Table 1 NGS statistics of collected samples before and after quality control
showing the number of reads, the N50, and the maximum contig length (bp)
Sample ID
|
County
|
AEZ
|
Reads before QC
|
Reads after QC
|
N50 after de novoassembly
|
Average length after de novoassembly
|
Max contig length
|
Tom 2
|
Kirinyaga
|
UM
|
740
|
593
|
147
|
148
|
1023
|
Tom 3
|
Kirinyaga
|
UM
|
319816
|
314602
|
157
|
157
|
5262
|
Tom 4
|
Kirinyaga
|
UM
|
712833
|
698797
|
172
|
171
|
8902
|
Tom 5
|
Kirinyaga
|
UM
|
478717
|
468508
|
235
|
231
|
13612
|
Tom 6
|
Meru
|
LM
|
926762
|
910347
|
182
|
178
|
10110
|
Tom 7
|
Kirinyaga
|
UM
|
685854
|
673575
|
182
|
179
|
7946
|
Tom 8
|
Nakuru
|
LH
|
228919
|
223686
|
180
|
178
|
7153
|
Tom 9
|
Nakuru
|
UM
|
234634
|
230096
|
183
|
182
|
6069
|
Tom 10
|
Kirinyaga
|
UM
|
666739
|
687749
|
184
|
182
|
6290
|
Tom 11
|
Kirinyaga
|
UM
|
513780
|
510356
|
175
|
175
|
7911
|
Tom 12
|
Nakuru
|
UM
|
518378
|
510356
|
175
|
175
|
6450
|
Tom 13
|
Baringo
|
LH
|
1294432
|
1274379
|
201
|
214
|
10139
|
Tom 14
|
Baringo
|
LH
|
1315827
|
1298815
|
201
|
207
|
44887
|
Tom 15
|
Baringo
|
LH
|
681944
|
672083
|
159
|
162
|
3864
|
Tom 16
|
Nakuru
|
UM
|
923671
|
908547
|
186
|
182
|
17400
|
Tom 17
|
Kwale
|
Coastal
|
534566
|
527106
|
162
|
162
|
7417
|
Tom 18
|
Nakuru
|
UM
|
352911
|
347096
|
181
|
181
|
11029
|
Tom 20
|
Baringo
|
LH
|
609870
|
597102
|
166
|
165
|
5871
|
Tom 21
|
Nakuru
|
UM
|
243975
|
240633
|
135
|
138
|
947
|
Tom 22
|
Baringo
|
LH
|
253971
|
251006
|
135
|
138
|
947
|
Tom 23
|
Meru
|
LM
|
989149
|
975057
|
163
|
164
|
7104
|
Tom 24
|
Meru
|
LM
|
786980
|
774322
|
171
|
171
|
7102
|
Tom 26
|
Baringo
|
LH
|
728499
|
719324
|
164
|
166
|
42790
|
Tom 27
|
Meru
|
LH
|
1058065
|
1039347
|
187
|
190
|
42301
|
Tom 28
|
Baringo
|
LH
|
339590
|
324853
|
170
|
173
|
7369
|
Tom 33
|
Makueni
|
UM
|
1093634
|
1078116
|
147
|
149
|
5805
|
Tom 34
|
Kirinyaga
|
UM
|
619068
|
610590
|
152
|
152
|
7151
|
Tom 35
|
Nakuru
|
LH
|
322666
|
317651
|
159
|
160
|
5398
|
Tom 36
|
Nakuru
|
LH
|
605642
|
597918
|
151
|
152
|
3604
|
Tom 37
|
Baringo
|
LH
|
161895
|
158650
|
201
|
206
|
3608
|
Tom 39
|
Makueni
|
LM
|
638580
|
630445
|
146
|
149
|
7957
|
Tom 40
|
