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Characterization of the virome of ancient pome fruit cultivars of Malus Mill. and Pyrus L. using high-throughput sequencing

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https://lib.uliege.be https://matheo.uliege.be

Characterization of the virome of ancient pome fruit cultivars of Malus Mill. and Pyrus L. using high-throughput sequencing

Auteur : Fontdevila Pareta, Núria Promoteur(s) : Massart, Sébastien

Faculté : Gembloux Agro-Bio Tech (GxABT)

Diplôme : Master en bioingénieur : sciences agronomiques, à finalité spécialisée Année académique : 2019-2020

URI/URL : http://hdl.handle.net/2268.2/9475

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ANNEX I: D ISTANCE M ATRIXES

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Table 1. Distance matrix of RdRp region at nucleotide level from complete sequences of apple stem pitting virus (ASPV) and apple green crinkle associated virus (AGCaV), downloaded from NCBI (https://www.ncbi.nlm.nih.gov/), and complete RdRp sequences from the three new ASPV isolates recovered from tree Q9.

KF32 1967

MK92 3755

MK92 3753

KY49 0039

MK23 9268

AB04 5371

KF31 9056

I3- Q9

MK92 3754

MK83 6301

MK92 3756

JF94 6772

JF94 6775

KJ52 2472

KF91 5809

I2- Q9

KY24 2757

AGCaV_K T835289

AGCaV_NC _018714

FR69 4186

LM99 9967

KF32 1966

KY70 2580

EU09 5327

I1- Q9

KY79 8310

LC47 5151

KY70 2581

D21 829

KU30 8398

LC47 5150

MG76 3895 KF321967 80,807 73,817

73,98 8 73,805

74,50 5

74,31 7

74,

049 73,324 74,027 74,331 74,25

0 74,34

1 74,20

8 76,09

7 74, 307

74,29

9 70,425 73,659

73,15 8 73,318

73,75 1

74,42 6

66,63 6

74, 101

73,56 8

73,81 2

74,77 1

73,4 13

73,88 8

76,26 4 74,311 MK923755

80,80

7 73,589

74,26 2 74,094

74,53 6

74,52 9

74,

490 74,495 74,270 74,164 73,13

8 73,39

7 74,04

0 76,03

6 74, 086

73,76

6 70,937 73,796

73,66 0 73,288

73,96 4

74,06 1

66,49 9

74, 452

74,17 7

73,46 1

74,14 7

73,5 65

73,69 0

76,73 7 74,174 MK923753

73,81 7 73,589

72,88 0 72,788

73,41 3

73,26 6

73,

572 73,367 73,309 74,025 75,70

1 76,64

5 72,74

8 73,08

3 73, 693

72,97

7 70,411 73,403

72,46 0 72,971

73,55 6

73,20 5

66,78 9

73, 541

72,70 2

72,51 9

72,82 4

72,9 13

72,65 7

74,62 3 72,974 KY490039

73,98

8 74,262 72,880 99,756 79,50

6 78,60

5 80,

230 80,299 75,659 77,615 73,95

2 74,12

0 78,66

7 75,60

2 75, 160

75,54

1 72,568 75,816

75,45 0 75,061

75,40 4

75,57 2

67,73 4

75, 816

75,70 9

75,63 3

75,84 6

75,2 17

75,63 3

77,26 4 75,217 MK239268

73,80

5 74,094 72,788 99,75

6

79,32 3

78,43 8

80,

093 80,146 75,553 77,432 73,81

5 73,99

8 78,50

0 75,41

9 74, 977

75,35

8 72,408 75,648

75,26 7 74,878

75,20 6

75,41 9

67,58 1

75, 633

75,54 1

75,43 5

75,66 3

75,0 34

75,46 5

77,03 6 75,050 AB045371

74,50

5 74,536 73,413 79,50

6 79,323

86,75 2

81,

305 81,199 75,095 75,339 74,83

6 75,09

5 77,66

1 75,45

0 75, 099

75,13

0 72,784 75,999

74,87 0 74,741

75,83 1

75,55 7

67,85 6

75, 602

74,64 2

74,26 0

75,37 4

75,4 76

76,34 9

78,01 2 75,995 KF319056

74,31

7 74,529 73,266 78,60

5 78,438 86,75

2

78,

948 79,015 75,969 75,665 74,36

8 74,29

2 76,18

4 75,97

1 76, 321

77,06

7 74,367 77,646

76,54 8 75,658

76,68 6

76,71 8

69,08 7

78, 103

78,17 9

77,44 8

79,47 3

77,6 41

76,38 2

79,39 7 76,606 Isolate 3 Q9

74,04

9 74,490 73,572 80,23

0 80,093 81,30

5 78,94

8 85,598 74,958 75,415 74,90

5 74,91

2 76,48

7 75,29

7 76, 121

75,26

7 73,315 76,388

75,44 2 75,411

75,93 0

75,70 9

67,47 4

75, 862

75,01 5

74,73 3

75,85 4

74,8 06

76,41 0

78,14 1 75,934 MK923754

73,32

4 74,495 73,367 80,29

9 80,146 81,19

9 79,01

5 85,

598 75,312 74,901

74,85 1

75,24 8

76,44 1

75,58 7

75, 450

75,23

6 73,013 76,273

74,50 5 74,497

75,38 9

75,65 1

67,09 3

75, 648

75,32 8

75,09 9

75,84 6

74,6 84

76,50 2

77,70 7 76,376 MK836301

74,02

7 74,270 73,309 75,65

9 75,553 75,09

5 75,96

9 74,

958 75,312 84,150

75,17 5

75,28 2

77,02 5

76,59 8

76, 354

76,84

2 72,761 75,698

76,17 0 75,248

76,70 5

76,49 3

69,03 0

77, 285

77,37 6

76,85 7

77,43 7

76,9 14

75,94 2

78,73 4 76,197 MK923756

74,33

1 74,164 74,025 77,61

5 77,432 75,33

9 75,66

5 75,

415 74,901 84,150

74,65 7

74,85 5

79,37 5

76,67 4

76, 636

76,41

5 73,026 76,003

76,64 3 75,111

76,27 8

76,32 5

69,41 1

77, 742

77,13 2

76,96 4

77,84 9

77,1 27

76,01 8

78,53 5 75,846 JF946772

74,25

0 73,138 75,701 73,95

2 73,815 74,83

6 74,36

8 74,

905 74,851 75,175 74,657

94,03 5

76,33 9

76,70 5

76, 255

76,15

6 73,313 76,552

76,01 8 75,903

77,04 0

77,34 6

70,64 7

76, 812

76,33 9

75,89 6

76,73 5

78,6 52

78,52 0

80,74 8 80,122 JF946775

74,34

1 73,397 76,645 74,12

0 73,998 75,09

5 74,29

2 74,

912 75,248 75,282 74,855 94,03

5

76,23 2

76,78 1

76, 262

76,04

9 73,397 76,659

76,15 5 75,720

76,87 3

77,20 8

71,51 6

77, 132

76,26 2

76,00 3

76,81 2

79,0 03

78,07 8

80,93 1 79,710 KJ522472

74,20

8 74,040 72,748 78,66

7 78,500 77,66

1 76,18

4 76,

487 76,441 77,025 79,375 76,33

9 76,23

2

78,51 0

78, 358

79,30

4 75,402 78,358

78,67 6 78,027

78,90 7

78,87 7

70,64 8

80, 708

79,68 6

79,16 7

79,71 6

79,8 93

78,11 4

80,99 8 78,047 KF915809

76,09

7 76,036 73,083 75,60

2 75,419 75,45

0 75,97

1 75,

297 75,587 76,598 76,674 76,70

5 76,78

1 78,51

0

78, 289

79,01

4 75,295 78,663

79,88 1 78,057

78,66 3

