein

222,375,521

3

272

55.8 bits/9e-07


CjSF261

FE968840

Serine hydroxymethyltransferase

261

1

676

218 bits/3e-55
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