Baringo
|
LH
|
359195
|
353997
|
201
|
208
|
40180
|
Tom 41
|
Machakos
|
LM
|
424094
|
418916
|
173
|
173
|
5839
|
Tom 42
|
Nakuru
|
LH
|
286302
|
282623
|
168
|
167
|
7249
|
Tom 43
|
Kirinyaga
|
UM
|
478583
|
470428
|
173
|
173
|
7405
|
Tom 44
|
Nakuru
|
LH
|
225820
|
222387
|
191
|
199
|
4190
|
Tom 45
|
Baringo
|
LH
|
547166
|
540173
|
208
|
211
|
9004
|
Tom 46
|
Meru
|
LM
|
484669
|
477311
|
176
|
178
|
6633
|
Tom 47
|
Meru
|
LM
|
492672
|
486329
|
161
|
162
|
4876
|
Tom 48
|
Meru
|
LM
|
656855
|
649550
|
270
|
237
|
14432
|
Tom 49
|
Meru
|
LM
|
99706
|
98214
|
168
|
169
|
5196
|
Tom 50
|
Kirinyaga
|
UM
|
576946
|
568993
|
166
|
167
|
7263
|
Tom 51
|
Nakuru
|
LH
|
236211
|
232201
|
160
|
162
|
7294
|
Tom 52
|
Baringo
|
LH
|
369927
|
364146
|
201
|
212
|
6670
|
Tom 53
|
Meru
|
LM
|
590600
|
581771
|
179
|
181
|
7083
|
Tom 54
|
Nakuru
|
UM
|
320207
|
314556
|
174
|
174
|
7225
|
Tom 55
|
Nakuru
|
LH
|
387684
|
382226
|
165
|
167
|
7218
|
Tom 56
|
Baringo
|
LH
|
219381
|
214875
|
224
|
223
|
8109
|
Lower Midland (LM), Upper Midland (UM), Lower Highland (LH)
Table 2 Percentage nucleic acid similarities between full and individual genomic regions of Tomato leaf curl Arusha virus-like isolates from Kenya with DNA-A component of tomato begomoviruses
Begomovirus
species a
|
Complete
genome
|
|
Genomic regions b
|
|
IR
|
V1
|
V2
|
C1
|
C2
|
C3
|
C4
|
ToLCArV
|
95.9-98.9
|
|
91.8-97.1
|
95.5-99.4
|
96.2-98.9
|
96.3-99.4
|
95.7-98.3
|
97.1-98.7
|
98.4-99.7
|
|
ToLCCMV
|
79.7-80.1
|
|
66.5-70.3
|
79.2-81.7
|
79.0-80.4
|
82.2-83.7
|
74.8-76.7
|
76.5-77.1
|
87.1-88.8
|
|
ToLCAnV
|
77.0-77.8
|
|
69.3-74.9
|
78.0-80.5
|
79.6-80.1
|
75.4-76.4
|
73.9-74.8
|
72.4-73.5
|
75.8-76.8
|
|
ToLCBaV/A
|
72.9-74.0
|
|
68.4-75.4
|
69.2-72.3
|
71.5-72.2
|
75.1-77.0
|
70.4-71.6
|
70.0-70.9
|
75.6-77.0
|
|
ToLCBV
|
74.7-75.5
|
|
64.8-67.5
|
75.6-77.8
|
74.0-75.1
|
77.1-78.1
|
68.7-72.1
|
70.6-72.6
|
75.0-76.0
|
|
ToLCKMV
|
79.5-80.3
|
|
75.6-80.6
|
82.6-84.4
|
82.3-82.9
|
77.3-78.2
|
73.9-75.6
|
74.2-74.9
|
76.6-77.9
|
|
ToLCDiV
|
75.9-77.2
|
|
64.6-67.1
|
73.6-75.3
|
74.7-75.9
|
79.8-81.4
|
73.9-75.7
|
74.9-76.0
|
86.2-86.8
|
|
ToLCGV
|
77.9-78.2
|
|
71.0-73.9
|
80.0-82.3
|
78.0-78.9
|