78,51 0

70,58 7

79, 563

79,47 2

78,69 4

80,93 7

79,2 98

78,29 7

81,09 0 78,108 Isolate 2 Q9

74,30

7 74,086 73,693 75,16

0 74,977 75,09

9 76,32

1 76,

121 75,450 76,354 76,636 76,25

5 76,26

2 78,35

8 78,28

9

82,45

6 76,165 79,556

78,84 4 79,216

79,82 3

79,68 6

70,26 7

79, 212

78,22 0

78,06 8

79,65 5

78,7 19

79,35 7

82,07 4 80,267 KY242757

74,29

9 73,766 72,977 75,54

1 75,358 75,13

0 77,06

7 75,

267 75,236 76,842 76,415 76,15

6 76,04

9 79,30

4 79,01

4 82,

456 75,745 79,075

79,53 0 79,658

79,33 5

80,29 6

70,98 4

80, 891

80,63 2

80,81 5

81,82 2

79,8 32

77,83 9

81,02 9 78,795 AGCaV_KT

835289 70,42

5 70,937 70,411 72,56

8 72,408 72,78

4 74,36

7 73,

315 73,013 72,761 73,026 73,31

3 73,39

7 75,40

2 75,29

5 76, 165

75,74

5 92,791

76,86 9 79,824

80,38 0

79,85 3

66,94 9

75, 908

74,67 7

75,24 9

78,84 4

75,2 76

76,27 7

79,05 0 76,786 AGCaV_NC

_018714 73,65

9 73,796 73,403 75,81

6 75,648 75,99

9 77,64

6 76,

388 76,273 75,698 76,003 76,55

2 76,65

9 78,35

8 78,66

3 79, 556

79,07

5 92,791

80,26 2 83,318

83,89 8

82,89 1

69,84 0

79, 289

77,96 1

78,55 6

82,35 7

78,6 12

80,31 1

82,03 6 79,314 FR694186

73,15

8 73,660 72,460 75,45

0 75,267 74,87

0 76,54

8 75,

442 74,505 76,170 76,643 76,01

8 76,15

5 78,67

6 79,88

1 78, 844

79,53

0 76,869 80,262 83,511

81,69 6

81,20 8

71,20 0

79, 515

79,25 6

78,72 2

81,31 5

81,1 56

78,43 2

81,66 6 78,442 LM999967

73,31

8 73,288 72,971 75,06

1 74,878 74,74

1 75,65

8 75,

411 74,497 75,248 75,111 75,90

3 75,72

0 78,02

7 78,05

7 79, 216

79,65

8 79,824 83,318

83,51 1

83,74 5

85,16 3

69,47 1

78, 866

77,67 6

77,76 8

80,74 1

78,6 47

78,54 5

81,42 7 78,936 KF321966

73,75

1 73,964 73,556 75,40

4 75,206 75,83

1 76,68

6 75,

930 75,389 76,705 76,278 77,04

0 76,87

3 78,90

7 78,66

3 79, 823

79,33

5 80,380 83,898

81,69 6 83,745

87,08 8

70,61 8

78, 953

78,61 7

79,38 0

81,36 4

79,1 15

79,19 7

82,32 6 79,924 KY702580

74,42

6 74,061 73,205 75,57

2 75,419 75,55

7 76,71

8 75,

709 75,651 76,493 76,325 77,34

6 77,20

8 78,87

7 78,51

0 79, 686

80,29

6 79,853 82,891

81,20 8 85,163

87,08 8

70,14 5

79, 350

78,95 3

78,73 9

81,34 9

79,0 69

79,12 1

82,37 2 80,702 EU095327

66,63

6 66,499 66,789 67,73

4 67,581 67,85

6 69,08

7 67,

474 67,093 69,030 69,411 70,64

7 71,51

6 70,64

8 70,58

7 70, 267

70,98

4 66,949 69,840

71,20 0 69,471

70,61 8

70,14 5

72, 143

71,28 9

71,71 6

72,25 0

82,3 26

70,28 2

73,80 6 69,915 Isolate 1 Q9

74,10

1 74,452 73,541 75,81

6 75,633 75,60

2 78,10

3 75,

862 75,648 77,285 77,742 76,81

2 77,13

2 80,70

8 79,56

3 79, 212

80,89

1 75,908 79,289

79,51 5 78,866

78,95 3

79,35 0

72,14 3

83,94 4

83,34 9

82,96 7

82,2 43

79,62 5

83,22 6 78,963 KY798310

73,56

8 74,177 72,702 75,70

9 75,541 74,64

2 78,17

9 75,

015 75,328 77,376 77,132 76,33

9 76,26

2 79,68

6 79,47

2 78, 220

80,63

2 74,677 77,961

79,25 6 77,676

78,61 7

78,95 3

71,28 9

83, 944

87,28 6

81,53 2

81,9 22

77,97 6

83,07 4 77,818 LC475151

73,81

2 73,461 72,519 75,63

3 75,435 74,26

0 77,44

8 74,

733 75,099 76,857 76,964 75,89

6 76,00

3 79,16

7 78,69

4 78, 068

80,81

5 75,249 78,556

78,72 2 77,768

79,38 0

78,73 9

71,71 6

83, 349

87,28 6

81,53 2

81,7 39

77,76 3

82,47 9 77,925 KY702581

74,77

1 74,147 72,824 75,84

6 75,663 75,37

4 79,47

3 75,

854 75,846 77,437 77,849 76,73

5 76,81

2 79,71

6 80,93

7 79, 655

81,82

2 78,844 82,357

81,31 5 80,741

81,36 4

81,34 9

72,25 0

82, 967

81,53 2

81,53 2

80,9 92

79,62 5

83,25 7 79,359 D21829

73,41

3 73,565 72,913 75,21

7 75,034 75,47

6 77,64

1 74,

806 74,684 76,914 77,127 78,65

2 79,00

3 79,89

3 79,29

8 78, 719

79,83

2 75,276 78,612

81,15 6 78,647

79,11 5

79,06 9

82,32 6

82, 243

81,92 2

81,73 9

80,99 2

78,78 0

83,95 1 78,728 KU308398

73,88

8 73,690 72,657 75,63

3 75,465 76,34

9 76,38

2 76,

410 76,502 75,942 76,018 78,52

0 78,07

8 78,11

4 78,29

7 79, 357

77,83

9 76,277 80,311

78,43 2 78,545

79,19 7

79,12 1

70,28 2

79, 625

77,97 6

77,76 3

79,62 5

78,7 80

87,85 1 85,919 LC475150

76,26

4 76,737 74,623 77,26

4 77,036 78,01

2 79,39

7 78,

141 77,707 78,734 78,535 80,74

8 80,93

1 80,99

8 81,09

0 82, 074

81,02

9 79,050 82,036

81,66 6 81,427

82,32 6

82,37 2

73,80 6

83, 226

83,07 4

82,47 9

83,25 7

83,9 51

87,85

1 89,184

(4)

Table 2. Distance matrix of RdRp region at aminoacid level from complete sequences of apple stem pitting virus (ASPV) and apple green crinkle associated virus (AGCaV), downloaded from NCBI (https://www.ncbi.nlm.nih.gov/), and complete RdRp sequences from the three new ASPV isolates recovered from tree Q9.

EU09 5327

AGCaV_A LV82119

MK92 3753

KF32 1967

MK92 3755

KY49 0039

MK23 9268

AB04 5371

KF31 9056

MK92 3754

I3- Q9

MK83 6301

MK92 3756

FR69 4186

JF94 6772

JF94 6775

AGCaV_B BJ56464

D21 829

KF91 5809

KJ52 2472

KU30 8398

LC47 5150

MG76 3895

KY24 2757

I2- Q9

I1- Q9

KY70 2581

LM99 9967

KF32 1966

KY70 2580

LC47 5151

KY79 8310

EU095327 62.383 65.812

67.07

9 66.850 67.170 66.941 68.11

5 68.70

7 67.566 67.

843 69.093 69.386 68.78

7 69.24

5 69.74

8 68.084

74.8 05

70.14 7

70.55 9 69.872

71.10

8 70.343 71.612 71.

127 71.

612 71.062 69.167 70.28

4 70.330 70.37

5 70.650 AGCaV_A

LV82119 62.38

3 74.746

75.83

4 76.475 78.033 77.804 78.78

5 79.18

0 78.968 78.

