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Table 3 Nucleotide diversity analysis and Ka/Ks ratios for the Pm3 alleles.

From: Wheat gene bank accessions as a source of new alleles of the powdery mildew resistance gene Pm3: a large scale allele mining project

Domain

Total number of sites aligned

Number of polymorphic sites

Average number of polymorphic sites per 100 bp

Nucleotide diversity (Ï€)

Number of synonymous substitutions (Ks)

Number of non-synonymous substitutions (Ka)

Ka/Ksratio

Hexaploid

       

Pm3 genes (excluding intron)

4242

299

7.03

0.01008

103

252

2.44

CC

474

0

0.00

0.00000

0

0

-

NBS

1062

80

7.51

0.00742

37

47

1.27

Interspacer

198

37

18.4

0.0379

12

28

2.33

LRR

2508

182

7.25

0.0109

54

177

3.27

Tetraploid

       

Pm3 genes (excluding intron)

4242

185

4.36

0.01113

43

147

3.41

CC

474

3

0.63

0.00086

1

2

2

NBS

1062

4

0.37

0.00045

1

3

3

Interspacer

198

31

15.65

0.02598

9

22

2.44

LRR

2508

147

5.86

0.01643

32

120

3.75

Hexaploid and tetraploid

    

Pm3 genes (excluding intron)

4242

356

8.38

0.01311

121

311

2.57

CC

474

3

0.63

0.00038

1

2

2.00

NBS

1062

84

7.90

0.00451

38

50

1.31

Interspacer

198

43

21.39

0.03273

16

38

2.37

LRR

2508

226

9.02

0.01761

66

221

3.34

  1. Nucleotide diversity was analyzed together as well as separately for Pm3 alleles isolated from hexaploid and tetraploid wheat, respectively. The domain positions correspond to that of consensus sequence Pm3CS and insertions/deletions were not counted as aligned sites. Synonymous and non-synonymous substitutions were determined by comparison of each codon in every sequence with the respective consensus sequence at that position. The number of polymorphic sites is lower than the sum of synonymous and non-synonymous substitutions because of multiple different bases in some polymorphic sites.