78.3-79.6
|
74.8-76.5
|
74.2-75.6
|
80.4-81.1
|
|
ToLCGdV
|
75.6-76.6
|
|
62.3-67.2
|
72.8-73.9
|
75.4-76.1
|
79.9-80.9
|
71.9-73.4
|
74.7-75.2
|
84.9-85.9
|
|
ToLCHaiV
|
73.2-74.0
|
|
61.2-65.2
|
75.8-76.6
|
71.7-72.5
|
77.9-78.9
|
71.5-73.7
|
70.5-71.5
|
80.7-81.4
|
|
ToLCHaV
|
74.4-75.1
|
|
66.3-74.4
|
75.8-77.0
|
73.7-74.0
|
77.5-78.8
|
70.1-71.3
|
70.0-70.8
|
75.7-77.3
|
|
ToLCIRV
|
73.8-74.6
|
|
64.2-72.0
|
75.3-76.8
|
71.5-72.3
|
77.5-78.4
|
72.0-73.5
|
70.4-72.0
|
76.0-77.3
|
|
ToLCJaV/A
|
76.1-76.9
|
|
65.5-71.0
|
73.8-75.0
|
74.1-75.1
|
80.9-82.0
|
71.9-72.7
|
71.3-72.2
|
83.9-85.3
|
|
ToLCV-K3
|
74.6-75.6
|
|
67.7-71.6
|
75.3-76.5
|
73.7-74.5
|
77.0-80.0
|
71.1-73.0
|
71.5-73.5
|
80.0-81.3
|
|
ToLCLV
|
74.5-75.4
|
|
63.5-68.6
|
69.6-71.8
|
74.0-75.2
|
78.1-79.5
|
71.7-73.4
|
72.1-73.8
|
81.4-82.7
|
|
ToLCMGV/Men
|
78.6-79.3
|
|
70.2-75.5
|
82.2-83.6
|
79.8-80.3
|
78.2-79.5
|
75.1-77.2
|
74.0-75.1
|
80.6-82.0
|
|
ToLCMiV
|
75.1-75.7
|
|
61.4-67.7
|
73.0-74.6
|
72.4-74.8
|
79.1-79.1
|
72.5-73.9
|
72.3-73.1
|
80.4-81.7
|
|
ToLCMohV
|
78.0-78.9
|
|
70.0-76.7
|
82.9-84.4
|
82.1-82.7
|
74.5-75.5
|
74.4-76.3
|
74.9-75.3
|
68.3-69.2
|
|
ToLCNaV
|
79.8-80.3
|
|
75.4-80.0
|
84.3-87.3
|
81.9-89.9
|
77.2-78.7
|
74.6-76.5
|
75.3-76.2
|
79.5-81.1
|
|
ToLCNDC2
|
73.6-74.3
|
|
66.7-69.8
|
71.1-73.6
|
72.1-73.3
|
76.9-77.8
|
73.0-74.2
|
70.0-72.9
|
79.5-80.1
|
|
ToLCNDC5
|
71.3-72.2
|
|
66.7-72.1
|
69.8-70.4
|
71.1-71.8
|
72.8-73.9
|
68.2-70.0
|
66.8-68.5
|
75.3-76.3
|
|
ToLCJV
|
71.9-73.4
|
|
58.3-69.8
|
68.8-71.0
|
73.3-74.4
|
76.1-78.1
|
66.2-68.6
|
68.7-70.5
|
78.6-79.3
|
|
ToLCKV2
|
74.1-74.8
|
|
71.9-76.0
|
67.7-69.3
|
72.1-73.0
|
78.1-79.2
|
72.5-73.5
|
70.4-72.2
|
76.6-78.0
|
|
ToLCKV3
|
73.4-74.0
|
|
62.9-71.3
|
73.5-75.8
|
72.3-73.2
|
75.7-76.5
|
70.9-71.5
|
70.2-72.0
|
77.3-78.6
|
|
ToLCNGV
|
78.1-78.9
|
|
68.4-71.9
|
78.8-80.7
|
78.8-79.9
|
78.8-80.1
|
75.1-77.0
|
74.2-78.1
|
83.0-83.6
|
|
ToLCPalV
|
70.1-70.5
|
|
61.6-65.4
|
67.7-68.3
|
70.8-71.5
|
70.9-72.1
|
68.9-70.6
|
70.3-72.2
|
75.0-76.3
|
|
ToLCPatV
|
74.5-75.1
|
|
62.1-65.7
|
72.6-73.2
|
73.6-74.2
|
78.7-79.6
|
71.2-73.1
|
70.6-71.3
|
78.5-79.8
|
|
ToLCRaV
|
72.4-72.9
|
|
62.8-69.4
|
75.1-76.2
|