970 78.903 78.746 79.60

0 78.08

9 78.22

6 81.498

79.8 74

80.46 1

80.96 4 81.010

82.98

0 81.339 81.148 81.

864 81.

148 83.163 82.055 83.85

0 83.850 79.86

5 80.094 MK923753

65.81

2 74.746

85.53

1 85.440 84.608 84.333 85.35

5 84.87

2 85.217 85.

586 84.936 85.151 81.51

0 86.04

1 86.27

0 81.970

82.8 38

83.97 4

83.92 9 83.974

85.07

3 84.851 84.524 85.

105 84.

844 84.295 82.891 84.75

3 84.570 83.42

5 83.700 KF321967

67.07

9 75.834 85.531 92.736 85.937 85.662

86.36 2

85.98 8 86.426

86.

364 85.956 86.401 83.79

1 84.43

2 84.47

8 84.222

85.3 48

87.12 8

85.79 9 85.479

86.85

3 85.943 85.479 86.

566 86.

441 86.257 84.211 86.25

7 86.185 84.97

5 85.937 MK923755

66.85

0 76.475 85.440 92.73

6 86.532 86.257

86.54 5

86.12 5 86.700

86.

867 86.048 85.806 83.56

2 84.57

0 84.66

1 84.437

84.8 44

87.40 3

86.21 2 85.616

87.03

6 86.218 86.028 86.

657 86.

441 86.532 84.073 86.57

8 86.414 85.29

5 85.937 KY490039

67.17

0 78.033 84.608 85.93

7 86.532 99.725

91.80 0

90.43 9 92.396

92.

077 88.365 88.273 85.94

3 85.66

8 85.62

3 87.090

86.7 67

88.36 5

89.51 0 88.365

89.73

9 88.553 88.639 88.

594 88.

960 88.777 86.362 88.45

6 88.181 86.94

5 87.723 MK239268

66.94

1 77.804 84.333 85.66

2 86.257 99.725

91.52 5

90.16 5 92.121

91.

802 88.090 87.998 85.66

8 85.39

4 85.34

8 86.875

86.4 93

88.09 0

89.23 5 88.090

89.46

4 88.278 88.365 88.

319 88.

685 88.502 86.087 88.18

1 87.907 86.67

0 87.448 AB045371

68.11

5 78.785 85.355 86.36

2 86.545 91.800 91.525

95.38 4 93.547

93.

000 88.924 88.777 85.95

6 85.91

0 86.23

1 87.789

87.3 74

88.83 3

89.29 1 88.879

89.84

0 88.609 87.872 88.

823 88.

924 88.696 86.877 89.19

9 89.062 87.50

6 87.689 KF319056

68.70

7 79.180 84.872 85.98

8 86.125 90.439 90.165 95.38

4 91.648

91.

593 88.498 88.808 86.79

8 85.15

3 85.42

7 87.594

88.3 51

88.75 7

88.89 4 88.894

90.53

9 89.402 89.260 89.

661 89.

854 89.808 87.443 89.44

2 89.457 88.11

7 88.574 MK923754

67.56

6 78.968 85.217 86.42

6 86.700 92.396 92.121 93.54

7 91.64

8

95.

105 88.346 88.243 86.36

8 86.23

1 86.27

6 87.144

86.8 71

88.42 1

88.83 3 88.879

89.97

7 88.975 87.872 88.

823 88.

787 88.787 86.831 89.24

5 88.985 87.41

4 87.689 Isolate 3 Q9

67.84

3 78.970 85.586 86.36

4 86.867 92.077 91.802 93.00

0 91.59

3 95.105 88.423 88.642 86.55

3 86.32

4 86.37

0 87.415

87.1 93

88.37 7

89.15 5 88.927

90.07

1 88.749 88.286 89.

512 88.

835 88.881 87.336 89.38

4 88.927 87.50

8 88.149 MK836301

69.09

3 78.903 84.936 85.95

6 86.048 88.365 88.090 88.92

4 88.49

8 88.346 88.

423 95.050

86.63 0

86.40 1

86.40

1 87.237

88.5 53

88.86 9

89.69 3 88.456

90.42

6 88.645 89.510 89.

821 90.

105 90.060 87.551 89.55

6 89.799 88.59

4 89.372 MK923756

69.38

6 78.746 85.151 86.40

1 85.806 88.273 87.998 88.77

7 88.80

8 88.243 88.

642 95.050

87.07 6

86.29 7

86.25

1 87.130

88.5 88

88.67 5

90.14 2 88.354

90.14

2 88.955 89.821 89.

684 90.

646 90.050 87.540 89.36

3 89.423 88.58

3 89.638 FR694186

68.78

7 79.600 81.510 83.79

1 83.562 85.943 85.668 85.95

6 86.79

8 86.368 86.

553 86.630 87.076

85.12 6

85.30

9 90.689

89.0 62

88.73 6

89.46 9 89.286

91.07

1 89.336 89.469 90.

513 90.

385 90.934 90.348 91.57

5 91.163 88.14

1 89.057 JF946772

69.24

5 78.089 86.041 84.43

2 84.570 85.668 85.394 85.91

0 85.15

3 86.231 86.

324 86.401 86.297 85.12

6

97.61

9 86.598

87.7 80

87.36 3

88.23 3 89.057

90.79

7 91.758 88.233 89.

047 87.

912 88.095 85.910 88.64

5 88.645 86.72

2 87.225 JF946775

69.74

8 78.226 86.270 84.47

8 84.661 85.623 85.348 86.23

1 85.42

7 86.276 86.

370 86.401 86.251 85.30

9 97.61

9 86.652

88.3 75

87.59 2

88.09 5 89.057

91.02

6 91.621 88.370 89.

047 88.

095 88.278 86.185 88.78

2 88.828 86.72

2 87.454 AGCaV_

NC_018714 68.08

4 81.498 81.970 84.22

2 84.437 87.090 86.875 87.78

9 87.59

4 87.144 87.

415 87.237 87.130 90.68

9 86.59

8 86.65

2

88.0 52

89.60 7

90.36 1 90.468

92.40

7 90.258 90.361 91.

007 90.

199 92.784 91.438 92.73

0 92.623 88.96

1 89.715 D21829

74.80

5 79.874 82.838 85.34

8 84.844 86.767 86.493 87.37

4 88.35

1 86.871 87.

193 88.553 88.588 89.06

2 87.78

0 88.37

5 88.052

90.70 5

91.16 3 90.293

92.58

2 90.847 91.758 91.

751 92.

720 91.896 88.838 90.38

5 91.071 91.52

9 91.667 KF915809

70.14

7 80.461 83.974 87.12

8 87.403 88.365 88.090 88.83

3 88.75

7 88.421 88.

377 88.869 88.675 88.73

6 87.36

3 87.59

2 89.607

90.7 05

90.74 7 90.380

92.44

2 90.888 91.800 91.

701 92.

808 92.304 89.474 91.02

2 91.205 90.74

7 91.113 KJ522472

70.55

9 80.964 83.929 85.79

9 86.212 89.510 89.235 89.29

1 88.89

4 88.833 89.

155 89.693 90.142 89.46

9 88.23

3 88.09

5 90.361

91.1 63

90.74

7 91.113

92.99

1 91.438 92.533 91.

976 92.

716 92.900 90.252 92.12

1 92.258 90.70

1 91.022 KU308398

69.87

2 81.010 83.974 85.47

9 85.616 88.365 88.090 88.87

9 88.89

4 88.879 88.

927 88.456 88.354 89.28

6 89.05

7 89.05

7 90.468

90.2 93

90.38 0

91.11 3

95.09

8 94.414 91.434 92.

618 91.

709 91.663 89.657 91.89

2 91.571 90.38

0 90.518 LC475150

71.10

8 82.980 85.073 86.85

3 87.036 89.739 89.464 89.84

0 90.53

9 89.977 90.

071 90.426 90.142 91.07

1 90.79

7 91.02

6 92.407

92.5 82

92.44 2

92.99

1 95.098 95.971 93.816 94.

