characterization of the virome of ancient pome fruit cultivars of … · 2020. 7. 11. ·...
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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: DISTANCE MATRIXES
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
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
62.383 74.746
75.834 76.475 78.033 77.804
78.785
79.180 78.968
78.970 78.903 78.746
79.600
78.089
78.226 81.498
79.874
80.461
80.964 81.010
82.980 81.339 81.148
81.864
81.148 83.163 82.055
83.850 83.850
79.865 80.094
MK923753
65.812 74.746
85.531 85.440 84.608 84.333
85.355
84.872 85.217
85.586 84.936 85.151
81.510
86.041
86.270 81.970
82.838
83.974
83.929 83.974
85.073 84.851 84.524
85.105
84.844 84.295 82.891
84.753 84.570
83.425 83.700
KF321967
67.079 75.834 85.531 92.736 85.937 85.662
86.362
85.988 86.426
86.364 85.956 86.401
83.791
84.432
84.478 84.222
85.348
87.128
85.799 85.479
86.853 85.943 85.479
86.566
86.441 86.257 84.211
86.257 86.185
84.975 85.937
MK923755
66.850 76.475 85.440
92.736 86.532 86.257
86.545
86.125 86.700
86.867 86.048 85.806
83.562
84.570
84.661 84.437
84.844
87.403
86.212 85.616
87.036 86.218 86.028
86.657
86.441 86.532 84.073
86.578 86.414
85.295 85.937
KY490039
67.170 78.033 84.608
85.937 86.532 99.725
91.800
90.439 92.396
92.077 88.365 88.273
85.943
85.668
85.623 87.090
86.767
88.365
89.510 88.365
89.739 88.553 88.639
88.594
88.960 88.777 86.362
88.456 88.181
86.945 87.723
MK239268
66.941 77.804 84.333
85.662 86.257 99.725
91.525
90.165 92.121
91.802 88.090 87.998
85.668
85.394
85.348 86.875
86.493
88.090
89.235 88.090
89.464 88.278 88.365
88.319
88.685 88.502 86.087
88.181 87.907
86.670 87.448
AB045371
68.115 78.785 85.355
86.362 86.545 91.800 91.525
95.384 93.547
93.000 88.924 88.777
85.956
85.910
86.231 87.789
87.374
88.833
89.291 88.879
89.840 88.609 87.872
88.823
88.924 88.696 86.877
89.199 89.062
87.506 87.689
KF319056
68.707 79.180 84.872
85.988 86.125 90.439 90.165
95.384 91.648
91.593 88.498 88.808
86.798
85.153
85.427 87.594
88.351
88.757
88.894 88.894
90.539 89.402 89.260
89.661
89.854 89.808 87.443
89.442 89.457
88.117 88.574
MK923754
67.566 78.968 85.217
86.426 86.700 92.396 92.121
93.547
91.648
95.105 88.346 88.243
86.368
86.231
86.276 87.144
86.871
88.421
88.833 88.879
89.977 88.975 87.872
88.823
88.787 88.787 86.831
89.245 88.985
87.414 87.689
Isolate 3 Q9
67.843 78.970 85.586
86.364 86.867 92.077 91.802
93.000
91.593 95.105 88.423 88.642
86.553
86.324
86.370 87.415
87.193
88.377
89.155 88.927
90.071 88.749 88.286
89.512
88.835 88.881 87.336
89.384 88.927
87.508 88.149
MK836301
69.093 78.903 84.936
85.956 86.048 88.365 88.090
88.924
88.498 88.346
88.423 95.050
86.630
86.401
86.401 87.237
88.553
88.869
89.693 88.456
90.426 88.645 89.510
89.821
90.105 90.060 87.551
89.556 89.799
88.594 89.372
MK923756
69.386 78.746 85.151
86.401 85.806 88.273 87.998
88.777
88.808 88.243
88.642 95.050
87.076
86.297
86.251 87.130
88.588
88.675
90.142 88.354
90.142 88.955 89.821
89.684
90.646 90.050 87.540
89.363 89.423
88.583 89.638
FR694186
68.787 79.600 81.510
83.791 83.562 85.943 85.668
85.956
86.798 86.368
86.553 86.630 87.076
85.126
85.309 90.689
89.062
88.736
89.469 89.286
91.071 89.336 89.469
90.513
90.385 90.934 90.348
91.575 91.163
88.141 89.057
JF946772
69.245 78.089 86.041
84.432 84.570 85.668 85.394
85.910
85.153 86.231
86.324 86.401 86.297
85.126
97.619 86.598
87.780
87.363
88.233 89.057
90.797 91.758 88.233
89.047
87.912 88.095 85.910
88.645 88.645
86.722 87.225
JF946775
69.748 78.226 86.270
84.478 84.661 85.623 85.348
86.231
85.427 86.276
86.370 86.401 86.251