73.4-74.2
|
73.0-74.9
|
69.5-71.6
|
70.1-71.1
|
73.1-74.4
|
|
ToLCSCV
|
76.7-77.4
|
|
69.7-73.3
|
83.3-85.2
|
80.4-80.9
|
73.5-75.0
|
72.6-75.4
|
72.1-73.5
|
65.7-67.0
|
|
ToLCLKV
|
73.8-74.4
|
|
68.3-73.7
|
68.8-70.0
|
71.6-72.5
|
77.7-78.5
|
71.8-73.7
|
70.4-72.1
|
79.2-80.6
|
|
ToLCTV/A
|
74.1-74.7
|
|
62.7-69.0
|
70.8-71.7
|
72.9-73.9
|
78.3-79.9
|
71.0-71.7
|
71.1-72.9
|
76.7-78.0
|
|
ToLCTZV
|
89.8-90.5
|
|
70.8-73.3
|
85.0-88.3
|
94.0-95.4
|
88.7-89.8
|
95.2-96.7
|
96.9-98.0
|
89.4-90.0
|
|
ToLCToV
|
95.9-98.9
|
|
75.9-81.7
|
73.8-75.9
|
83.4-84.6
|
91.4-92.5
|
94.7-96.0
|
95.1-96.7
|
92.6-93.6
|
|
ToLCUV
|
78.9-79.3
|
|
75.0-76.7
|
83.5-86.2
|
82.5-83.3
|
74.4-75.0
|
76.5-78.1
|
74.4-75.6
|
65.3-66.3
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
a ToLCArV: Tomato leaf curl virus Arusha virus, ToLCCMV: Tomato leaf curl Cameroon virus, ToLCAnV: Tomato leaf curl Anjouan virus, ToLCBaV/A: Tomato leaf curl Bangalore virus, ToLCBV: Tomato leaf curl Bangladesh virus, ToLCKMV: Tomato leaf curl Comoros virus, ToLCDiV: Tomato leaf curl Diana virus, ToLCGV: Tomato leaf curl Ghana virus, ToLCGdV: Tomato leaf curl Guangdong virus, ToLCHaiV: Tomato leaf curl Hainan virus, ToLCHaV: Tomato leaf curl Hanoi virus, ToLCIRV: Tomato leaf curl Iran virus, ToLCJaV/A: Tomato leaf curl Java virus, ToLCV-K3: Tomato leaf curl Kerala virus, TLCV-LA: Tomato leaf curl Laos virus, ToLCMGV: Tomato leaf curl Madagascar virus, ToLCMiV: Tomato leaf curl Mindanao virus, ToLCMohV: Tomato leaf curl Moheli virus, ToLCNaV: Tomato leaf curl Namakely virus, ToLCNDC2: Tomato leaf curl New Delhi virus 2, ToLCNDC5: Tomato leaf curl New Delhi virus 5, ToLCJV: Tomato leaf curl Joydebpur virus, ToLCKV2: Tomato leaf curl Karnataka virus 2, ToLCKV3: Tomato leaf curl Karnataka virus 3, ToLCNGV: Tomato leaf curl Nigeria virus, ToLCPalV: Tomato leaf curl Palampur virus, ToLCPatV: Tomato leaf curl Patna virus, ToLCRaV: Tomato leaf curl Rajasthan virus, ToLCSCV: Tomato leaf curl Seychelles virus, ToLCLKV: Tomato leaf curl Sri Lanka virus, ToLCTV/A: Tomato leaf curl Taiwan virus, ToLCTZV: Tomato leaf curl Arusha virus, ToLCToV: Tomato leaf curl Toliara virus, ToLCUV: Tomato leaf curl Uganda virus.