865 93.

953 94.182 92.128 94.27

4 94.320 92.62

5 93.083 MG763895

70.34

3 81.339 84.851 85.94

3 86.218 88.553 88.278 88.60

9 89.40

2 88.975 88.

749 88.645 88.955 89.33

6 91.75

8 91.62

1 90.258

90.8 47

90.88 8

91.43 8 94.414

95.97

1 91.941

93.

309 91.

987 92.308 90.256 92.49

1 92.674 90.29

3 90.888 KY242757

71.61

2 81.148 84.524 85.47

9 86.028 88.639 88.365 87.87

2 89.26

0 87.872 88.

286 89.510 89.821 89.46

9 88.23

3 88.37

0 90.361

91.7 58

91.80 0

92.53 3 91.434

93.81 6 91.941

95.

002 93.

678 93.953 90.389 92.35

0 92.533 92.12

1 92.900 Isolate 2 Q9

71.12

7 81.864 85.105 86.56

6 86.657 88.594 88.319 88.82

3 89.66

1 88.823 89.

512 89.821 89.684 90.51

3 89.04

7 89.04

7 91.007

91.7 51

91.70 1

91.97 6 92.618

94.86

5 93.309 95.002 93.

122 93.122 91.388 93.16

8 93.306 91.42

6 91.884 Isolate 1 Q9

71.61

2 81.148 84.844 86.44

1 86.441 88.960 88.685 88.92

4 89.85

4 88.787 88.

835 90.105 90.646 90.38

5 87.91

2 88.09

5 90.199

92.7 20

92.80 8

92.71 6 91.709

93.95

3 91.987 93.678 93.

122 94.411 90.755 92.44

2 92.945 93.12

9 93.770 KY702581

71.06

2 83.163 84.295 86.25

7 86.532 88.777 88.502 88.69

6 89.80

8 88.787 88.

881 90.060 90.050 90.93

4 88.09

5 88.27

8 92.784

91.8 96

92.30 4

92.90 0 91.663

94.18

2 92.308 93.953 93.

122 94.

411 92.449

94.41 1 94.503

91.98 4 92.579 LM999967

69.16

7 82.055 82.891 84.21

1 84.073 86.362 86.087 86.87

7 87.44

3 86.831 87.

336 87.551 87.540 90.34

8 85.91

0 86.18

5 91.438

88.8 38

89.47 4

90.25 2 89.657

92.12

8 90.256 90.389 91.

388 90.

755 92.449

93.04 3 93.867

88.83 3 89.291 KF321966

70.28

4 83.850 84.753 86.25

7 86.578 88.456 88.181 89.19

9 89.44

2 89.245 89.

384 89.556 89.363 91.57

5 88.64

5 88.78

2 92.730

90.3 85

91.02 2

92.12 1 91.892

94.27

4 92.491 92.350 93.

168 92.

442 94.411 93.043 96.290 90.56

3 90.884 KY702580

70.33

0 83.850 84.570 86.18

5 86.414 88.181 87.907 89.06

2 89.45

7 88.985 88.

927 89.799 89.423 91.16

3 88.64

5 88.82

8 92.623

91.0 71

91.20 5

92.25 8 91.571

94.32

0 92.674 92.533 93.

306 92.

945 94.503 93.867 96.29

0

90.97 6 91.342 LC475151

70.37

5 79.865 83.425 84.97

5 85.295 86.945 86.670 87.50

6 88.11

7 87.414 87.

508 88.594 88.583 88.14

1 86.72

2 86.72

2 88.961

91.5 29

90.74 7

90.70 1 90.380

92.62

5 90.293 92.121 91.

426 93.

129 91.984 88.833 90.56

3 90.976 93.907

(5)

Table 3. Distance matrix of CP region at nucleotide level from complete sequences of apple stem pitting virus (ASPV) and apple green crinkle associated virus (AGCaV), downloaded from NCBI (https://www.ncbi.nlm.nih.gov/), and complete CP sequences from the three new ASPV isolates recovered from tree Q9.

LM99 9967

MK92 3753

KY24 2757

JF94 6775

JF94 6772

MK92 3755

KF32 1967

AGCaV_H E963831

AGCaV_K T835289

MG76 3895

KF31 9056

KJ52 2472

KY70 2580

I2- Q9

KY79 8310

LC47 5151

I1- Q9

FR69 4186

AB04 5371

I3- Q9

MK92 3754

MK92 3756

KF91 5809

MK83 6301

KF32 1966

KY49 0039

MK23 9268

KU30 8398

KY70 2581

LC47 5150

D21 829

EU09 5327

LM999967 75.870 77.250 66.24

0 65.99

0 63.387 64.43

5 62.440 61.089 63.483

65.38 5

63.62 2 64.173

66.

613 63.738 63.01

9 68.

517 65.86

6 64.56

7 65.

668 66.114 64.173 64.17

3 65.433 64.17

3 64.789 64.623 64.677 65.617 67.73

7 64.2

35 59.65

8 MK923753 75.870 88.372

66.34 8

65.69 8 64.026

64.26

8 61.422 60.596 61.981

65.79 8

64.81 2 64.577

65.

885 65.245 64.92

4 67.

106 66.77

7 64.57

7 65.

460 66.117 65.909 64.18

5 64.655 63.55

8 64.056 63.891 64.851 66.447 66.45

4 62.9

04 58.96

2 KY242757 77.250 88.372

67.45 7

65.90 4 65.830

65.18

2 61.840 60.853 63.622

67.63 0

67.71 3 67.217

66.

309 65.109 64.46

4 67.

795 67.05

2 66.96

9 67.

022 67.135 67.382 66.22

6 68.538 66.22

6 64.822 64.657 64.988 68.126 68.70

4 63.7

15 59.28

0 JF946775 66.240 66.348 67.457

90.06 6 65.590

63.24

7 65.425 63.860 65.481

66.88 5

66.55 9 65.997

67.

779 64.000 62.96

0 67.

884 68.63

1 66.80

1 68.

182 67.967 68.489 68.65

0 68.167 67.44

4 68.465 68.299 68.631 69.959 69.29

3 65.1

31 60.00

0 JF946772 65.990 65.698 65.904

90.06

6 64.459

64.21

1 65.830 64.143 65.319

66.88 5

67.70 0 67.292

67.

292 64.400 64.64

0 68.

548 68.63

1 67.53

7 67.

839 68.216 69.005 68.51

5 69.168 66.55

8 67.303 67.137 68.465 70.290 70.14

7 65.6

87 61.06

1 MK923755 63.387 64.026 65.830

65.59 0

64.45 9

79.26

8 63.622 62.634 65.360

67.23 9

66.99 3 66.830

68.

056 66.825 64.84

1 69.

199 68.38

2 68.21

9 68.

017 68.709 68.412 69.06

7 70.434 68.87

3 68.056 67.892 67.484 70.016 71.32

4 66.1

19 61.97

4 KF321967 64.435 64.268 65.182

63.24 7

64.21

1 79.268 66.026 64.476 66.000

68.30 1

67.64 7 67.974

68.

791 66.587 65.07

9 69.

118 69.11

8 67.56

5 67.

806 68.627 67.974 67.97

4 68.301 67.56

5 67.484 67.320 66.912 69.281 71.07

8 65.7

28 61.00

3 AGCaV_

NC_018714 62.440 61.422 61.840 65.42

5 65.83

0 63.622 66.02

6 95.765 75.470

69.35 0

67.96 7 67.561

68.

374 63.608 63.05

9 68.

537 67.80

5 67.88

6 67.

926 70.000 68.293 67.15

4 68.049 69.10

6 69.593 69.431 66.504 69.919 70.32

5 64.0

97 57.89

0 AGCaV_K

T835289 61.089 60.596 60.853 63.86

0 64.14

3 62.634 64.47

6 95.765 73.194

67.20 9

66.32 8 65.962

66.

965 62.810 62.13

1 67.

263 66.39

6 66.31

4 66.