85.309
97.619 86.652
88.375
87.592
88.095 89.057
91.026 91.621 88.370
89.047
88.095 88.278 86.185
88.782 88.828
86.722 87.454
AGCaV_
NC_018714
68.084 81.498 81.970
84.222 84.437 87.090 86.875
87.789
87.594 87.144
87.415 87.237 87.130
90.689
86.598
86.652
88.052
89.607
90.361 90.468
92.407 90.258 90.361
91.007
90.199 92.784 91.438
92.730 92.623
88.961 89.715
D21829
74.805 79.874 82.838
85.348 84.844 86.767 86.493
87.374
88.351 86.871
87.193 88.553 88.588
89.062
87.780
88.375 88.052
90.705
91.163 90.293
92.582 90.847 91.758
91.751
92.720 91.896 88.838
90.385 91.071
91.529 91.667
KF915809
70.147 80.461 83.974
87.128 87.403 88.365 88.090
88.833
88.757 88.421
88.377 88.869 88.675
88.736
87.363
87.592 89.607
90.705
90.747 90.380
92.442 90.888 91.800
91.701
92.808 92.304 89.474
91.022 91.205
90.747 91.113
KJ522472
70.559 80.964 83.929
85.799 86.212 89.510 89.235
89.291
88.894 88.833
89.155 89.693 90.142
89.469
88.233
88.095 90.361
91.163
90.747 91.113
92.991 91.438 92.533
91.976
92.716 92.900 90.252
92.121 92.258
90.701 91.022
KU308398
69.872 81.010 83.974
85.479 85.616 88.365 88.090
88.879
88.894 88.879
88.927 88.456 88.354
89.286
89.057
89.057 90.468
90.293
90.380
91.113
95.098 94.414 91.434
92.618
91.709 91.663 89.657
91.892 91.571
90.380 90.518
LC475150
71.108 82.980 85.073
86.853 87.036 89.739 89.464
89.840
90.539 89.977
90.071 90.426 90.142
91.071
90.797
91.026 92.407
92.582
92.442
92.991 95.098 95.971 93.816
94.865
93.953 94.182 92.128
94.274 94.320
92.625 93.083
MG763895
70.343 81.339 84.851
85.943 86.218 88.553 88.278
88.609
89.402 88.975
88.749 88.645 88.955
89.336
91.758
91.621 90.258
90.847
90.888
91.438 94.414
95.971 91.941
93.309
91.987 92.308 90.256
92.491 92.674
90.293 90.888
KY242757
71.612 81.148 84.524
85.479 86.028 88.639 88.365
87.872
89.260 87.872
88.286 89.510 89.821
89.469
88.233
88.370 90.361
91.758
91.800
92.533 91.434
93.816 91.941
95.002
93.678 93.953 90.389
92.350 92.533
92.121 92.900
Isolate 2 Q9
71.127 81.864 85.105
86.566 86.657 88.594 88.319
88.823
89.661 88.823
89.512 89.821 89.684
90.513
89.047
89.047 91.007
91.751
91.701
91.976 92.618
94.865 93.309 95.002
93.122 93.122 91.388
93.168 93.306
91.426 91.884
Isolate 1 Q9
71.612 81.148 84.844
86.441 86.441 88.960 88.685
88.924
89.854 88.787
88.835 90.105 90.646
90.385
87.912
88.095 90.199
92.720
92.808
92.716 91.709
93.953 91.987 93.678
93.122 94.411 90.755
92.442 92.945
93.129 93.770
KY702581
71.062 83.163 84.295
86.257 86.532 88.777 88.502
88.696
89.808 88.787
88.881 90.060 90.050
90.934
88.095
88.278 92.784
91.896
92.304
92.900 91.663
94.182 92.308 93.953
93.122
94.411 92.449
94.411 94.503
91.984 92.579
LM999967
69.167 82.055 82.891
84.211 84.073 86.362 86.087
86.877
87.443 86.831
87.336 87.551 87.540
90.348
85.910
86.185 91.438
88.838
89.474
90.252 89.657
92.128 90.256 90.389
91.388
90.755 92.449
93.043 93.867
88.833 89.291
KF321966
70.284 83.850 84.753
86.257 86.578 88.456 88.181
89.199
89.442 89.245
89.384 89.556 89.363
91.575
88.645
88.782 92.730
90.385
91.022
92.121 91.892
94.274 92.491 92.350
93.168
92.442 94.411 93.043 96.290
90.563 90.884
KY702580
70.330 83.850 84.570
86.185 86.414 88.181 87.907
89.062
89.457 88.985
88.927 89.799 89.423
91.163
88.645
88.828 92.623
91.071
91.205
92.258 91.571
94.320 92.674 92.533
93.306
92.945 94.503 93.867
96.290
90.976 91.342
LC475151
70.375 79.865 83.425
84.975 85.295 86.945 86.670
87.506
88.117 87.414
87.508 88.594 88.583
88.141
86.722
86.722 88.961
91.529
90.747
90.701 90.380
92.625 90.293 92.121
91.426
93.129 91.984 88.833
90.563 90.976 93.907
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
