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Table 2 Substitutions between the genomes of PVS isolates H95 and H00

From: Construction and characterization of an infectious cDNA clone of potato virus S developed from selected populations that survived genetic bottlenecks

 

ORF1

ORF2

ORF3

ORF4

ORF5

ORF6

Total

Nt

(%)

Nt

(%)

Nt

(%)

Nt

(%)

Nt

(%)

Nt

(%)

Nt

(%)

Nucleotide substitutions

Ti

260

81.0

22

81.5

12

85.7

4

100

3

100

1

100

302

81.6

Tv

61

19.0

5

18.5

2

14.3

0

0

0

0

0

0

68

18.4

Ti/Tv

4.26

4.40

6.00

–

–

–

4.44

S

232

72.3

18

66.7

13

92.9

3

75

2

66.7

0

0

268

72.4

NS

89

27.7

9

33.3

1

7.1

1

25

1

33.3

1

100

102

27.6

Ka/Ks

0.38

0.50

0.08

0.33

0.50

–

0.38

Total

321

5.4

27

3.9

14

4.3

4

2.0

3

0.3

1

0.4

370

4.4

 

Replicase

TGBp1

TGBp2

TGBp3

CP

CRP

Total

Aa

(%)

Aa

(%)

Aa

(%)

Aa

(%)

Aa

(%)

Aa

(%)

Aa

(%)

Amino acids substitutionsa

0–3

22

27.5

2

28.6

0

0

0

0

0

0

1

100

25

27.5

4

22

27.5

0

0

0

0

0

0

1

100

0

0

23

25.3

5

36

45.0

5

71.4

1

100

1

100

0

0

0

0

43

47.3

Total

80

4.1

7

3.1

1

0.9

1

1.5

1

0.3

1

1.1

91

3.3

  1. Percentage in italic letters indicate the proportion of different substitutions shown in the left column to the total substitutions
  2. aSubstitutions were evaluated using the Structure-Genetic (SG) scoring system. The SG values range from 0 (most drastic change) to 5 (most frequent substitution)
  3. Nt Nucleotides, Aa Amino acids, Ti Transition, Tv Transversion, S Synonymous, NS Nonsynonymous,
  4. Ka/Ks: The ratio of nonsynonymous to synonymous substitution rate
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Virology Journal

ISSN: 1743-422X