261 68.631 67.087 65.50

1 66.436 67.61

5 67.710 67.547 64.770 68.144 68.46

9 62.5

52 56.41

4 MG763895 63.483 61.981 63.622

65.48 1

65.31 9 65.360

66.00

0 75.470 73.194

66.31 5

67.37 0 66.964

66.

071 62.569 63.43

0 66.

883 67.45

1 66.55

8 66.

178 68.101 66.234 66.55

8 67.695 66.80

2 66.477 66.315 64.367 68.994 73.13

3 63.9

97 58.85

7 KF319056 65.385 65.798 67.630

66.88 5

66.88 5 67.239

68.30

1 69.350 67.209 66.315

77.19 7 76.202

77.

446 72.977 72.24

9 77.

162 77.49

8 77.61

2 78.

472 78.925 74.627 76.03

6 74.627 76.03

6 74.475 74.475 73.971 76.574 77.03

2 71.1

65 66.00

7 KJ522472 63.622 64.812 67.713

66.55 9

67.70 0 66.993

67.64

7 67.967 66.328 67.370

77.19

7 96.772

78.

272 74.595 72.41

1 78.

505 78.17

0 76.63

5 78.

733 79.513 75.120 74.40

2 73.764 73.84

4 75.231 75.063 73.132 74.727 76.42

3 71.3

25 66.00

7 KY702580 64.173 64.577 67.217

65.99 7

67.29 2 66.830

67.97

4 67.561 65.962 66.964

76.20 2

96.77 2

78.

107 74.029 72.33

0 77.

582 77.75

0 76.31

6 78.

819 78.841 74.561 74.16

3 73.764 72.72

7 74.727 74.559 72.544 75.231 76.01

6 71.2

45 65.34

7 Isolate 2 Q9 66.613 65.885 66.309

67.77 9

67.29 2 68.056

68.79

1 68.374 66.965 66.071

77.44 6

78.27

2 78.107 74.676

72.49 2

80.

017 79.76

5 79.67

1 81.

076 80.017 77.942 78.35

4 77.449 77.11

9 79.093 78.925 75.399 78.505 79.83

5 75.0

20 69.47

2 KY798310 63.738 65.245 65.109

64.00 0

64.40 0 66.825

66.58

7 63.608 62.810 62.569

72.97 7

74.59 5 74.029

74.

676

82.28 2

78.

398 78.15

5 73.78

6 74.

812 74.110 71.764 72.97

7 72.654 72.08

7 70.469 70.307 71.278 72.006 75.80

9 69.1

47 64.18

3 LC475151 63.019 64.924 64.464

62.96 0

64.64 0 64.841

65.07

9 63.059 62.131 63.430

72.24 9

72.41 1 72.330

72.

492 82.282

76.

214 76.29

4 72.08

7 72.

891 72.654 70.550 72.08

7 71.521 70.79

3 70.388 70.227 71.197 70.227 73.86

7 67.3

64 62.74

0 Isolate 1 Q9 68.517 67.106 67.795

67.88 4

68.54 8 69.199

69.11

8 68.537 67.263 66.883

77.16 2

78.50 5 77.582

80.

017 78.398 76.21

4

83.96 3

79.59 7

79.

384 80.353 76.742 76.91

0 77.666 77.75

0 77.498 77.330 74.979 76.574 79.09

3 73.6

55 68.66

2 FR694186 65.866 66.777 67.052

68.63 1

68.63 1 68.382

69.11

8 67.805 66.396 67.451

77.49 8

78.17 0 77.750

79.

765 78.155 76.29

4 83.

963

81.78 0

81.

424 80.101 76.406 77.75

0 78.170 77.07

8 77.834 77.750 75.903 78.086 79.93

3 73.0

12 66.83

3 AB045371 64.567 64.577 66.969

66.80 1

67.53 7 68.219

67.56

5 67.886 66.314 66.558

77.61 2

76.63 5 76.316

79.

671 73.786 72.08

7 79.

597 81.78

0

82.

161 83.375 76.156 75.99

7 76.874 75.67

8 77.246 77.162 75.315 79.177 76.58

5 73.0

92 68.06

9 Isolate 3 Q9 65.668 65.460 67.022

68.18 2

67.83 9 68.017

67.80

6 67.926 66.261 66.178

78.47 2

78.73 3 78.819

81.

076 74.812 72.89

1 79.

384 81.42

4 82.16

1 86.285 77.865

77.73 4 78.342

77.47

4 78.819 78.733 74.826 77.170 77.99

5 74.5

66 70.31

5 MK923754 66.114 66.117 67.135

67.96 7

68.21 6 68.709

68.62

7 70.000 68.631 68.101

78.92 5

79.51 3 78.841

80.

017 74.110 72.65

4 80.

353 80.10

1 83.37

5 86.

285 77.750

78.84 1 78.338

79.26

1 79.177 79.009 74.391 79.261 79.00

9 73.7

35 68.32

9 MK923756 64.173 65.909 67.382

68.48 9

69.00 5 68.412

67.97

4 68.293 67.087 66.234

74.62 7

75.12 0 74.561

77.

942 71.764 70.55

0 76.

742 76.40

6 76.15

6 77.

865 77.750

83.61 3 84.307

77.35

2 77.246 77.246 76.490 78.589 78.37

4 74.9

40 69.30

7 KF915809 64.173 64.185 66.226

68.65 0

68.51 5 69.067

67.97

4 67.154 65.501 66.558

76.03 6

74.40 2 74.163

78.

354 72.977 72.08

7 76.

910 77.75

0 75.99

7 77.

734 78.841 83.613 86.890 77.35

2 78.673 78.589 78.002 80.688 79.67

5 76.2

25 69.38

9 MK836301 65.433 64.655 68.538

68.16 7

69.16 8 70.434

68.30

1 68.049 66.436 67.695

74.62 7

73.76 4 73.764

77.

449 72.654 71.52

1 77.

666 78.17

0 76.87

4 78.

342 78.338 84.307 86.89

0

78.46

9 78.086 78.002 78.505 80.772 79.26

8 76.3

05 70.29

7 KF321966 64.173 63.558 66.226

67.44 4

66.55 8 68.873

67.56

5 69.106 67.615 66.802

76.03 6

73.84 4 72.727

77.

119 72.087 70.79

3 77.

750 77.07

8 75.67

8 77.

474 79.261 77.352 77.35

2 78.469 87.741 87.573 80.269 81.528 82.35

8 78.0

72 72.27

7 KY490039 64.789 64.056 64.822

68.46 5

67.30 3 68.056

67.48

4 69.593 67.710 66.477

74.47 5

75.23 1 74.727

79.

093 70.469 70.38

8 77.

498 77.83

4 77.24

6 78.

819 79.177 77.246 78.67

3 78.086 87.74

1 99.832 80.101 81.612 82.28

4 77.5

10 71.07

2 MK239268 64.623 63.891 64.657

68.29 9

67.13 7 67.892

67.32

0 69.431 67.547 66.315

74.47 5

75.06 3 74.559

78.

925 70.307 70.22

7 77.

330 77.75

0 77.16

2 78.

733 79.009 77.246 78.58

9 78.002 87.57

3 99.832 80.185 81.444 82.11

6 77.3

49 70.90

6 KU308398 64.677 64.851 64.988

68.63 1

68.46 5 67.484

66.91

2 66.504 64.770 64.367

73.97 1

73.13 2 72.544

75.

399 71.278 71.19

7 74.

979 75.90

3 75.31

5 74.

826 74.391 76.490 78.00

2 78.505 80.26

9 80.101 80.185 79.849 82.95

5 77.3

49 71.15

5 KY702581 65.617 66.447 68.126

69.95 9

70.29 0 70.016

69.28

1 69.919 68.144 68.994

76.57 4

74.72 7 75.231

78.

505 72.006 70.22

7 76.

574 78.08

6 79.17

7 77.

170 79.261 78.589 80.68

8 80.772 81.52

8 81.612 81.444 79.849

83.79 5

76.8 67

71.48 8 LC475150 67.737 66.454 68.704

69.29 3

70.14 7 71.324

71.07

8 70.325 68.469 73.133

77.03 2

76.42 3 76.016

79.