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
30.345 83.375 77.329 74.510
74.510
68.558 67.612
72.059
68.545
73.775 73.529
71.814
72.549
72.304
72.794
74.177 74.020 72.794
73.039 73.775 73.529
73.775 72.304 72.059 69.118
72.794
72.794
72.794 71.463 69.756 70.488
AGCaV_
NC_018714
30.115 83.375 91.473 74.510
75.000
68.558 69.031
73.775
69.249
74.510 75.000
73.284
74.265
74.265
74.265
74.684 75.245 74.265
74.265 74.755 75.490
73.529 74.265 74.020 70.588
72.794
72.059
72.059 70.732 70.488 71.220
AGCaV_K
T835289
27.701 77.329 91.473 69.274
69.519
63.969 64.206
68.772
64.693
69.262 69.753
68.527
69.262
69.017
69.017
69.758 69.998 68.527
68.772 69.262 70.243
68.772 69.753 69.508 65.831
68.037
67.792
67.057 66.729 65.998 66.729
MK923755
33.563 74.510 74.510 69.274
88.206
70.213 70.922
75.000
71.596
77.451 76.225
76.471
76.961
77.696
78.186
78.987 80.147 78.378
78.378 78.870 77.941
78.186 77.206 76.961 72.794
77.206
71.253
71.744 70.244 71.951 71.951
KF321967
32.874 74.510 75.000 69.519 88.206
69.976 70.449
74.020
70.657
75.980 74.755
75.245
76.225
76.471
76.961
77.919 77.696 76.716
76.225 77.451 76.471
77.451 76.225 75.980 70.588
76.225
69.608
70.098 70.000 70.976 70.976
LC475151
38.118 68.558 68.558 63.969 70.213
69.976 81.752
74.939
77.885
77.859 76.886
79.805
78.589
81.265
79.562
80.151 79.075 78.102
78.589 78.345 77.859
79.075 78.345 78.345 75.669
79.075
67.150
67.874 67.874 68.599 68.357
KY798310
37.412 67.612 69.031 64.206 70.922
70.449
81.752
76.642
80.529
77.616 77.129
82.238
81.022
82.238
81.509
82.663 82.968 79.319
80.049 80.535 80.049
80.292 79.319 79.075 78.832
81.022
68.116
67.874 68.599 68.357 68.841
KF319056
34.507 72.059 73.775 68.772 75.000
74.020
74.939 76.642
77.053
82.045 81.297
82.828
83.042
83.081
83.791
84.595 86.111 81.546
82.045 81.796 85.354
82.793 83.333 83.081 79.545
81.546
71.040
69.802 69.136 72.593 73.000
D21829
48.700 68.545 69.249 64.693 71.596
70.657
77.885 80.529
77.053
78.019 77.053
80.193
82.126
80.193
80.435
80.798 81.884 80.193
81.401 82.126 83.333
81.884 81.884 81.643 82.609
85.749
69.544
70.264 69.378 70.574 70.813
KJ522472
36.150 73.775 74.510 69.262 77.451
75.980
77.859 77.616
82.045
78.019 98.058
83.333
84.901
86.111
83.738
88.512 87.879 83.738
84.709 83.738 85.101
82.039 84.091 83.838 79.798
81.907
69.417
69.458 69.231 71.394 73.000
KY702580
35.211 73.529 75.000 69.753 76.225
74.755
76.886 77.129
81.297
77.053
98.058
82.576
84.406
85.101
82.524
87.467 86.869 82.767
83.738 82.767 84.091
80.583 83.586 83.333 79.293
81.418
69.903
69.951 68.510 70.192 72.250
Isolate 1 Q9
37.825 71.814 73.284 68.527 76.471
75.245
79.805 82.238
82.828
80.193
83.333 82.576
88.131
89.646
89.394
88.251 88.384 85.859
86.364 87.121 86.616
85.354 87.121 86.869 81.313
84.596
70.175
70.426 70.000 72.250 72.000
Isolate 2 Q9
38.732 72.549 74.265 69.262 76.961
76.225
78.589 81.022
83.042
82.126
84.901 84.406
88.131
88.889
88.366
89.817 89.141 87.129
86.634 87.871 88.636
85.149 87.374 87.121 82.828
85.891
71.744
70.936 69.363 71.569 72.750
FR694186
37.116 72.304 74.265 69.017 77.696
76.471
81.265 82.238
83.081
80.193
86.111 85.101
89.646
88.889
88.636
90.078 88.384 86.111
87.879 87.879 86.869
86.111 86.364 86.111 81.818
86.364
70.677
70.677 70.250 71.750 71.500
AB045371
38.263 72.794 74.265 69.017 78.186
76.961
79.562 81.509
83.791
80.435
83.738 82.524
89.394
88.366
88.636
91.906 92.424 86.571
85.132 85.372 88.384
83.453 86.616 86.364 82.323
83.374
69.903
70.197 67.458 71.259 74.000
Isolate 3 Q9
37.317 74.177 74.684 69.758 78.987
77.919
80.151 82.663
84.595
80.798
88.512 87.467
88.251
89.817
90.078
91.906 93.734 89.556
