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Table 6 Differential allelic expression

From: Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

Gene_id

SNP

Control

Stress

SNP

TAIR gene

position

Allele-A

Allele-B

Freq1

Allele-A

Allele-B

Freq

Annotation

Annotation

Eucgr.I01495

25151384

36

1

0.97

15

589

0.02

syn

basic chitinase

Eucgr.I02395

34587565

10

3

0.77

40

85

0.32

5'UTR

heat repeat-containing

Eucgr.I02395

34586749

8

16

0.33

177

6804

0.03

non-syn

dehydrin lea

Eucgr.F00644

8551578

5

44

0.10

56

2036

0.03

non-syn

GA requiring 3

Eucgr.D00606

11184666

6

3

0.67

33

266

0.11

syn

dormancy-associated

Eucgr.B03987

63762855

22

25

0.47

111

430

0.21

3'UTR

glycosyl transferase

Eucgr.B03987

63762861

20

29

0.41

96

382

0.20

3'UTR

glycosyl transferase

Eucgr.A02790

38441055

8

2

0.80

121

579

0.17

non-syn

low-temperature-induced

Eucgr.A02790

38441184

4

11

0.27

31

738

0.04

non-syn

low-temperature-induced

Eucgr.C01388

22208472

1114

155

0.88

8

7

0.53

syn

lipid transfer protein

Eucgr.I01393

24399270

28

1

0.97

39

158

0.20

non-syn

dnaj heat shock

Eucgr.I01393

24399277

28

3

0.90

40

162

0.20

non-syn

dnaj heat shock

Eucgr.I01393

24399018

4

6

0.40

205

11

0.95

non-syn

dnaj heat shock

Eucgr.C01031

16478607

7

6

0.54

101

748

0.12

syn

unknown protein

Eucgr.H00189

1874619

7

1

0.88

6

94

0.06

syn

cellulose synthase

Eucgr.G01188

19918572

5

12

0.29

24

390

0.06

syn

ethylene-dependent

Eucgr.K01389

17036132

49

19

0.72

259

1030

0.20

syn

xerico

Eucgr.K01389

17035852

7

53

0.12

34

1275

0.03

5'UTR

xerico

Eucgr.K01389

17035854

21

34

0.38

797

547

0.59

5'UTR

xerico

Eucgr.K01389

17036141

16

51

0.24

817

386

0.68

syn

xerico

Eucgr.E03875

67744315

114

123

0.48

6

28

0.18

non-syn

methyltransferase

Eucgr.C02590

49489875

35

1

0.97

87

324

0.21

non-syn

cipk6

Eucgr.C02590

49489315

14

0

1.00

26

62

0.30

5'UTR

cipk6

Eucgr.C02590

49489916

54

1

0.98

153

271

0.36

non-syn

cipk6

Eucgr.C02590

49489924

55

2

0.96

154

242

0.39

syn

cipk6

Eucgr.C02590

49489939

15

7

0.68

39

211

0.16

syn

cipk6

Eucgr.A02077

31568814

24

22

0.52

177

435

0.29

non-syn

oxidoreductase

Eucgr.I01579

25696053

36

5

0.88

10

18

0.36

syn

naringenin-chalcone synthase

Eucgr.I01579

25696038

30

4

0.88

15

17

0.47

syn

naringenin-chalcone synthase

  1. 1Freq – Frequency of allele-A.
  2. SNPs with significant differential allelic expression between samples at the beginning (S0) and at the end of stress (S1) treatment. Genes with these SNPs also showed significant differential gene expression between control (C1) and stress (S1) treatments. E. grandis genes overlapping SNP positions are shown. Gene annotations are based on Arabidopsis homologs of the Eucalyptus transcripts. More details are shown in Additional file 5.
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BMC Genomics

ISSN: 1471-2164

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