Introduction
Results
Detection of TBTV, TVDV and TBTD-associated RNA in different sources of tobacco with tobacco bushy top disease
5’-RACE and 3’-RACE of TBTV from JiangChuan and MiDu
Comparison of the sequences of the three new TBTV isolates and five previously published sequences
TBTV-JC | TBTV-MD-I | TBTV-MD-II | TBTV-Ch | TBTV-YWSh | TBTV-YYXi | TBTV-YLLi | TBTV-YWDu | |
---|---|---|---|---|---|---|---|---|
(KM016224) | (KM016225) | (KM067277) | (NC004366) | (FN256356) | (FN597051) | (FM242699) | (FM242700) | |
TBTV-JC | 97.3 | 94.8 | 96.6 | 97.3 | 95.4 | 97.2 | 89.2 | |
TBTV-MD-I | 97.3 | 94.9 | 96.8 | 97.8 | 95.8 | 99.0 | 89. | |
TBTV-MD-II | 94.7 | 94.9 | 95.5 | 96.2 | 94.6 | 95.4 | 89.0 | |
TBTV-Ch | 96.7 | 96.9 | 94.7 | 98.9 | 96.5 | 97.3 | 90.9 | |
TBTV-YWSh | 97.7 | 98.5 | 96.0 | 98.5 | 97.1 | 98.2 | 90.6 | |
TBTV-YYXi | 96.7 | 97.5 | 95.0 | 98.8 | 98.6 | 96.4 | 89.7 | |
TBTV-YLLi | 97.5 | 98.9 | 95.4 | 97.7 | 99.2 | 98.3 | 90.0 | |
TBTV-YWDu | 96.6 | 96.7 | 94.6 | 99.8 | 98.3 | 98.6 | 97.5 |
TBTV-JC | TBTV-MD-I | TBTV-MD-II | TBTV-Ch | TBTV-YWSh | TBTV-YYXi | TBTV-YLLi | TBTV-YWDu | |
---|---|---|---|---|---|---|---|---|
TBTV-JC | 96.0 | 90.9 | 94.9 | 95.9 | 92.4 | 96.4 | 75.0 | |
(96.5) | (94.3) | (94.6) | (95.9) | (93.0) | (97.1) | (73.7) | ||
TBTV-MD-I | 97.3 | 90.5 | 94.3 | 95.9 | 92.5 | 99.2 | 75.7 | |
(98.9) | (92.7) | (92.7) | (94.0) | (92.4) | (98.7) | (73.7) | ||
TBTV-MD-II | 95.6 | 95.6 | 92.3 | 92.8 | 90.6 | 90.5 | 76.1 | |
(98.2) | (97.6) | (94.9) | (95.9) | (91.4) | (93.3) | (74.9) | ||
TBTV-Ch | 97.3 | 97.7 | 96.6 | 98.4 | 93.3 | 94.8 | 76.0 | |
(99.5) | (98.7) | (98.7) | (98.1) | (92.4) | (93.3) | (74.3) | ||
TBTV-YWSh | 97.5 | 98.0 | 96.9 | 99.5 | 94.4 | 96.4 | 76.7 | |
(99.3) | (98.9) | (98.7) | (99.8) | (94.0) | (94.6) | (74.3) | ||
TBTV-YYXi | 96.4 | 96.6 | 95.9 | 97.9 | 98.2 | 93.0 | 76.4 | |
(99.1) | (98.4) | (98.4) | (99.6) | (99.5) | (93.0) | (74.3) | ||
TBTV-YLLi | 96.9 | 98.4 | 96.8 | 98.0 | 98.3 | 97.4 | 75.9 | |
(98.9) | (99.3) | (98.0) | (99.1) | (99.3) | (98.7) | (74.0) | ||
TBTV-YWDu | 90.5 | 90.4 | 89.7 | 91.1 | 91.2 | 90.7 | 90.8 | |
(96.4) | (95.8) | (95.8) | (96.5) | (96.5) | (96.4) | (95.8) | ||