89.817 90.339 87.467
86.945 86.945 86.684 82.768
85.640
73.316
72.021 72.093 73.127 73.643
MK923754
38.298 74.020 75.245 69.998 80.147
77.696
79.075 82.968
86.111
81.884
87.879 86.869
88.384
89.141
88.384
92.424
93.734 89.141
89.394 89.646 89.141
87.879 87.626 87.374 82.323
86.869
72.431
72.431 72.000 73.750 74.500
MK923756
37.089 72.794 74.265 68.527 78.378
76.716
78.102 79.319
81.546
80.193
83.738 82.767
85.859
87.129
86.111
86.571
89.556 89.141
90.865 91.106 87.879
83.453 85.606 85.859 82.828
83.619
70.560
70.617 67.458 70.309 72.500
KF915809
38.498 73.039 74.265 68.772 78.378
76.225
78.589 80.049
82.045
81.401
84.709 83.738
86.364
86.634
87.879
85.132
89.817 89.394 90.865 91.587 89.141
83.213 85.859 86.111 82.828
84.108
70.316
71.111 68.409 70.546 72.750
MK836301
38.028 73.775 74.755 69.262 78.870
77.451
78.345 80.535
81.796
82.126
83.738 82.767
87.121
87.871
87.879
85.372
90.339 89.646 91.106
91.587 89.141
84.412 86.616 86.869 83.333
84.841
71.951
72.346 69.834 70.309 73.750
KY702581
39.716 73.529 75.490 70.243 77.941
76.471
77.859 80.049
85.354
83.333
85.101 84.091
86.616
88.636
86.869
88.384
87.467 89.141 87.879
89.141 89.141
88.889 89.394 89.141 85.606
88.384
71.930
72.180 71.250 74.250 74.250
KF321966
38.263 73.775 73.529 68.772 78.186
77.451
79.075 80.292
82.793
81.884
82.039 80.583
85.354
85.149
86.111
83.453
86.945 87.879 83.453
83.213 84.412 88.889 92.929 92.677 83.586
86.308
70.631
70.443 68.646 70.071 73.250
KY490039
38.061 72.304 74.265 69.753 77.206
76.225
78.345 79.319
83.333
81.884
84.091 83.586
87.121
87.374
86.364
86.616
86.945 87.626 85.606
85.859 86.616 89.394
92.929 99.747 84.596
87.374
71.429
70.677 70.750 72.500 72.750
MK239268
38.298 72.059 74.020 69.508 76.961
75.980
78.345 79.075
83.081
81.643
83.838 83.333
86.869
87.121
86.111
86.364
86.684 87.374 85.859
86.111 86.869 89.141
92.677 99.747 84.848
87.121
71.178
70.426 70.500 72.250 72.500
KU308398
38.061 69.118 70.588 65.831 72.794
70.588
75.669 78.832
79.545
82.609
79.798 79.293
81.313
82.828
81.818
82.323
82.768 82.323 82.828
82.828 83.333 85.606
83.586 84.596 84.848
88.131
72.180
73.684 70.500 72.500 72.000
LC475150
39.671 72.794 72.794 68.037 77.206
76.225
79.075 81.022
81.546
85.749
81.907 81.418
84.596
85.891
86.364
83.374
85.640 86.869 83.619
84.108 84.841 88.384
86.308 87.374 87.121 88.131
71.845
73.645 70.944 72.639 74.250
JF946775
30.070 72.794 72.059 67.792 71.253
69.608
67.150 68.116
71.040
69.544
69.417 69.903
70.175
71.744
70.677
69.903
73.316 72.431 70.560
70.316 71.951 71.930
70.631 71.429 71.178 72.180
71.845
91.605 73.913 73.188 76.559
JF946772
30.769 72.794 72.059 67.057 71.744
70.098
67.874 67.874
69.802
70.264
69.458 69.951
70.426
70.936
70.677
70.197
72.021 72.431 70.617
71.111 72.346 72.180
70.443 70.677 70.426 73.684
73.645
91.605 74.510 73.039 75.810
LM999967
30.465 71.463 70.732 66.729 70.244
70.000
67.874 68.599
69.136
69.378
69.231 68.510
70.000
69.363
70.250
67.458
72.093 72.000 67.458
68.409 69.834 71.250
68.646 70.750 70.500 70.500
70.944
73.913
74.510 79.529 85.213
MK923753
32.558 69.756 70.488 65.998 71.951
70.976
68.599 68.357
72.593
70.574
71.394 70.192
72.250
71.569
71.750
71.259
73.127 73.750 70.309
70.546 70.309 74.250
70.071 72.500 72.250 72.500
72.639
73.188
73.039 79.529 93.216
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
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
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
Table 11. Distance matrix of complete sequences of apple stem grooving virus (ASGV) downloaded from NCBI (https://www.ncbi.nlm.nih.gov/), at nucleotide level.