835 75.809 73.86

7 79.

093 79.93

3 76.58

5 77.

995 79.009 78.374 79.67

5 79.268 82.35

8 82.284 82.116 82.955 83.795

80.9 64

75.00 0 D21829 64.235 62.904 63.715

65.13 1

65.68 7 66.119

65.72

8 64.097 62.552 63.997

71.16 5

71.32 5 71.245

75.

020 69.147 67.36

4 73.

655 73.01

2 73.09

2 74.

566 73.735 74.940 76.22

5 76.305 78.07

2 77.510 77.349 77.349 76.867 80.96

4

89.85 9

(6)

Table 4. Distance matrix of CP region at aminoacid level from complete sequences of apple stem pitting virus (ASPV) and apple green crinkle associated virus (AGCaV), downloaded from NCBI (https://www.ncbi.nlm.nih.gov/), and complete CP sequences from the three new ASPV isolates recovered from tree Q9.

EU09 5327

MG76 3895

AGCaV_H E963831

AGCaV_K T835289

MK92 3755

KF32 1967

LC47 5151

KY79 8310

KF31 9056

D21 829

KJ52 2472

KY70 2580

I1- Q9

I2- Q9

FR69 4186

AB04 5371

I3- Q9

MK92 3754

MK92 3756

KF91 5809

MK83 6301

KY70 2581

KF32 1966

KY49 0039

MK23 9268

KU30 8398

LC47 5150

JF94 6775

JF94 6772

LM99 9967

MK92 3753

KY24 2757 EU095327 30.345 30.115 27.701 33.563

32.87 4

38.11 8 37.412

34.50 7

48.7 00

36.15 0 35.211

37.

825 38.

732 37.11

6 38.26

3 37.

317 38.298 37.089 38.49

8 38.028 39.716 38.26

3 38.061 38.298 38.061 39.67

1 30.07

0 30.76

9 30.465 32.558 32.553 MG763895

30.34

5 83.375 77.329 74.510

74.51 0

68.55 8 67.612

72.05 9

68.5 45

73.77 5 73.529

71.

814 72.

549 72.30

4 72.79

4 74.

177 74.020 72.794 73.03

9 73.775 73.529 73.77

5 72.304 72.059 69.118 72.79

4 72.79

4 72.79

4 71.463 69.756 70.488 AGCaV_

NC_018714 30.11

5 83.375 91.473 74.510

75.00 0

68.55 8 69.031

73.77 5

69.2 49

74.51 0 75.000

73.

284 74.

265 74.26

5 74.26

5 74.

684 75.245 74.265 74.26

5 74.755 75.490 73.52

9 74.265 74.020 70.588 72.79

4 72.05

9 72.05

9 70.732 70.488 71.220 AGCaV_K

T835289 27.70

1 77.329 91.473 69.274

69.51 9

63.96 9 64.206

68.77 2

64.6 93

69.26 2 69.753

68.

527 69.

262 69.01

7 69.01

7 69.

758 69.998 68.527 68.77

2 69.262 70.243 68.77

2 69.753 69.508 65.831 68.03

7 67.79

2 67.05

7 66.729 65.998 66.729 MK923755

33.56

3 74.510 74.510 69.274

88.20 6

70.21 3 70.922

75.00 0

71.5 96

77.45 1 76.225

76.

471 76.

961 77.69

6 78.18

6 78.

987 80.147 78.378 78.37

8 78.870 77.941 78.18

6 77.206 76.961 72.794 77.20

6 71.25

3 71.74

4 70.244 71.951 71.951 KF321967

32.87

4 74.510 75.000 69.519 88.206

69.97 6 70.449

74.02 0

70.6 57

75.98 0 74.755

75.

245 76.

225 76.47

1 76.96

1 77.

919 77.696 76.716 76.22

5 77.451 76.471 77.45

1 76.225 75.980 70.588 76.22

5 69.60

8 70.09

8 70.000 70.976 70.976 LC475151

38.11

8 68.558 68.558 63.969 70.213 69.97

6 81.752

74.93 9

77.8 85

77.85 9 76.886

79.

805 78.

589 81.26

5 79.56

2 80.

151 79.075 78.102 78.58

9 78.345 77.859 79.07

5 78.345 78.345 75.669 79.07

5 67.15

0 67.87

4 67.874 68.599 68.357 KY798310

37.41

2 67.612 69.031 64.206 70.922 70.44

9 81.75

2

76.64 2

80.5 29

77.61 6 77.129

82.

238 81.

022 82.23

8 81.50

9 82.

663 82.968 79.319 80.04

9 80.535 80.049 80.29

2 79.319 79.075 78.832 81.02

2 68.11

6 67.87

4 68.599 68.357 68.841 KF319056

34.50

7 72.059 73.775 68.772 75.000 74.02

0 74.93

9 76.642

77.0 53

82.04 5 81.297

82.

828 83.

042 83.08

1 83.79

1 84.

595 86.111 81.546 82.04

5 81.796 85.354 82.79

3 83.333 83.081 79.545 81.54

6 71.04

0 69.80

2 69.136 72.593 73.000 D21829

48.70

0 68.545 69.249 64.693 71.596 70.65

7 77.88

5 80.529 77.05

3

78.01 9 77.053

80.

193 82.

126 80.19

3 80.43

5 80.

798 81.884 80.193 81.40

1 82.126 83.333 81.88

4 81.884 81.643 82.609 85.74

9 69.54

4 70.26

4 69.378 70.574 70.813 KJ522472

36.15

0 73.775 74.510 69.262 77.451 75.98

0 77.85

9 77.616 82.04

5 78.0

19 98.058

83.

333 84.

901 86.11

1 83.73

8 88.

512 87.879 83.738 84.70

9 83.738 85.101 82.03

9 84.091 83.838 79.798 81.90

7 69.41

7 69.45

8 69.231 71.394 73.000 KY702580

35.21

1 73.529 75.000 69.753 76.225 74.75

5 76.88

6 77.129 81.29

7 77.0

53 98.05

8

82.

576 84.

406 85.10

1 82.52

4 87.

467 86.869 82.767 83.73

8 82.767 84.091 80.58

3 83.586 83.333 79.293 81.41

8 69.90

3 69.95

1 68.510 70.192 72.250 Isolate 1 Q9

37.82

5 71.814 73.284 68.527 76.471 75.24

5 79.80

5 82.238 82.82

8 80.1

93 83.33

3 82.576 88.

131 89.64

6 89.39

4 88.

251 88.384 85.859 86.36

4 87.121 86.616 85.35

4 87.121 86.869 81.313 84.59

6 70.17

5 70.42

6 70.000 72.250 72.000 Isolate 2 Q9

38.73

2 72.549 74.265 69.262 76.961 76.22

5 78.58

9 81.022 83.04

2 82.1

26 84.90

1 84.406 88.

131

88.88 9

88.36 6

89.

817 89.141 87.129 86.63

4 87.871 88.636 85.14

9 87.374 87.121 82.828 85.89

1 71.74

4 70.93

6 69.363 71.569 72.750 FR694186

37.11

6 72.304 74.265 69.017 77.696 76.47

1 81.26

5 82.238 83.08

1 80.1

93 86.11

1 85.101 89.

646 88.

889

88.63 6

90.

078 88.384 86.111 87.87

9 87.879 86.869 86.11

1 86.364 86.111 81.818 86.36

4 70.67

7 70.67

7 70.250 71.750 71.500 AB045371

38.26

3 72.794 74.265 69.017 78.186 76.96

1 79.56

2 81.509 83.79

1 80.4

35 83.73

8 82.524 89.

394 88.

366 88.63

6

91.

906 92.424 86.571 85.13

2 85.372 88.384 83.45

3 86.616 86.364 82.323 83.37

4 69.90

3 70.19

7 67.458 71.259 74.000 Isolate 3 Q9

37.31

7 74.177 74.684 69.758 78.987 77.91

9 80.15

1 82.663 84.59

5 80.7

98 88.51

2 87.467 88.