b IR: Intergenic region, V1: Movement protein gene, V2: Coat protein gene, C1: Replication-associated protein gene, C2: Transcriptional activator protein gene, C3: Replication enhancer protein gene, C4: C4 protein gene
Table 3 Percentage amino acid sequence similarities between open reading frames of Tomato leaf curl Arusha virus-like isolates from Kenya with DNA-A component of tomato begomoviruses
Begomovirus
|
Genomic regions b
|
species a
|
V1
|
V2
|
C1
|
C2
|
C3
|
C4
|
ToLCArV
|
93.3-99.1
|
97.3-98.9
|
95.4-98.6
|
94.2-97.8
|
96.0-98.0
|
97.1-100.0
|
ToLCCMV
|
74.5-76.3
|
86.6-87.8
|
81.9-85.4
|
64.3-68.6
|
66.2-68.2
|
69.2-73.1
|
ToLCAnV
|
75.0-76.7
|
88.2-88.9
|
70.6-72.2
|
62.1-64.3
|
65.2-68.1
|
50.6-53.3
|
ToLCBaV/A
|
63.0-64.7
|
73.9-74.3
|
75.3-76.9
|
58.5-60.0
|
63.0-65.2
|
52.9-56.5
|
ToLCBV
|
67.7-68.6
|
78.1-79.3
|
75.7-77.6
|
57.0-59.3
|
65.2-68.8
|
50.0-52.9
|
ToLCKMV
|
80.6-82.3
|
93.1-93.9
|
76.5-77.9
|
63.6-65.0
|
66.0-69.6
|
54.8-56.7
|
ToLCDiV
|
66.3-67.2
|
81.7-82.9
|
80.1-81.7
|
64.7-66.9
|
71.9-74.8
|
72.5-73.5
|
ToLCGV
|
74.8-76.5
|
86.2-87.4
|
78.2-80.1
|
64.7-68.4
|
67.5-69.6
|
56.7-58.6
|
ToLCGdV
|
71.4-73.1
|
79.0-80.5
|
80.7-81.6
|
61.0-63.2
|
62.7-66.7
|
72.9-76.5
|
ToLCHaiV
|
71.2-74.3
|
75.5-75.9
|
79.3-80.7
|
59.2-60.0
|
57.3-59.4
|
60.8-61.7
|
ToLCHaV
|
72.2-73.9
|
79.0-80.1
|
76.4-77.8
|
56.3-58.5
|
63.0-64.5
|
46.1-50.9
|
ToLCIRV
|
67.7-68.6
|
73.5-73.9
|
73.3-74.4
|
59.2-61.5
|
65.2-66.7
|
48.1-51.0
|
ToLCJaV/A
|
67.7-69.5
|
78.2-79.4
|
81.8-82.9
|
56.6-58.8
|
65.9-66.7
|
70.6-73.5
|
ToLCV-K3
|
67.7-68.6
|
76.2-77.4
|
75.1-76.8
|
62.9-64.4
|
65.2-66.7
|
58.6-62.1
|
ToLCLV
|
55.0-56.7
|
81.2-82.4
|
77.4-78.6
|
56.6-59.5
|
62.0-65.2
|
59.6-62.5
|
ToLCMGV/Men
|
82.5-84.2
|
88.5-90.0
|
77.7-78.5
|
67.1-69.3
|
66.2-68.8
|
57.6-61.2
|
ToLCMiV
|
68.6-69.4
|
77.8-79.0
|
77.5-78.9
|
59.5-61.7
|
65.2-66.7
|
62.5-65.4
|
ToLCMohV
|
79.8-84.0
|
91.6-92.4
|
-
|
65.4-66.9
|
66.0-69.6
|
37.5-38.5
|
ToLCNaV
|
81.5-83.2
|
91.6-92.4
|
76.8-78.2
|
66.1-66.9
|
70.2-73.2
|
60.0-64.7
|
ToLCNDC2
|
61.0-63.5
|
76.6-77.8
|
78.0-79.7
|
61.1-63.3
|
56.8-58.9
|
56.7-58.6
|
ToLCNDC5
|
61.4-62.2
|
79.3-80.1
|
73.8-75.7
|
50.7-51.5
|
54.6-57.3
|
62.1-67.2
|
ToLCJV
|
70.8-73.5
|
78.3-78.7
|
75.5-77.6
|
52.0-54.4
|
55.7-57.2
|
55.1-56.5
|
ToLCKV2
|
56.7-57.6
|
77.8-78.5
|
77.6-78.7
|
62.2-63.7
|
64.5-66.7