KU94
7036
KR10
6996
AY59
6172
LC48
0456
MH10
8985
KX98
8001
Isol
ate
Q9
LT160
740
LC08
4659
KR18
5346
MH14
4342
MF61
6381
KX68
6100
MH10
8986
KJ579
253
KU60
5672
LC14
3387
D16
681
MK59
9421
KC58
8948
KX66
8488
D14
995
MH14
4343
LC18
4612
JQ308
181
LC47
5148
MK59
9422
JN701
424
KU947
036 78.749 78.343 78.784 79.131 78.689
79.2
1 78.752 78.878 79.842 78.437 78.485 78.627 79.21 80.823 78.784 79.115
78.7
2 79.352 79.479 78.673
79.0
05 78.878 79.147 78.626 81.058 78.768 79.052
KR106
996 78.749 78.451 78.965 79.028 78.569
79.3
13 78.933 79.282 79.234 79.434 78.69 78.848 78.902 79.049 78.632 79.028
78.7
59 78.997 79.155 79.139
78.8
38 79.123 79.424 78.743 81.149 79.234 78.822
AY596
172 78.343 78.451 78.758 79.058 80.022
79.4
06 79.263 78.857 79.659 78.894 79.289 79.479 79.753 79.795 79.026 80.275
80.1
33 79.343 79.532 79.769
79.4
06 79.327 79.453 79.469 82.511 79.611 79.343
LC480
456 78.784 78.965 78.758 81.387 80.833
81.1
65 80.785 80.851 81.925 81.022 80.879 80.99 81.371 81.517 81.339 81.402
81.1
97 82.289 81.671 81.608
81.8
3 81.846 81.956 81.592 83.531 81.861 81.766
MH10
8985 79.131 79.028 79.058 81.387 81.323
81.6
08 81.497 81.436 83.017 81.971 80.943 81.211 81.481 80.932 81.402 81.687
81.1
49 81.703 82.02 81.371
81.5
61 81.276 81.893 81.022 84.022 81.117 80.801
KX988
001 78.689 78.569 80.022 80.833 81.323
81.9
25 81.402 81.689 81.846 81.591 81.037 81.385 81.814 81.501 80.928 81.751
81.1
81 81.561 81.387 81.624
81.4
5 81.497 81.814 81.133 84.101 81.07 80.896
Isolate
Q9 79.21 79.313 79.406 81.165 81.608 81.925 96.249 81.009 82.336 81.971 81.069 81.18 81.671 82.022 80.421 81.624
81.1
17 81.687 81.513 81.402
81.9
25 81.307 81.719 80.912 83.966 81.402 81.117
LT160
740 78.752 78.933 79.263 80.785 81.497 81.402
96.2
49 80.898 82.004 82.951 82.145 81.322 81.323 81.943 80.405 81.481
80.8
01 81.64 81.276 82.13
81.9
09 81.26 81.687 80.753 84.156 81.434 81.212
LC084
659 78.878 79.282 78.857 80.851 81.436 81.689
81.0
09 80.898 81.025 80.351 81.173 81.584 80.614 81.864 80.946 81.325
80.8
67 82.1 82.084 80.993
81.3
88 81.104 81.863 81.025 84.401 81.293 81.199
KR185
346 79.842 79.234 79.659 81.925 83.017 81.846
82.3
36 82.004 81.025 82.129 81.575 81.544 81.909 82.18 84.156 83.033
82.2
1 82.494 82.653 82.21
82.6
05 82.273 82.368 82.067 84.758 82.494 82.368
MH14
4342 78.437 79.434 78.894 81.022 81.971 81.591
81.9
71 82.951 80.351 82.129 87.179 86.689 81.923 81.926 81.275 81.812
81.4
64 81.876 81.892 83.821
82.1
92 81.876 82.176 81.101 85.292 81.844 81.544
MF616
381 78.485 78.69 79.289 80.879 80.943 81.037
81.0
69 82.145 81.173 81.575 87.179 90.06 81.464 82.999 81.512 82.398
82.1
45 82.666 82.445 84.485
82.4
45 82.587 83.03 84.786 86.707 86.177 86.067
KX686
100 78.627 78.848 79.479 80.99 81.211 81.385
81.1
8 81.322 81.584 81.544 86.689 90.06 80.974 81.847 80.705 81.496
81.4
96 81.085 81.101 83.647
81.0
69 81.18 81.243 82.603 84.651 81.37 81.322
MH10
8986 79.21 78.902 79.753 81.371 81.481 81.814
81.6
71 81.323 80.614 81.909 81.923 81.464 80.974 84.107 83.65 83.555
83.0
48 86.008 86.467 84.473
85.7
55 86.91 86.293 83.397 86.546 84.41 84.188
KJ579
253 80.823 79.049 79.795 81.517 80.932 81.501
82.0
22 81.943 81.864 82.18 81.926 82.999 81.847 84.107 83.918 82.859
82.4
8 86.367 86.256 85.055
86.3
67 85.861 86.667 82.686 86.532 83.886 83.965
KU605
672 78.784 78.632 79.026 81.339 81.402 80.928
80.4
21 80.405 80.946 84.156 81.275 81.512 80.705 83.65 83.918 82.605
82.1
46 86.325 86.499 85.771
87.3
54 86.61 86.768 83.966 86.436 84.457 84.837
LC143
387 79.115 79.028 80.275 81.402 81.687 81.751
81.6
24 81.481 81.325 83.033 81.812 82.398 81.496 83.555 82.859 82.605
94.7
77 83.143 83.713 82.02
83.0
33 83.46 83.349 83.175 88.264 83.476 84.489
D1668
1 78.72 78.759 80.133 81.197 81.149 81.181
81.1
17 80.801 80.867 82.21 81.464 82.145 81.496 83.048 82.48 82.146 94.777 82.574 83.001 82.067
82.5
89 82.7 82.605 82.779 87.409 82.906 83.697
MK59