251 89.

817 90.07

8 91.90

6 93.734 89.556

89.81

7 90.339 87.467 86.94

5 86.945 86.684 82.768 85.64

0 73.31

6 72.02

1 72.093 73.127 73.643 MK923754

38.29

8 74.020 75.245 69.998 80.147 77.69

6 79.07

5 82.968 86.11

1 81.8

84 87.87

9 86.869 88.

384 89.

141 88.38

4 92.42

4 93.

734 89.141

89.39

4 89.646 89.141 87.87

9 87.626 87.374 82.323 86.86

9 72.43

1 72.43

1 72.000 73.750 74.500 MK923756

37.08

9 72.794 74.265 68.527 78.378 76.71

6 78.10

2 79.319 81.54

6 80.1

93 83.73

8 82.767 85.

859 87.

129 86.11

1 86.57

1 89.

556 89.141

90.86

5 91.106 87.879 83.45

3 85.606 85.859 82.828 83.61

9 70.56

0 70.61

7 67.458 70.309 72.500 KF915809

38.49

8 73.039 74.265 68.772 78.378 76.22

5 78.58

9 80.049 82.04

5 81.4

01 84.70

9 83.738 86.

364 86.

634 87.87

9 85.13

2 89.

817 89.394 90.865 91.587 89.141 83.21

3 85.859 86.111 82.828 84.10

8 70.31

6 71.11

1 68.409 70.546 72.750 MK836301

38.02

8 73.775 74.755 69.262 78.870 77.45

1 78.34

5 80.535 81.79

6 82.1

26 83.73

8 82.767 87.

121 87.

871 87.87

9 85.37

2 90.

339 89.646 91.106 91.58

7 89.141

84.41

2 86.616 86.869 83.333 84.84

1 71.95

1 72.34

6 69.834 70.309 73.750 KY702581

39.71

6 73.529 75.490 70.243 77.941 76.47

1 77.85

9 80.049 85.35

4 83.3

33 85.10

1 84.091 86.

616 88.

636 86.86

9 88.38

4 87.

467 89.141 87.879 89.14

1 89.141

88.88

9 89.394 89.141 85.606 88.38

4 71.93

0 72.18

0 71.250 74.250 74.250 KF321966

38.26

3 73.775 73.529 68.772 78.186 77.45

1 79.07

5 80.292 82.79

3 81.8

84 82.03

9 80.583 85.

354 85.

149 86.11

1 83.45

3 86.

945 87.879 83.453 83.21

3 84.412 88.889 92.929 92.677 83.586 86.30

8 70.63

1 70.44

3 68.646 70.071 73.250 KY490039

38.06

1 72.304 74.265 69.753 77.206 76.22

5 78.34

5 79.319 83.33

3 81.8

84 84.09

1 83.586 87.

121 87.

374 86.36

4 86.61

6 86.

945 87.626 85.606 85.85

9 86.616 89.394 92.92

9 99.747 84.596

87.37 4

71.42 9

70.67

7 70.750 72.500 72.750 MK239268

38.29

8 72.059 74.020 69.508 76.961 75.98

0 78.34

5 79.075 83.08

1 81.6

43 83.83

8 83.333 86.

869 87.

121 86.11

1 86.36

4 86.

684 87.374 85.859 86.11

1 86.869 89.141 92.67

7 99.747 84.848

87.12 1

71.17 8

70.42

6 70.500 72.250 72.500 KU308398

38.06

1 69.118 70.588 65.831 72.794 70.58

8 75.66

9 78.832 79.54

5 82.6

09 79.79

8 79.293 81.

313 82.

828 81.81

8 82.32

3 82.

768 82.323 82.828 82.82

8 83.333 85.606 83.58

6 84.596 84.848

88.13 1

72.18 0

73.68

4 70.500 72.500 72.000 LC475150

39.67

1 72.794 72.794 68.037 77.206 76.22

5 79.07

5 81.022 81.54

6 85.7

49 81.90

7 81.418 84.

596 85.

891 86.36

4 83.37

4 85.

640 86.869 83.619 84.10

8 84.841 88.384 86.30

8 87.374 87.121 88.131

71.84 5

73.64

5 70.944 72.639 74.250 JF946775

30.07

0 72.794 72.059 67.792 71.253 69.60

8 67.15

0 68.116 71.04

0 69.5

44 69.41

7 69.903 70.

175 71.

744 70.67

7 69.90

3 73.

316 72.431 70.560 70.31

6 71.951 71.930 70.63

1 71.429 71.178 72.180 71.84

5

91.60

5 73.913 73.188 76.559 JF946772

30.76

9 72.794 72.059 67.057 71.744 70.09

8 67.87

4 67.874 69.80

2 70.2

64 69.45

8 69.951 70.

426 70.

936 70.67

7 70.19

7 72.

021 72.431 70.617 71.11

1 72.346 72.180 70.44

3 70.677 70.426 73.684 73.64

5 91.60

5 74.510 73.039 75.810 LM999967

30.46

5 71.463 70.732 66.729 70.244 70.00

0 67.87

4 68.599 69.13

6 69.3

78 69.23

1 68.510 70.

000 69.

363 70.25

0 67.45

8 72.

093 72.000 67.458 68.40

9 69.834 71.250 68.64

6 70.750 70.500 70.500 70.94

4 73.91

3 74.51

0 79.529 85.213

MK923753 32.55

8 69.756 70.488 65.998 71.951 70.97

6 68.59

9 68.357 72.59

3 70.5

74 71.39

4 70.192 72.

250 71.

569 71.75

0 71.25

9 73.

127 73.750 70.309 70.54

6 70.309 74.250 70.07

1 72.500 72.250 72.500 72.63

9 73.18

8 73.03

9 79.529 93.216

(7)

Table 5. Distance matrix of segment L at nucleotide level from apple rubbery wood virus-1 (ARWV-1) and apple rubbery wood virus-2 (ARWV-2) complete sequences downloaded from NCBI (https://www.ncbi.nlm.nih.gov/).

ARWV-2 MK936230

ARWV-2 MF062144

ARWV-2 MF062128

ARWV-2 MF062133

ARWV-2 MF062139

ARWV-1 MK936227

ARWV-1 MF062130

Isolate Q9

ARWV-1 MF062136

ARWV-1 MF062125 ARWV-2

MK936230 95.867 96.641 96.035 96.175 62.081 62.316 62.476 62.558 62.517

ARWV-2

MF062144 95.867 97.802 97.728 97.911 62.919 63.186 63.361 63.429 63.361

ARWV-2

MF062128 96.641 97.802 98.195 98.321 62.937 63.108 63.350 63.446 63.446

ARWV-2

MF062133 96.035 97.728 98.195 99.060 63.029 63.186 63.456 63.511 63.470

ARWV-2

MF062139 96.175 97.911 98.321 99.060 63.016 63.173 63.374 63.456 63.415

ARWV-1

MK936227 62.081 62.919 62.937 63.029 63.016 93.387 94.850 94.920 95.075

ARWV-1

MF062130 62.316 63.186 63.108 63.186 63.173 93.387 94.723 94.779 94.835

Isolate Q9 62.476 63.361 63.350 63.456 63.374 94.850 94.723 98.782 98.824

ARWV-1

MF062136 62.558 63.429 63.446 63.511 63.456 94.920 94.779 98.782 99.286

ARWV-1

MF062125 62.517 63.361 63.446 63.470 63.415 95.075 94.835 98.824 99.286

Table 6. Distance matrix of segment L at aminoacid level from apple rubbery wood virus-1 (ARWV-1) and apple rubbery wood virus-2 (ARWV-2) complete sequences downloaded from NCBI (https://www.ncbi.nlm.nih.gov/).

