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Table 2 Putative function of 164 genes preferentially expressed in cold stored peach fruits.

From: Isolation and functional characterization of cold-regulated promoters, by digitally identifying peach fruit cold-induced genes from a large EST dataset

Contig

E3

E1+E2+E4

AC test1

Putative Function;Arabidopsis ortholog2

Biological process unknown (GO:0000004)

C517

10

6

E4

NC domain-containing protein (located in mitochondrion); At5g06370

C675

12

4

E2; E4

Expressed protein; At3g03870↓

C774*

11

4

E2; E4

Novel gene

C2089

20

0

E1; E2; E4

Expressed protein (located in endomembrane system); At5g64820

C2112

31

2

E1; E2; E4

Cupin family protein (nutrient reservoir activity); At1g07750

C2139

12

0

E1; E2; E4

Novel gene

C4065

13

8

E2

Expressed protein; At5g52870↑

C273

5

2

 

Expressed protein; At5g24660↓

C477

7

6

 

Expressed protein (located in endomembrane system); At5g64510↓

C1207*

8

7

 

Novel gene

C2134

3

2

 

Expressed protein; At1g71080

C2148

4

1

 

Novel gene

C2155

4

1

 

Expressed protein; At5g11730

C2167

3

2

 

RWD domain-containing protein; At1g51730

C2173

7

1

 

Expressed protein (located in mitochondrion);At5g60680↑

C2193

3

2

 

Novel gene

C2211

8

1

 

Ankyrin repeat family protein (protein binding); At2g28840

C2241

6

2

 

Expressed protein (located in mitochondrion); At5g51040

C2267

7

0

 

Integral membrane family protein; At4g15610

C2315

5

3

 

Expressed protein; At1g70780

C2318

3

2

 

Ribosome associated membrane protein RAMP4; At1g27350

C2343

9

9

 

Novel gene

C2560

6

1

 

Expressed protein; At3g27880↑

C2591

6

1

 

Expressed protein (located in mitochondrion); At5g24600

C2682*

4

2

 

N-methyl-D-aspartate receptor-associated protein; At4g15470

C2713

4

1

 

Glycine-rich protein; At4g22740

C2778

12

7

 

Zinc finger (AN1-like) family (DNA and zinc ion binding); At3g52800↑

C2806

8

2

 

C2 domain-containing protein; At1g22610

C3094

3

2

 

Reticulon family protein (located in ER and mitochondrion); At3g10260↓

Cell homeostasis (GO:0019725)

C2265

91

38

E1; E2; E4

Metallothionein-like protein; At5g02380

C2202*

5

1

 

Metallothionein-like protein; NSM4

Cell organization and biogenesis (GO:0016043)

C734

17

9

E2; E4

Proline-rich/extensin family; At2g27380

C1240

62

20

E1; E2; E4

Proline-rich/extensin family; At1g54215

C2494*

10

3

E2

Actin-depolymerizing factor 4; At5g59890

C2831

20

6

E1; E2; E4

Leucine-rich repeat/extensin family; At4g13340↑

C3041

12

5

E2; E4

Leucine-rich repeat/extensin family; At4g13340↑

C831

4

2

 

BON1-associated protein (BAP2); At2g45760↑

C1062

4

1

 

Invertase/pectin methylesterase inhibitor family; At5g62360↑

C2060

7

3

 

Expansin family; At4g38400↑

C2086*

6

1

 

Arabinogalactan-protein; At5g64310

C2073

6

2

 

Zinc finger protein (CYO1); At3g19220

C2574

7

3

 

Invertase/pectin methylesterase inhibitor family; At2g01610

C2762*

4

1

 

Profilin 4; At2g19770

C2815

4

1

 

Phytochelatin synthetase; At4g16120

Cellular protein metabolism (GO:0044267)

C228*

112

51

E1; E2; E4

DJ-1 family protein/protease-related; At3g02720↓

C379*

50

21

E1; E2; E4

DJ-1 family protein/protease-related; At3g02720↓

C1027*

47

46

E1; E2; E4

Heat shock cognate 70 kDa protein 1; At5g02500

C1660

51

25

E1; E2; E4

Cysteine proteinase inhibitor-related; At2g31980↓

C2099*

13

1

E1; E2; E4

DJ-1 family protein/protease-related; At3g02720↓

C2436

17

3

E1; E2; E4

Rhomboid family protein; At1g63120

C2715

41

21

E1; E2; E4

Luminal binding protein 1 (BiP-1); At5g28540

C2066*

3

2

 

60S ribosomal protein L23A; At3g55280↑

Cellular protein metabolism (GO:0044267)

C2072*

6

2

 

DNAJ heat shock protein; At3g44110

C2217*

7

3

 

20S proteasome beta subunit A; At4g31300

C2308*

9

0

 

Heat shock protein 70; At3g12580↓

C2345*

4

2

 

Ubiquitin carrier protein E2; At2g02760

C2364

5

2

 

Phosphatase-related (SGT1B); At4g11260

C2388

5

3

 

F-box family protein (AtSKP2;2); At1g77000

C2593

4

1

 