|
49.0-51.9
|
ToLCKV3
|
63.5-64.4
|
79.7-80.4
|
74.3-77.3
|
52.9-53.7
|
62.0-63.7
|
50.0-52.9
|
ToLCNGV
|
73.9-75.6
|
87.4-88.5
|
78.6-80.7
|
67.6-69.1
|
67.5-68.9
|
62.7-63.7
|
ToLCPalV
|
56.8-58.5
|
76.2-77.4
|
72.0-73.4
|
52.9-54.5
|
60.0-62.3
|
62.1-67.2
|
ToLCPatV
|
70.3-74.5
|
79.4-80.1
|
76.6-77.7
|
59.5-61.7
|
56.7-60.9
|
56.3-59.7
|
ToLCRaV
|
62.5-66.1
|
78.9-79.3
|
72.7-74.4
|
51.5-52.2
|
60.0-62.3
|
62.1-67.2
|
ToLCSCV
|
81.7-84.2
|
90.8-91.2
|
71.3-73.0
|
65.6-68.5
|
63.1-66.7
|
35.0-39.0
|
ToLCLKV
|
63.6-65.4
|
73.5-73.9
|
76.1-77.5
|
59.7-61.8
|
61.4-63.6
|
51.7-55.3
|
ToLCTV/A
|
67.7-68.6
|
77.1-77.8
|
73.9-75.3
|
55.8-58.1
|
58.0-63.0
|
50.9-53.8
|
ToLCTZV
|
82.5-84.1
|
96.2-97.3
|
88.2-89.8
|
93.6-95.0
|
95.3-98.5
|
78.8-79.8
|
ToLCToV
|
68.3-70.9
|
82.8-84.0
|
88.6-90.3
|
93.6-95.0
|
91.3-94.2
|
85.3-88.2
|
ToLCUV
|
79.8-81.5
|
93.1-93.5
|
72.6-74.6
|
65.0-66.4
|
67.5-69.6
|
31.7-33.6
|
a ToLCArV: Tomato leaf curl virus Arusha virus, ToLCCMV: Tomato leaf curl Cameroon virus, ToLCAnV: Tomato leaf curl Anjouan virus, ToLCBaV/A: Tomato leaf curl Bangalore virus, ToLCBV: Tomato leaf curl Bangladesh virus, ToLCKMV: Tomato leaf curl Comoros virus, ToLCDiV: Tomato leaf curl Diana virus, ToLCGV: Tomato leaf curl Ghana virus, ToLCGdV: Tomato leaf curl Guangdong virus, ToLCHaiV: Tomato leaf curl Hainan virus, ToLCHaV: Tomato leaf curl Hanoi virus, ToLCIRV: Tomato leaf curl Iran virus, ToLCJaV/A: Tomato leaf curl Java virus, ToLCV-K3: Tomato leaf curl Kerala virus, TLCV-LA: Tomato leaf curl Laos virus, ToLCMGV: Tomato leaf curl Madagascar virus, ToLCMiV: Tomato leaf curl Mindanao virus, ToLCMohV: Tomato leaf curl Moheli virus, ToLCNaV: Tomato leaf curl Namakely virus, ToLCNDC2: Tomato leaf curl New Delhi virus 2, ToLCNDC5: Tomato leaf curl New Delhi virus 5, ToLCJV: Tomato leaf curl Joydebpur virus, ToLCKV2: Tomato leaf curl Karnataka virus 2, ToLCKV3: Tomato leaf curl Karnataka virus 3, ToLCNGV: Tomato leaf curl Nigeria virus, ToLCPalV: Tomato leaf curl Palampur virus, ToLCPatV: Tomato leaf curl Patna virus, ToLCRaV: Tomato leaf curl Rajasthan virus, ToLCSCV: Tomato leaf curl Seychelles virus, ToLCLKV: Tomato leaf curl Sri Lanka virus, ToLCTV/A: Tomato leaf curl Taiwan virus, ToLCTZV: Tomato leaf curl Arusha virus, ToLCToV: Tomato leaf curl Toliara virus, ToLCUV: Tomato leaf curl Uganda virus.