TBTV-JC | 98.6 | 97.3 | 97.2 | 98.3 | 95.8 | 98.5 | 96.9 | |
(96.2) | (93.7) | (92.4) | (95.8) | (89.9) | (96.2) | (92.0) | ||
TBTV-MD-I | 98.6 | 98.5 | 98.5 | 99.4 | 97.1 | 99.9 | 98.2 | |
(99.6) | (96.6) | (95.8) | (98.7) | (93.3) | (100) | (95.4) | ||
TBTV-MD-II | 97.4 | 98.5 | 97.8 | 98.7 | 96.9 | 98.6 | 97.5 | |
(98.8) | (99.2) | (94.1) | 97.1) | (93.3) | (96.6) | (93.7) | ||
TBTV-Ch | 97.3 | 98.5 | 97.8 | 98.9 | 96.4 | 98.6 | 99.7 | |
(98.8) | (99.2) | (99.1) | (96.6) | (91.1) | (95.8) | (99.6) | ||
TBTV-YWSh | 98.4 | 99.5 | 98.8 | 98.9 | 96.9 | 99.6 | 98.6 | |
(99.2) | (99.6) | (99.6) | (99.6) | (93.3) | (98.7) | (96.2) | ||
TBTV-YYXi | 95.5 | 96.6 | 96.5 | 95.9 | 96.5 | 96.9 | 96.1 | |
(96.7) | (97.1) | (96.3) | (96.3) | (96.7) | (93.3) | (90.7) | ||
TBTV-YLLi | 98.5 | 99.9 | 98.6 | 98.6 | 99.6 | 96.5 | 98.3 | |
(99.2) | (99.6) | (99.6) | (99.6) | (100) | (96.7) | (95.4) | ||
TBTV-YWDu | 97.0 | 98.2 | 97.6 | 99.7 | 98.6 | 95.7 | 98.7 | |
(98.0) | (98.4) | (98.4) | (99.2) | (98.8) | (95.5) | (98.8) |
Phylogenetic relationship among all TBTV isolates
Recombination analysis of the TBTV isolates
Event number | Recombinant Sequence(s) | Breakpoint position | Parental sequence (s) | Recombinant score | P-Value for the six detection methods in RDP4 | |||||
---|---|---|---|---|---|---|---|---|---|---|
Begin/End | Minor/Major | RDP | GENECONV | BootScan | MaxChi | Chimaera | SiScan | |||
1 | TBTV-JC | 616/965 | YYXi/MD-II | 0.472 | NS | NS | NS | 8.76E-03 | 1.68E-02 | 4.07E-03 |
2 | TBTV-MD-I | 241/1464 | JC/YYXi | 0.469 | 2.71E-02 | 1.06E-02 | 1.11E-02 | 1.93E-05 | 4.78E-04 | 1.19E-09 |
3 | TBTV-MD-I | 616/965 | YYXi/MD-II | 0.472 | NS | NS | NS | 8.76E-03 | 1.68E-02 | 4.07E-03 |
4 | TBTV-MD-I | 629/3207 | JC/YYXi | 0.608 | 3.07E-02 | NS | 2.97E-02 | 1.65E-03 | 6.97E-03 | 5.17E-08 |
5 | TBTV-MD-II | 279/519 | JC/Unknown (YYXi) | 0.482 | 1.81E-03 | NS | 1.95E-02 | 3.48E-05 | 7.87E-06 | 3.56E-05 |
6 | TBTV-MD-II | 2716/3511 | YWDu/Unknown (YYXi) | 0.426 | 7.26E-04 | NS | 1.11E-02 | 1.22E-06 | 3.49E-06 | NS |
7 | TBTV-Ch | 210/618 | MD-I/YYXi | 0.426 | NS | 3.18E-02 | 2.76E-02 | 7.31E-03 | 3.32E-02 | 4.49E-06 |
8 | TBTV-Ch | 211/652 | JC/YYXi | 0.482 | 1.81E-03 | NS | 1.95E-02 | 3.48E-05 | 7.87E-06 | 3.56E-05 |