C3HC4-type RING finger family protein; At1g26800↓

C2597

6

2

 

26S proteasome regulatory subunit S3; At1g20200

C2691

7

6

 

C3HC4-type RING finger family protein; At5g47610

C2360

10

7

 

Structural constituent of ribosome; At5g15260

C2735

9

4

 

40S ribosomal protein S9; At5g39850

C3022

6

2

 

Translation initiation factor IF5; At1g36730

C3051*

5

2

 

DJ-1 family protein/protease-related; At3g02720↓

C3520

4

1

 

60S ribosomal protein L36; At3g53740

C3551*

11

4

 

Cysteine proteinase inhibitor; At3g12490↑

C3656

6

4

 

40S ribosomal protein S26; At3g56340

C4131

3

2

 

C3HC4-type RING finger family protein; At5g48655

Development (GO:0007275)

C2802

10

2

E1

Senescence-associated protein; At1g78020↓

C2919

10

1

E1; E2

Senescence-associated protein; At5g20700

C1113

6

3

 

Auxin-responsive protein; At3g25290↓

C3887*

4

1

 

Maternal effect embryo arrest 60; At5g05950

C3942

6

4

 

SIAMESE, cyclin binding protein; At5g04470↓

C2457

6

0

 

Nodulin MtN3 family protein; At5g13170↑

Generation of precursor metabolites and energy (GO:0006091)

C2304

7

1

 

NADH dehydrogenase; At4g05020↑

C2541

8

1

 

Uclacyanin I; At2g32300↓

C2552

5

0

 

Flavin-containing monooxygenase family protein; At1g48910↑

Metabolism (GO:0008152) 3

C1017

15

9

E2

Xyloglucan endotransglycosylase; At4g25810↓ (carbohydrate)

C1258*

19

2

E1; E2; E4

Phosphoesterase family protein; At3g03520↓ (phospholipid)

C2373

15

8

E2; E4

β-alanine-pyruvate aminotransferase; At2g38400↓ (amino acid)

C2397*

27

9

E1; E2; E4

S-adenosylmethionine decarboxylase; At3g02470 (polyamine)

C2554*

17

3

E1; E2; E4

UDP-glucoronosyl/UDP-glucosyl transferase; At5g65550 (anthocyanin)

C2957

11

0

E1; E2; E4

Glycosyl hydrolase family 3; At5g49360↓ (carbohydrate)

C2669

61

28

E1; E2; E4

Phosphoserine aminotransferase; At4g35630 (amino acid)

C656

4

3

 

Nucleoside diphosphate kinase 3; At4g11010 (nucleotide)

C821*

4

1

 

UDP-glucoronosyl/UDP-glucosyl transferase; At5g49690↑ (anthocyanin)

C926*

7

6

 

(1-4)-β-mannan endohydrolase; At5g66460↑ (carbohydrate)

C1000*

8

2

 

Alkaline alpha galactosidase; At1g55740 (carbohydrate)

C1693

9

3

 

Haloacid dehalogenase-like hydrolase; At5g02230↓

C1943

4

3

 

2-oxoglutarate-dependent dioxygenase; At1g06620 (ethylene)

C2424

5

0

 

β-amylase; At4g17090↑ (starch)

C2495

8

1

 

Cinnamoyl-CoA reductase; At4g30470 (lignin)

C2522

11

8

 

Glycosyl hydrolase family 5; At1g13130↑ (carbohydrate)

C2569

7

1

 

Short-chain dehydrogenase/reductase family; At3g61220↓

C2602

5

0

 

Short-chain dehydrogenase/reductase family; At4g13250

C2610

5

0

 

Galactinol synthase; At3g28340↑ (carbohydrate)

C2222

6

0

 

Carboxyesterase 5; At1g49660↓

C2635

6

4

 

GNS1/SUR4 membrane family protein; At4g36830 (fatty acid)

C2705

7

4

 

DSBA oxidoreductase family protein; At5g38900 (organic acid)

C669

4

2

 

Dehydrogenase; At5g10730

C2936

4

1

 

Pyruvate decarboxylase; At5g17380 (glycolisis)

C2940

4

1

 

Farnesyl pyrophosphate synthetase 1; At5g47770 (lipid)

C2976

6

1

 

Aminoalcoholphosphotransferase; At1g13560 (phospholipid)

C3047*

7

4

 

Dienelactone hydrolase; At3g23600 (alkene)

Metabolism (GO:0008152 ) 3

C3058*

5

1

 

Cellulose synthase; At4g39350 (cellulose)

C3152

8

3

 

Purple acid phosphatase; At3g52820 (phosphate)

C3225

4

1

 

Acyl-activating enzyme 12; At1g65890 (phospholipid)

C4127

6

2

 

Ω-3fatty acid desaturase; At5g05580 (fatty acid)

C86

6

3

 

Embryo-abundant protein; At2g41380↑

C677

4

2

 

Cyclic phosphodiesterase; At4g18930 (RNA)

C802

4

3

 

RNA recognition motif-containing protein; At5g04600 (RNA)

C2798

3

2

 

Small nuclear ribonucleoprotein G; At2g23930↑ (RNA)

