Table 2.
Potato spindle tuber viroid (PSTVd) sequence variant population structure, occurrence frequency and nucleotide variation in PSTVd isolate FN-infected tomato plants.
| Sequence variant | Size (nt) | Occurrence frequency (%) | Nucleotide difference from the reference sequence a | |
|---|---|---|---|---|
| Plant 1 | Plant 2 | |||
| EF044303 | 358 | n/a | n/a | n/a |
| I | 358 | 15.2 | 44.8 | No variation |
| II | 358 | 15.2 | 6.9 | 120 (C to U) |
| III | 357 | 3.0 | 0 | 120 (C to U), 236 (C to deletion) |
| IV | 358 | 3.0 | 0 | 18 (U to C), 120 (C to U) |
| V | 358 | 3.0 | 0 | 40 (U to A), 120 (C to U) |
| VI | 358 | 27.3 | 0 | 120 (C to U), 253 (G to A) |
| VII | 357 | 30.3 | 0 | 120 (C to U), 127 (G to A), between 145 and 146 (insertion of C), 200 (G to U), 211 (C to deletion), 212 (G to A), 232 (C to deletion), 255 (C to U), 306 (C to U), 307 (U to C), 310 (C to U) |
| VIII | 356 | 3.0 | 0 | 200 (G to U), 211 (C to deletion), 212 (G to A), 232 (C to deletion), 255 (C to U), 306 (C to U), 307 (U to C), 310 ( C to U) |
| IX | 357 | 0 | 3.4 | 277 (G to deletion) |
| X | 359 | 0 | 3.4 | Between 145 and 146 (insertion of C) |
| XI | 358 | 0 | 3.4 | 173 (G to A), 306 (C to U), 307 (U to C), 310 (C to U) |
| XII | 358 | 0 | 3.4 | 306 (C to U), 307 (U to C), 310 (C to U) |
| XIII | 357 | 0 | 6.9 | 120 (C to U), 127 (G to A), between 145 and 146 (insertion of C), 200 (G to U), 211 (C to deletion), 212 (G to A), 232 (C to deletion), 343 (A to G) |
| XIV | 357 | 0 | 6.9 | 120 (C to U), 127 (G to A), between 145 and 146 (insertion of C), 200 (G to U), 211 (C to deletion), 212 (G to A), 232 (C to deletion) |
| XV | 357 | 0 | 20.7 | 120 (C to U), 127 (G to A), between 145 and 146 (insertion of C), 200 (G to U), 211 (C to deletion), 212 (G to A), 232 (C to deletion), 306 (C to U), 307 (U to C), 310 ( C to U) |
| Haplotype diversity b | 0.799 ± 0.034 | 0.697 ± 0.078 | ||
| Nucleotide diversity c | 0.01130 ± 0.00103 | 0.00944 ± 0.00115 | ||
a EF044303 was used as a reference sequence. Nucleotide differences in each variant were indicated in relation to the reference sequence at positions in the reference; b/c Haplotype and nucleotide diversities were calculated using the software DnaSP v5; n/a: not applicable.