9 | TBTV-Ch | 253/385 | MD-II/YLLi | 0.419 | NS | NS | NS | 3.24E-02 | NS | NS |
10 | TBTV-Ch | 652/3207 | YYXi/JC | 0.608 | 3.07E-02 | NS | 2.97E-02 | 1.65E-03 | 6.97E-03 | 5.17E-08 |
11 | TBTV-Ch | 3574/142 | YYXi/MD-I | 0.461 | 1.23E-02 | NS | 1.37E-02 | 1.37E-02 | 1.62E-04 | NS |
12 | TBTV-YWSh | 211/793 | JC/YYXi | 0.483 | 1.04E-02 | NS | 1.00E-02 | 4.09E-02 | 1.23E-02 | 1.09E-06 |
13 | TBTV-YWSh | 253/385 | MD-II/YLLi | 0.419 | NS | NS | NS | 3.24E-02 | NS | NS |
14 | TBTV-YWSh | 384/666 | MD-I/YYXi | 0.426 | NS | 3.18E-02 | 2.76E-02 | 7.31E-03 | 3.32E-02 | 4.49E-06 |
15 | TBTV-YWSh | 652/3207 | YYXi/JC | 0.608 | 3.07E-02 | NS | 2.97E-02 | 1.65E-03 | 6.97E-03 | 5.17E-08 |
16 | TBTV-YYXi | 183/2070 | MD-II/JC | 0.593 | 2.95E-03 | 3.16E-02 | 8.25E-05 | NS | NS | 6.63E-05 |
17 | TBTV-YYXi | 1355/1687 | YWSh/Unknown (MD-II) | 0.420 | NS | 1.41E-02 | NS | 4.78E-02 | NS | 6.90E-06 |
18 | TBTV-YYXi | 2571/3508 | Unknown (MD-II)/Ch | 0.443 | NS | NS | NS | 1.53E-04 | NS | NS |
19 | TBTV-YYXi | 3155/3603 | Unknown (MD-II)/ YLLi | 0.615 | 1.03E-02 | 4.02E-04 | 2.49E-04 | 9.70E-04 | 7.29E-04 | 4.44E-05 |
20 | TBTV-YYXi | 3207/3514 | Unknown(JC)/YWDu | 0.841 | 3.26E-04 | 2.37E-02 | NS | 6.50E-04 | 1.63E-02 | NS |
21 | TBTV-YYXi | 3538/209 | Ch/Unknown(MD-I) | 0.534 | NS | NS | NS | 7.38E-06 | 4.47E-04 | NS |
22 | TBTV-YLLi | 211/1515 | JC/YYXi | 0.608 | 3.07E-02 | NS | 2.97E-02 | 1.65E-03 | 6.97E-03 | 5.17E-08 |
23 | TBTV-YLLi | 616/965 | YYXi/MD-II | 0.472 | NS | NS | NS | 8.76E-03 | 1.68E-02 | 4.07E-03 |
24 | TBTV-YLLi | 1533/1986 | MD-II/MD-I | 0.741 | 1.21E-08 | 3.18E-04 | 9.88E-09 | 8.14E-04 | 5.48E-04 | NS |
25 | TBTV-YLLi | 1533/2480 | YYXi/MD-I | 0.731 | 1.31E-03 | NS | 2.93E-02 | 3.86E-08 | 3.61E-05 | NS |
26 | TBTV-YLLi | 1554/1971 | Ch/MD-I | 0.611 | NS | NS | 3.56E-04 | 1.26E-03 | NS | NS |
27 | TBTV-YWDu | 2027/11 | Ch/Unknown(MD-II) | 0.632 | 3.34E-42 | 6.13E-42 | 1.08E-39 | 5.51E-19 | 7.16E-19 | 2.38E-23 |
28 | TBTV-YWDu | 2042/3170 | Ch/Unknown(MD-II) | 0.601 | 5.12E-23 | 1.81E-23 | 7.17E-25 | 3.99E-09 | 3.28E-11 | 1.92E-09 |
29 | TBTV-YWDu | 3171/4140 | Ch/Unknown(MD-II) | 0.545 | 3.34E-42 | 6.13E-42 | 1.08E-39 | 5.42E-06 | 5.80E-06 | 1.13E-14 |