Table 5.
Number and relative frequency (%) of the different types of mutations found in begomovirus mutant spectra.
| Type of mutationa | Repb | C4 | IR | V2 | CP | TOTAL | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| n | % | n | % | n | % | n | % | n | % | n | % | |
| TRANSITIONS | ||||||||||||
| A → G | 2 | 7.7 | 2 | 18.2 | 2 | 5.7 | 0 | 0 | 2 | 2.6 | 5 | 3.6 |
| G → A | 5 | 19.2 | 0 | 0.0 | 4 | 11.4 | 4 | 19.0 | 13 | 16.7 | 18 | 12.9 |
| C → T | 10 | 38.5 | 6 | 54.5 | 9 | 25.7 | 10 | 47.6 | 23 | 29.5 | 30 | 21.6 |
| T → C | 1 | 3.8 | 1 | 9.1 | 3 | 8.6 | 1 | 4.8 | 6 | 7.7 | 8 | 5.8 |
| Total | 18 | 69.2 | 9 | 81.8 | 18 | 51.4 | 15 | 71.4 | 44 | 56.4 | 61 | 43.9 |
| TRANSVERSIONS | ||||||||||||
| A → C | 0 | 0.0 | 0 | 0.0 | 4 | 11.4 | 2 | 9.5 | 5 | 6.4 | 8 | 5.8 |
| C → A | 0 | 0.0 | 0 | 0.0 | 1 | 2.9 | 3 | 14.3 | 9 | 11.5 | 8 | 5.8 |
| A → T | 0 | 0.0 | 2 | 18.2 | 7 | 20.0 | 0 | 0.0 | 6 | 7.7 | 11 | 7.9 |
| T → A | 3 | 11.5 | 1 | 9.1 | 1 | 2.9 | 2 | 9.5 | 5 | 6.4 | 7 | 5.0 |
| C → G | 4 | 15.4 | 1 | 9.1 | 1 | 2.9 | 1 | 4.8 | 3 | 3.8 | 4 | 2.9 |
| G → C | 1 | 3.8 | 2 | 18.2 | 1 | 2.9 | 1 | 4.8 | 1 | 1.3 | 3 | 2.2 |
| G → T | 7 | 26.9 | 2 | 18.2 | 4 | 11.4 | 3 | 14.3 | 18 | 23.1 | 19 | 13.7 |
| T → G | 2 | 7.7 | 0 | 0.0 | 2 | 5.7 | 0 | 0.0 | 3 | 3.8 | 7 | 5.0 |
| Total | 17 | 65.4 | 8 | 72.7 | 21 | 60.0 | 12 | 57.1 | 39 | 50.0 | 67 | 48.2 |
| Ts/Tvc | 1.1 | 1.1 | 0.9 | 1.3 | 1.1 | 0.9 | ||||||
| Substitutions | 35 | 92.1 | 17 | 100.0 | 39 | 86.7 | 27 | 93.1 | 83 | 94.3 | 128 | 88.9 |
| Insertions | 1 | 2.6 | 0 | 0.0 | 5 | 11.1 | 1 | 3.4 | 2 | 2.3 | 9 | 6.3 |
| Deletions | 2 | 5.3 | 0 | 0.0 | 1 | 2.2 | 1 | 3.4 | 3 | 3.4 | 7 | 4.9 |
| Total | 38 | 17 | 45 | 29 | 88 | 144 | ||||||
| Nonsynonymous | 17 | 65.4 | 10 | 76.9 | 0 | 0.0 | 19 | 79.2 | 60 | 75.0 | 106 | 74.1 |
| Missense | 14 | 53.8 | 8 | 61.5 | Nad | Na | 16 | 66.7 | 54 | 67.5 | 92 | 64.3 |
| Nonsense | 0 | 0.0 | 1 | 7.7 | Na | Na | 2 | 8.3 | 2 | 2.5 | 5 | 3.5 |
| Frameshift | 3 | 11.5 | 1 | 7.7 | Na | Na | 0 | 0.0 | 4 | 5.0 | 8 | 5.6 |
| Readthrough | 0 | 0.0 | 0 | 0.0 | Na | Na | 1 | 4.2 | 0 | 0.0 | 1 | 0.7 |
| Synonymous | 9 | 34.6 | 3 | 23.1 | Na | Na | 5 | 20.8 | 20 | 25.0 | 37 | 25.9 |
a
Mutations found in tomato yellow leaf curl Sardinia virus, tomato yellow leaf curl virus and tomato yellow leaf curl Malaga virus mutant spectra after 15, 30, and 45 days post inoculation of infectious clones. Mutations were scored with respect to the consensus sequence.
b
Genomic regions were defined by the following nucleotide positions: Rep from 2,262 to 2,619, C4 from 2,262 to 2,462, IR from 2,619 to 149, V2 from 309 to 496 and CP from 309 to 1,082. Positions refer to the TYLCSV sequence [ES:Mur1:92] (Z25751) (Noris et al., 1994).
c
Ts:Tv, transition:transversion ratio.
d
Na, not applicable.