9421 79.352 78.997 79.343 82.289 81.703 81.561
81.6
87 81.64 82.1 82.494 81.876 82.666 81.085 86.008 86.367 86.325 83.143
82.5
74 90.519 88.24
90.5
67 90.139 90.994 86.103 89.031 87.749 87.512
KC588
948 79.479 79.155 79.532 81.671 82.02 81.387
81.5
13 81.276 82.084 82.653 81.892 82.445 81.101 86.467 86.256 86.499 83.713
83.0
01 90.519 88.066
90.8
83 90.63 91.295 85.502 88.81 86.151 86.151
KX668
488 78.673 79.139 79.769 81.608 81.371 81.624
81.4
02 82.13 80.993 82.21 83.821 84.485 83.647 84.473 85.055 85.771 82.02
82.0
67 88.24 88.066
92.1
02 89.649 89.981 85.818 88.628 86.483 85.897
D1499
5 79.005 78.838 79.406 81.83 81.561 81.45
81.9
25 81.909 81.388 82.605 82.192 82.445 81.069 85.755 86.367 87.354 83.033
82.5
89 90.567 90.883 92.102 92.26 92.941 86.103 89.364 86.515 86.831
MH14
4343 78.878 79.123 79.327 81.846 81.276 81.497
81.3
07 81.26 81.104 82.273 81.876 82.587 81.18 86.91 85.861 86.61 83.46 82.7 90.139 90.63 89.649
92.2
6 92.988 85.723 89.38 86.752 86.958
LC184
612 79.147 79.424 79.453 81.956 81.893 81.814
81.7
19 81.687 81.863 82.368 82.176 83.03 81.243 86.293 86.667 86.768 83.349
82.6
05 90.994 91.295 89.981
92.9
41 92.988 85.723 89.957 86.689 86.847
JQ308
181 78.626 78.743 79.469 81.592 81.022 81.133
80.9
12 80.753 81.025 82.067 81.101 84.786 82.603 83.397 82.686 83.966 83.175
82.7
79 86.103 85.502 85.818
86.1
03 85.723 85.723 89.055 88.841 90.393
LC475
148 81.058 81.149 82.511 83.531 84.022 84.101
83.9
66 84.156 84.401 84.758 85.292 86.707 84.651 86.546 86.532 86.436 88.264
87.4
09 89.031 88.81 88.628
89.3
64 89.38 89.957 89.055 89.182 90.543
MK59
9422 78.768 79.234 79.611 81.861 81.117 81.07
81.4
02 81.434 81.293 82.494 81.844 86.177 81.37 84.41 83.886 84.457 83.476
82.9
06 87.749 86.151 86.483
86.5
15 86.752 86.689 88.841 89.182 91.231
JN701
424 79.052 78.822 79.343 81.766 80.801 80.896
81.1
17 81.212 81.199 82.368 81.544 86.067 81.322 84.188 83.965 84.837 84.489
83.6
97 87.512 86.151 85.897
86.8
31 86.958 86.847 90.393 90.543 91.231
Table 12. Distance matrix of complete sequences of apple stem grooving virus (ASGV) downloaded from NCBI (https://www.ncbi.nlm.nih.gov/), at aminoacid level,
KU94
7036
AY59
6172
KR10
6996
LC08
4659
KX98
8001
Iso-
Q9
LT160
740
LC48
0456
MH10
8985
KJ579
253
KR18
5346
KU60
5672
MH10
8986
LC14
3387
D16
681
MK59
9422
MH14
4342
LC47
5148
MK59
9421
KC58
8948
MH14
4343
LC18
4612
D14
995
JQ308
181
JN701
424
KX66
8488
MF61
6381
KX68
6100
KU947
036 84.276 83.658 84.988 84.038 85.796
85.6
06 84.941 85.036 85.891 85.891 84.466 85.701 85.416 84.941
84.8
93 85.131 86.746 85.178 85.083 85.416 85.416 85.463
84.8
46 85.131 85.036 84.846 84.656
AY596
172 84.276 85.321 85.416 85.701
86.9
36 86.461 84.893 85.368 86.413 85.843 84.466 85.416 85.083
84.3
23 86.033 85.891 87.696 85.653 85.083 86.033 85.606
85.8
91 84.513 84.941 85.748 85.701 84.988
KR106
996 83.658 85.321 84.893 84.703
85.3
21 85.321 84.798 85.178 84.846 85.036 84.513 84.371 84.608
84.0
38 85.321 85.463 87.363 84.798 84.798 84.893 84.941
84.6
56 84.133 84.656 85.511 85.321 84.846
LC084
659 84.988 85.416 84.893 86.793
87.7
91 87.886 86.461 87.268 87.221 86.746 85.701 86.793 87.031
86.5
08 87.316 86.508 89.121 88.171 87.411 86.983 87.648
87.8
86 86.033 86.698 87.268 87.126 86.793
KX988
001 84.038 85.701 84.703 86.793
87.3
16 86.841 86.603 86.461 87.363 87.743 86.271 87.838 87.126
86.1
76 87.316 87.601 89.359 88.076 87.791 87.696 88.124
87.7
43 86.366 86.508 87.553 87.268 86.651
Isolate
Q9 85.796 86.936 85.321 87.791 87.316 97.625 87.126 87.268 87.981 88.029 86.698 86.793 87.126
86.5
08 87.981 87.411 89.501 87.696 87.078 87.316 87.316
88.0
76 87.078 87.506 87.506 87.981 87.126
LT160
740 85.606 86.461 85.321 87.886 86.841
97.6
25 86.841 87.078 87.506 88.029 86.081 86.413 87.411
86.7
46 87.648 87.696 89.549 87.126 86.651 87.078 86.888
87.5
06 86.651 87.363 87.411 87.981 87.363
LC480
456 84.941 84.893 84.798 86.461 86.603
87.1
26 86.841 86.128 86.746 87.363 86.508 87.411 87.648