b V1: Movement protein gene, V2: Coat protein gene, C1: Replication-associated protein gene, C2: Transcriptional activator protein gene, C3: Replication enhancer protein gene, C4: C4 protein gene
Table 4 Percentage pairwise sequence identities among the twelve Tomato leaf curl virus Arusha virus-like isolates form Kenya
Segment b
|
Nucleotide (%)
|
Amino acid (%)
|
Genome
|
95.7-99.7
|
-
|
V1
|
95.0-100
|
94.1-100
|
V2
|
95.0-100
|
98.5-100
|
C1
|
95.7-99.6
|
94.1-99.4
|
C2
|
95.0-100
|
94.3-100
|
C3
|
96.8-100
|
95.6-100
|
C4
|
98.7-100
|
95.1-100
|
b V1: Movement protein gene, V2: Coat protein gene, C1: Replication-associated protein gene, C2: Transcriptional activator protein gene, C3: Replication enhancer protein gene, C4: C4 protein gene
Table 5 Recombination events identified in Tomato leaf curl virus Arusha virus-like isolates from Kenya using algorithms within the RDP 4 software
Event
|
Recombinants a
|
Potential parents b
|
Recombination
breakpoints
|
Average p values in detecting algorithms c
|
Minor
|
Major
|
R
|
G
|
B
|
M
|
C
|
S
|
T
|
1
|
ToLCArV
Tom5a-Kenya
(MN894493)
|
ToLCArV
Tom45-Kenya
(MN894498)
|
ToLCArV
Tom28-Kenya
(MN894452)
|
60-570
|
1.00E-02
|
-
|
-
|
1.01E-04
|
-
|
6.80E-07
|
9.32E-07
|
2
|
ToLCArV
Tom39-Kenya
(MN894499)
|
ToLCArV Tom35-Kenya (MN894451)
|
ToLCArV
AFTT23-Tanzania
(EF194760)
|
1386-1974
|
-
|
7.86E-04
|
-
|
8.81E-06
|
-
|
1.61E-04
|
5.20E-05
|
3
|
ToLCArV
TZTen05-Tanzania
(DQ519575)
|
ToLCArV Tom5a-Kenya (MN894493)
|
ToLCUV
Iganga-Uganda
(DQ127170)
|
158-524
|
2.42E-06
|
2.04E-04
|
-
|
7.13E-09
|
4.67E-10
|
-
|
1.68E-12
|
4
|
ToLCDiV
Namakely-Madagascar
(AM701765)
|
ToLCArV Tom39-Kenya (MN894499)
|
ToLCMohV
Moheli-Comoros
(AM701763)
|
1091-1583
|
1.48E-12
|
4.75E-12
|
1.32E-10
|
1.04E-10
|
1.17E-05
|
-
|
4.29E-04
|
a ToLCArV: Tomato leaf curl virus Arusha virus, ToLCDiV: Tomato leaf curl Diana virus.
b ToLCUV: ToLCUV: Tomato leaf curl Uganda virus, ToLCMohV: ToLCMohV: Tomato leaf curl Moheli virus.