ARWV-2 MK936230

ARWV-2 MF062144

ARWV-2 MF062128

ARWV-2 MF062133

ARWV-2 MF062139

ARWV-1 MK936227

ARWV-1 MF062130

Isolate Q9

ARWV-1 MF062136

ARWV-1 MF062125 ARWV-2

MK936230 95.481 95.904 95.650 95.776 57.427 58.138 58.430 58.220 58.472

ARWV-2

MF062144 95.481 97.435 97.938 97.938 58.664 59.330 59.538 59.370 59.538

ARWV-2

MF062128 95.904 97.435 98.024 97.982 58.624 59.374 59.624 59.456 59.666

ARWV-2

MF062133 95.650 97.938 98.024 99.158 58.917 59.708 59.832 59.664 59.874

ARWV-2

MF062139 95.776 97.938 97.982 99.158 58.833 59.540 59.748 59.580 59.790

ARWV-1

MK936227 57.427 58.664 58.624 58.917 58.833 93.775 94.662 94.704 94.789

ARWV-1

MF062130 58.138 59.330 59.374 59.708 59.540 93.775 95.336 95.294 95.252

Isolate Q9 58.430 59.538 59.624 59.832 59.748 94.662 95.336 98.865 98.865

ARWV-1

MF062136 58.220 59.370 59.456 59.664 59.580 94.704 95.294 98.865 99.033

ARWV-1

MF062125 58.472 59.538 59.666 59.874 59.790 94.789 95.252 98.865 99.033

(8)

Table 7. Distance matrix of segment M at nucleotide level from apple rubbery wood virus-1 (ARWV-1) and apple rubbery wood virus-2 (ARWV-2) complete sequences downloaded from NCBI (https://www.ncbi.nlm.nih.gov/).

ARWV-1 MF062131

ARWV-1

MK936226 Isolate Q9

ARWV-1 MF062137

ARWV-1 MF062126

ARWV-2 MF062134

ARWV-2 MF062143

ARWV-2 MF062142

ARWV-2 MF062145

ARWV-2 MK936229

ARWV-1 MF062131 94.480 95.247 95.844 95.759 62.935 63.109 63.880 63.462 62.521

ARWV-1 MK936226 94.480 95.396 96.164 95.908 62.675 62.510 63.109 62.689 62.521

Isolate Q9 95.247 95.396 98.721 98.636 63.088 62.758 63.277 62.857 62.689

ARWV-1 MF062137 95.844 96.164 98.721 99.233 63.254 62.923 63.613 63.193 63.025

ARWV-1 MF062126 95.759 95.908 98.636 99.233 63.088 62.758 63.445 63.025 62.857

ARWV-2 MF062134 62.935 62.675 63.088 63.254 63.088 98.731 65.465 65.801 60.272

ARWV-2 MF062143 63.109 62.510 62.758 62.923 62.758 98.731 65.375 65.712 65.375

ARWV-2 MF062142 63.880 63.109 63.277 63.613 63.445 65.465 65.375 98.246 97.982

ARWV-2 MF062145 63.462 62.689 62.857 63.193 63.025 65.801 65.712 98.246 97.982

ARWV-2 MK936229 62.521 62.521 62.689 63.025 62.857 60.272 65.375 97.982 97.982

Table 8. Distance matrix of segment M at aminoacid level from apple rubbery wood virus-1 (ARWV-1) and apple rubbery wood virus-2 (ARWV-2) complete sequences downloaded from NCBI (https://www.ncbi.nlm.nih.gov/).

ARWV-1 MK936226

ARWV-1

MF062131 Isolate Q9

ARWV-1 MF062137

ARWV-1 MF062126

ARWV-2 MF062134

ARWV-2 MF062143

ARWV-2 MF062145

ARWV-2 MK936229

ARWV-2 MF062142

ARWV-1 MK936226 93.590 93.846 94.872 94.615 57.289 57.545 58.462 58.718 58.974

ARWV-1 MF062131 93.590 94.359 95.385 95.128 57.975 58.228 59.184 59.439 59.694

Isolate Q9 93.846 94.359 97.949 98.205 57.033 57.289 59.487 59.487 59.744

ARWV-1 MF062137 94.872 95.385 97.949 98.718 58.056 58.312 60.256 60.513 60.769

ARWV-1 MF062126 94.615 95.128 98.205 98.718 57.545 57.801 59.744 60.000 60.256

ARWV-2 MF062134 57.289 57.975 57.033 58.056 57.545 98.473 67.263 67.008 67.519

ARWV-2 MF062143 57.545 58.228 57.289 58.312 57.801 98.473 66.496 66.240 66.752

ARWV-2 MF062145 58.462 59.184 59.487 60.256 59.744 67.263 66.496 97.361 98.417

ARWV-2 MK936229 58.718 59.439 59.487 60.513 60.000 67.008 66.240 97.361 98.417

ARWV-2 MF062142 58.974 59.694 59.744 60.769 60.256 67.519 66.752 98.417 98.417

(9)

Table 9. Distance matrix of segment S at nucleotide level from apple rubbery wood virus-1 (ARWV-1) and apple rubbery wood virus-2 (ARWV-2) complete sequences downloaded from NCBI (https://www.ncbi.nlm.nih.gov/).

ARWV-1 MF062132

Isolate Q9

ARWV-1 MK936225

ARWV-1 MF062138

ARWV-1 MF062127

ARWV-2 MF062129

ARWV-2 MF062135

ARWV-2 MF062146

ARWV-2 MF062140

ARWV-2 MK936228 ARWV-1

MF062132 98.511 95.876 96.220 96.449 68.114 68.104 68.785 68.104 68.672

Isolate Q9 98.511 95.074 95.647 95.876 68.571 68.331 69.012 68.331 68.899

ARWV-1

MK936225 95.876 95.074 96.678 96.907 68.914 69.240 69.467 69.240 69.580

ARWV-1

MF062138 96.220 95.647 96.678 99.542 68.114 68.785 69.012 68.785 69.126

ARWV-1

MF062127 96.449 95.876 96.907 99.542 68.000 69.012 69.240 69.012 69.353

ARWV-2

MF062129 68.114 68.571 68.914 68.114 68.000 69.738 69.852 69.852 69.625

ARWV-2

MF062135 68.104 68.331 69.240 68.785 69.012 69.738 98.616 98.962 98.847

ARWV-2

MF062146 68.785 69.012 69.467 69.012 69.240 69.852 98.616 98.962 99.077

ARWV-2

MF062140 68.104 68.331 69.240 68.785 69.012 69.852 98.962 98.962 99.193

ARWV-2

MK936228 68.672 68.899 69.580 69.126 69.353 69.625 98.847 99.077 99.193

Table 10. Distance matrix of segment S at aminoacid level from apple rubbery wood virus-1 (ARWV-1) and apple rubbery wood virus-2 (ARWV-2) complete sequences downloaded from NCBI (https://www.ncbi.nlm.nih.gov/).

ARWV-1 MF062138

ARWV-1 MF062127

ARWV-1 MK936225

ARWV-1 MF062132

Isolate Q9

ARWV-2 MF062129

ARWV-2 MF062146

ARWV-2 MF062135

ARWV-2 MK936228

ARWV-2 MF062140 ARWV-1

MF062138 99.310 97.241 97.931 97.586 67.958 68.836 68.836 68.493 68.151

ARWV-1

MF062127 99.310 97.241 97.931 97.586 67.958 68.836 68.836 68.493 68.151

ARWV-1

MK936225 97.241 97.241 97.931 97.586 69.014 69.521 69.521 69.178 68.836

ARWV-1

MF062132 97.931 97.931 97.931 99.655 68.310 68.836 68.836 68.493 68.151

Isolate Q9 97.586 97.586 97.586 99.655 68.662 68.836 68.836 68.493 68.151

ARWV-2

MF062129 67.958 67.958 69.014 68.310 68.662 78.322 77.622 77.972 77.972

ARWV-2

MF062146 68.836 68.836 69.521 68.836 68.836 78.322 98.611 99.306 98.958

ARWV-2

MF062135 68.836 68.836 69.521 68.836 68.836 77.622 98.611 99.306 98.958

ARWV-2

MK936228 68.493 68.493 69.178 68.493 68.493 77.972 99.306 99.306 99.653

ARWV-2

MF062140 68.151 68.151 68.836 68.151 68.151 77.972 98.958 98.958 99.653

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