86.8
88 87.838 87.743 89.644 88.599 86.936 87.458 88.076
88.3
14 86.888 87.743 87.981 87.933 87.363
MH10
8985 85.036 85.368 85.178 87.268 86.461
87.2
68 87.078 86.128 86.793 87.886 86.366 87.173 87.648
86.6
51 87.173 88.124 89.691 87.268 87.506 87.078 88.219
87.4
58 87.031 87.126 87.648 87.078 86.603
KJ579
253 85.891 86.413 84.846 87.221 87.363
87.9
81 87.506 86.746 86.793 87.648 87.981 88.266 88.076
86.9
36 88.931 87.221 90.024 88.694 88.694 89.121 88.931
88.9
79 87.126 88.456 88.219 87.553 87.173
KR185
346 85.891 85.843 85.036 86.746 87.743
88.0
29 88.029 87.363 87.886 87.648 92.209 88.171 88.599
87.6
96 88.361 88.029 90.309 87.838 87.743 88.266 88.171
88.3
14 87.886 88.551 88.694 88.314 87.316
KU605
672 84.466 84.466 84.513 85.701 86.271
86.6
98 86.081 86.508 86.366 87.981 92.209 87.933 87.743
86.9
83 88.219 86.793 90.784 89.501 89.264 89.786 89.834
90.4
51 87.696 88.361 89.596 86.888 86.651
MH10
8986 85.701 85.416 84.371 86.793 87.838
86.7
93 86.413 87.411 87.173 88.266 88.171 87.933 88.599
87.3
63 88.741 87.648 91.069 90.689 90.451 91.781 90.499
90.4
51 87.981 88.741 88.836 87.268 86.413
LC143
387 85.416 85.083 84.608 87.031 87.126
87.1
26 87.411 87.648 87.648 88.076 88.599 87.743 88.599
95.5
82 89.121 87.268 92.494 89.691 89.169 89.454 89.216
90.0
24 89.359 90.309 88.694 87.601 87.173
D1668
1 84.941 84.323 84.038 86.508 86.176
86.5
08 86.746 86.888 86.651 86.936 87.696 86.983 87.363 95.582 88.551 86.556 91.259 88.409 87.886 87.981 87.838
88.5
04 88.409 89.264 88.124 87.553 86.508
MK59
9422 84.893 86.033 85.321 87.316 87.316
87.9
81 87.648 87.838 87.173 88.931 88.361 88.219 88.741 89.121
88.5
51 87.363 92.542 90.404 89.691 89.596 89.976
90.2
61 91.401 91.021 90.499 89.359 87.601
MH14
4342 85.131 85.891 85.463 86.508 87.601
87.4
11 87.696 87.743 88.124 87.221 88.029 86.793 87.648 87.268
86.5
56 87.363 90.166 87.601 87.411 87.791 88.076
87.7
43 86.793 86.983 90.594 92.589 91.971
LC475
148 86.746 87.696 87.363 89.121 89.359
89.5
01 89.549 89.644 89.691 90.024 90.309 90.784 91.069 92.494
91.2
59 92.542 90.166 93.777 92.922 93.444 93.872
93.7
77 92.684 93.349 93.112 90.926 89.739
MK59
9421 85.178 85.653 84.798 88.171 88.076
87.6
96 87.126 88.599 87.268 88.694 87.838 89.501 90.689 89.691
88.4
09 90.404 87.601 93.777 93.017 92.969 94.062
93.6
82 89.976 90.926 90.594 88.029 87.316
KC588
948 85.083 85.083 84.798 87.411 87.791
87.0
78 86.651 86.936 87.506 88.694 87.743 89.264 90.451 89.169
87.8
86 89.691 87.411 92.922 93.017 93.017 94.252
93.9
67 89.501 89.454 90.594 87.791 86.936
MH14
4343 85.416 86.033 84.893 86.983 87.696
87.3
16 87.078 87.458 87.078 89.121 88.266 89.786 91.781 89.454
87.9
81 89.596 87.791 93.444 92.969 93.017 94.489
94.0
14 89.881 90.166 90.926 87.981 87.126
LC184
612 85.416 85.606 84.941 87.648 88.124
87.3
16 86.888 88.076 88.219 88.931 88.171 89.834 90.499 89.216
87.8
38 89.976 88.076 93.872 94.062 94.252 94.489
94.9
17 89.929 90.309 91.069 88.219 87.458
D1499
5 85.463 85.891 84.656 87.886 87.743
88.0
76 87.506 88.314 87.458 88.979 88.314 90.451 90.451 90.024
88.5
04 90.261 87.743 93.777 93.682 93.967 94.014 94.917 90.594 90.736 92.257 88.029 87.363
JQ308
181 84.846 84.513 84.133 86.033 86.366
87.0
78 86.651 86.888 87.031 87.126 87.886 87.696 87.981 89.359
88.4
09 91.401 86.793 92.684 89.976 89.501 89.881 89.929
90.5
94 93.539 89.216 88.741 86.413
JN701
424 85.131 84.941 84.656 86.698 86.508
87.5
06 87.363 87.743 87.126 88.456 88.551 88.361 88.741 90.309
89.2
64 91.021 86.983 93.349 90.926 89.454 90.166 90.309
90.7
36 93.539 89.406 88.219 86.651
KX668
488 85.036 85.748 85.511 87.268 87.553
87.5
06 87.411 87.981 87.648 88.219 88.694 89.596 88.836 88.694
88.1
24 90.499 90.594 93.112 90.594 90.594 90.926 91.069
92.2
57 89.216 89.406 93.207 92.494
MF616
381 84.846 85.701 85.321 87.126 87.268
87.9
81 87.981 87.933 87.078 87.553 88.314 86.888 87.268 87.601
87.5