c R: RDP, G: GENCOV, B: BoostScan, M: MaxChi, C: Chimera, S: SiScan, T: 3Seq
Table 6 Genetic variability determinants and neutrality tests on Tomato leaf curl virus Arusha virus-like populations from Kenya with other worldwide tomato begomoviruses
Population
|
Gene a
|
N b
|
h c
|
S d
|
Hd e
|
Eta f
|
π g
|
k h
|
θ-W i
|
θ-Eta j
|
Tajima's D
|
Fu and Li's D
|
Fu and Li's F
|
Tomato begomoviruses
|
Genome
|
2920
|
46
|
1666
|
1.000
|
2985
|
0.22424
|
569.5749
|
0.14924
|
0.2674
|
-0.5971
|
-0.2912
|
-0.4859
|
(n=46)
|
V1
|
372
|
43
|
241
|
0.996
|
419
|
0.22538
|
76.1768
|
0.16224
|
0.28206
|
-0.7389
|
-0.8229
|
-0.9463
|
|
V2
|
1261
|
46
|
752
|
1.000
|
1334
|
0.22421
|
271.971
|
0.14106
|
0.25023
|
-0.3842
|
-0.0052
|
-0.1764
|
|
C1
|
1179
|
46
|
692
|
1.000
|
1213
|
0.21165
|
225.4106
|
0.14784
|
0.25915
|
-0.6771
|
-0.3609
|
-0.5737
|
|
C2
|
431
|
45
|
264
|
0.999
|
458
|
0.23777
|
97.486
|
0.14651
|
0.25417
|
-0.2374
|
-0.0923
|
-0.1752
|
|
C3
|
469
|
45
|
303
|
0.999
|
550
|
0.24589
|
108.1903
|
0.15669
|
0.28442
|
-0.4989
|
-0.3631
|
-0.4949
|
|
C4
|
316
|
44
|
210
|
0.997
|
360
|
0.21015
|
65.1459
|
0.15414
|
0.26423
|
-0.7516
|
-0.4512
|
-0.6736
|
Kenyan ToLCArV-like
|
Genome
|
2766
|
12
|
211
|
1.000
|
224
|
0.0264
|
72.955
|
0.0253
|
0.0268
|
-0.0774
|
-0.4189
|
-0.3751
|
isolates (n=12)
|
V1
|
360
|
9
|
22
|
0.939
|
24
|
0.02298
|
8.2727
|
0.02024
|
0.02208
|
0.1819
|
0.1216
|
0.1564
|
|
V2
|
1239
|
12
|
71
|
1.000
|
72
|
0.0209
|
25.8788
|
0.01899
|
0.01926
|
0.3958
|
-0.0631
|
0.0659
|
|
C1
|
1116
|
12
|
94
|
1.000
|
102
|
0.02744
|
30.6212
|
0.02789
|
0.03027
|
-0.4355
|
-0.7775
|
-0.7841
|
|
C2
|
422
|
11
|
39
|
0.985
|
40
|
0.02761
|
11.6515
|
0.0306
|
0.03139
|
-0.5481
|
-1.072
|
-1.065
|
|
C3
|
450
|
11
|
23
|
0.985
|
23
|
0.01872
|
8.4242
|
0.01692
|
0.01692
|
0.4703
|
-0.3193
|
-0.1286
|
|
C4
|
312
|
10
|
11
|
0.955
|
11
|
0.00869
|
2.7121
|
0.01167
|
0.01167
|
-1.0628
|
-1.4718
|
-1.552
|
a V1: Movement protein gene, V2: Coat protein gene, C1: Replication-associated protein gene, C2: Transcriptional activator protein gene, C3: Replication enhancer protein gene, C4: C4 protein gene
b N: Number of nucleotide sites
c h: Haplotype number
d S: Total number of variable or segregation sites
e Hd: Haplotype diversity
f Eta: Total number of mutations
g π: Nucleotide diversity
h k: Average number of nucleotide differences between sequences
i θ-W: Waterson’s estimate of population mutation rate based on the total number of segregating sites
j θ-Eta: Waterson’s estimate of population mutation rate based on the total number of mutations
Table 7 Estimates of selection pressure on the coding regions of twelve Tomato leaf curl virus Arusha virus -like isolates from Kenya
Coding
region a
|
Total number
of sites
|
|
|
|
|
Number of sites b
|
log L
|
dN
|
dS
|
dN/dS
|
Positive or diversifying selection
|
Negative or purifying selection
|
V1
|
114
|
-651.20
|
0.0363
|
0.1757
|
0.2067
|
0
|
1
|
V2
|
258
|
-1483.95
|
0.0150
|
0.2212
|
0.0677
|
0
|
3
|
C1
|
364
|
-2392.81
|
0.0847
|
0.2124
|
0.3986
|
0
|
11
|
C2
|
135
|
-856.05
|
0.0607
|
0.2085
|
0.2908
|
0
|
1
|
C3
|
134
|
-708.30
|
0.0307
|
0.1184
|
0.2590
|
0
|
2
|
C4
|
85
|
-509.31
|
0.0392
|
0.0341
|
1.1491
|
0
|
0
|
a V1: Movement protein gene, V2: Coat protein gene, C1: Replication-associated protein gene, C2: Transcriptional activator protein gene, C3: Replication enhancer protein gene, C4: C4 protein gene.
b Selected at p≤0.1