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Table 1 Variation for each gene region showing the P. trichocarpa gene models used as reference, the number of Salix genotypes and Populus species studied, the total number of SNPs detected, the number of SNPs within Salix and within Populus; the number of insertions/deletions

From: High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources

Gene region

P. trichocarpa reference(Phytozome gene model)a

No.ofSalix genotypes studied

No.ofPopulus species studied(See Table2)

Predicted Exons/intronsa

Studied length (bp)

Total SNPs per kbpb

SNPs withinSalix per kbpc

SNPs withinPopulus per kbpc

Total Indels

Total non synonymous sites amongSalix per kbp

A) DIRECT SEQUENCING

 

C3H1

Potri.006G033300

23

5

Exon

347

118

63

40

0

6

Intron

0

/

/

/

/

 

C4H

Potri.013G157900

13

6

Exon

609

76

16

21

0

3

Intron

0

/

/

/

/

 

CesA2

Potri.005G194200

22

4

Exon

244

53

20

20

0

0

Intron

87

195

92

11

2

 

Pal1

Potri.006G126800

20

6

Exon

474

99

46

40

0

0

Intron

0

/

/

/

/

 

CesA1

Potri.002G257900

20

6

Exon

629

68

11

38

0

2

Intron

130

208

146

31

3

 

Knat7

Potri.001G112200

17

2

Exon

120

25

8

8

0

0

Intron

95

284

221

42

3

 

Kor1

Potri.003G151700

23

5

Exon

192

63

10

36

0

0

Intron

117

179

111

17

0

 

SAD

Potri.016G078300

15

4

Exon

395

142

78

30

1

28

Intron

19

158

0

158

0

 

B) COMBINED RESULTS (from direct sequencing and cloning)

 

CesA1

Potri.002G257900

20

6

Exon

629

107

33

54

0

14

Intron

130

315

177

46

8

 

Knat7

Potri.001G112200

17

2

Exon

372

70

38

30

0

13

Intron

392

209

117

56

15

 

Kor1

Potri.003G151700

23

5

Exon

319

94

38

34

0

19

Intron

438

201

98

23

11

 

SAD

Potri.016G078300

15

4

Exon

582

165

93

24

1

38

Intron

217

475

207

69

4

 

C) CLONING

 

4CL2

Potri.019G049500

7

2

Exon

249

116

48

8

0

20

Intron

289

325

83

35

14

 

GA-20

Potri.015G134600

6

2

Exon

620

176

58

105

0

27

Intron

290

462

117

210

31

 

CAD

Potri.009G095800

7

2

Exon

439

125

96

16

1

34

Intron

436

273

128

76

21

 

Mybr2r3

Potri.015G033600

6

2

Exon

351

117

23

26

1

11

    

Intron

259

228

108

31

11

 
  1. aBased on P. trichocarpa v3 assembly retrieved from Phytozome (http://www.phytozome.net/poplar).
  2. b(No. total SNPs / length) × 1,000.
  3. c(No. SNPs within Salix or within Populus / length) × 1,000.
  4. Both direct sequencing and cloning techniques were used.