Response to stress (GO:0006950)

C30

57

27

E1; E2; E4

Cold acclimation WCOR413-like protein; At3g50830

C254

71

10

E1; E2; E4

Dehydrin Xero2; At3g50970↑

C304*

189

124

E1; E2; E4

Type II dehydrin SKII; (ERD14) At1g76180↑

C910

126

38

E1; E2; E4

Class III acidic endochitinase; At5g24090

C1479

96

25

E1; E2; E4

Harpin inducing protein; At5g06320↑

C1708

30

12

E1; E2; E4

Thaumatin-like protein; At1g20030↑

C2131

65

2

E1; E2; E4

Class Ib basic endochitinase; At3g12500↑

C2177

15

4

E1; E4

Thaumatin-like protein; At1g20030↑

C2317

67

6

E1; E2; E4

Thaumatin-like protein; At1g20030↑

C2514*

20

15

E2

Glutathione peroxidase; At4g11600↑

C2528

22

7

E1; E2; E4

Hevein-like protein; At3g04720↓

C2655*

10

6

E4

DREPP plasma membrane polypeptide; At4g20260

C2988*

37

6

E1; E2; E4

Polygalacturonase inhibiting protein; At5g06860↑

C2473*

10

0

E1; E2; E4

Major allergen Pru p 1; At1g24020

C2147

8

0

 

Thaumatin-like protein; At1g20030↑

C2441

8

1

 

Class IV chitinase; At3g54420

C2507

5

2

 

Pyridoxine biosynthesis protein; At5g01410

C2556

5

0

 

4-aminobutyrate aminotransferase; At3g22200

C2578

3

2

 

Aldehyde dehydrogenase; At1g44170

C2926

7

2

 

Wounding stress inducimg protein; At4g24220

C3613*

3

2

 

Harpin inducing protein; At3g11660

C1889*

5

4

 

Major allergen Pru p 1; At1g24020

C3858*

4

2

 

Late embryogenesis abundant protein 3; At4g02380↑

Signal transduction (GO:0007165)

C815

9

1

 

Leucine-rich repeat family protein; At3g49750

C1192*

6

5

 

CBL-interacting protein kinase 12; At4g18700↑

C2205

5

4

 

Ser/Thr kinase; At2g47060↓

C2312*

8

3

 

Touch-responsive/calmodulin-related protein 3; At2g41100↓

C2430*

6

6

 

Remorin family protein; At5g23750↓

C2548

10

6

 

Fringe-related protein; At4g00300

C2829*

3

2

 

Protein kinase, 41K; At5g66880↓

C2853

5

3

 

GTP-binding protein Rab2; At4g17170

C3690*

10

8

 

Ser/Thr kinase; At4g40010

Transcription (GO:0006350)

C452

4

2

 

Myb family; At5g45420

C2742*

5

1

 

DREB subfamily A-6; At1g78080↓

C3420*

8

4

 

MADS-box protein (AGL9); At1g24260

C3812

3

2

 

WRKY family; At4g31550↑

Transport (GO:0006810)

C716

13

5

E2; E4

Proton-dependent oligopeptide transport family; At5g62680↓

C1846

15

10

E4

Auxin efflux carrier family protein; At2g17500↓

C2091

18

0

E1; E2; E4

Protease inhibitor/seed storage/lipid transfer family; At1g62790

C163

4

1

 

Vesicle-associated membrane protein; At1g08820

C208

9

2

 

GTP-binding secretory factor SAR1A; At4g02080

C235

5

4

 

Sugar transporter; At1g54730↓

C484

11

6

 

Porin; At5g67500

C1526

5

4

 

emp24/gp25L/p24 protein; At3g22845

Transport (GO:0006810)

C2062

3

2

 

Ripening-responsive protein; At1g47530

C2236

3

2

 

Ras-related GTP-binding protein; At4g35860

C2476

9

1

 

Bet1 gene family; At4g14450↑

C2679

5

0

 

Sulfate transporter ST1; At3g51895↑

C3063

4

2

 

Amino acid carrier; At1g77380↑

C3066

4

1

 

Sulfate transporter; At3g15990

C3099

3

2

 

Ras-related GTP-binding protein; At1g52280

  1. 1 Statistically significant cold-induced contigs detected with the Audic and Claverie test (p < 0.01) vs. E1, E2 or E4 cDNA libraries. The column shows the cDNA library with differences to E3.
  2. 2The column described the locus identifier (id) of the Arabidopsis most similar protein. The locus ids with ↑ [37] are the Arabidopsis cold response genes similarly up-regulated; the locus ids with ↓ [31] are the genes with opposite response, down-regulated in Arabidopsis (ColdArrayDB; http://cold.stanford.edu/cgi-bin/data.cgi).
  3. 3Between parentheses: the principal subcategory of the biological process "metabolism" associated to the annotation.
  4. 4NSM: Not significant match (E value < 10-10) with A. thaliana sequences.
  5. * Contigs that shown significant sequence homology (e value > 10-10) with contigs from others hierarchical clusters.
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BMC Plant Biology

ISSN: 1471-2229

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