53 89.359 92.589 90.926 88.029 87.791 87.981 88.219
88.0
29 88.741 88.219 93.207 96.152
KX686
100 84.656 84.988 84.846 86.793 86.651
87.1
26 87.363 87.363 86.603 87.173 87.316 86.651 86.413 87.173
86.5
08 87.601 91.971 89.739 87.316 86.936 87.126 87.458
87.3
63 86.413 86.651 92.494 96.152
ANNEX II: CAPTURE OF GENEIOUS PARAMETERS
Figure 1. Parameters used during the DeNovo assembly of all reads from sample Q9 (Table 5) with SPAdes Assembler in Geneious.
Figure 2. Parameters used during the mapping on Geneious of all reads from sample Q9 (Table 5) to the reference genomes of Apricot
latent virus (ApLV), Apple green crinkle associated virus (AGCaV), and Apple stem pitting virus (APSV) simultaneously to avoid multiple
mapping of the same read into two or more sequences.
Figure 3. Parameters used during pairwise or multiple alignments on Geneious with MUSCLE Alignment.
Figure 4. Extension of contigs obtained after the DeNovo assembly with Geneious assembler allowing 5% of mismatches by mapping
all reads from sample Q9 (Table 5) using the contigs as reference.
Figure 5. Parameters used during mapping of all extended contigs, from previous step, to the reference sequence of Apple stem pitting
virus (ASPV) at a Medium-Low Sensitivity, which allows a 20% of mismatches and with data from sample Q9 (Table 5).
Figure 6. Parameters used during the DeNovo assembly of the extracted Foveavirus reads from sample Q9 (Table 5), with Geneious
assembler allowing 20% of mismatches.
Figure 7. Parameters used during the DeNovo assembly of the extracted Foveavirus reads from sample Q9 (Table 5), with Geneious
assembler allowing 10% of mismatches.
Figure 8. Parameters used during the DeNovo assembly of the extracted Foveavirus reads from sample Q9 (Table 5), with Geneious
assembler allowing 5% of mismatches.
Figure 9. Parameters used during the mapping of all reads from sample Q9 (Table 5) to contigs 2, 3, 5, and 7 produced by the DeNovo
assembly with Geneious assembler allowing 10% of mismatches which correspond to the RdRp and CP fragments of new ASPV isolates
2 and 3, respectively.
Figure 10. Parameters used during the mapping, allowing 28% of mismatches, of contigs obtained after a DeNovo assembly with
Geneious assembler allowing 10% of mismatches.
Figure 11. Parameters used during the mapping on Geneious of extracted virus reads from Kraken to the reference sequence of Apple
stem grooving virus (ASGV), allowing a 20% of mismatches and iterating twenty-five times.
Figure 12. Parameters used during the mapping on Geneious of all reads from sample Q9 (Figure 11) to the three reference genome
sequences of Apple rubbery wood virus-1 Isolate BR-Mishima.
Figure 13. Parameters used during the DeNovo assembly with SPAdes of the used reads during the previous mapping to three reference
genome sequences of ARWV-1 Isolate BR-Mishima (Figure 12).
Figure 14. Parameters used to build phylogenetic trees, with the genetic distance model Jukes-Cantor and the tree build method
UPGMA.
Figure 15. Parameters used during the DeNovo assembly with Geneious assembler allowing 10% of mismatches of the reads from
pooled samples extracted with double-stranded RNA (dsRNA) and VANA protocols.
Figure 16. Parameters used during the mapping, allowing 20% of mismatches, of reads from sample 8 Error! Reference source not
found.), where some reads from Apple hammerhead viroid-like RNA (AHVd-like RNA) were detected.
Figure 17. Parameters used during the mapping of reads from sample 9 (Table 4), where numerous reads were assigned to Apple
luteovirus-1 (ALV-1), to the reference genome sequence of ALV-1. The mapping was done allowing 20% of mismatches.
Figure 18. Parameters used during the mapping of reads from individual samples extracted with double-stranded RNA (dsRNA) protocol
to the reference genome sequence of ALV-1 allowing 20% of mismatches, to test presence of ALV-1 within the individual samples.