Table 1.
Recombination events among 50 sugarcane yellow leaf virus (SCYLV) isolates using RDP4 software.
| Putative recombinanta | Major × minor putative parents a | Recombination breakpointb | Detection methodc | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Begin | End | R | G | B | M | C | S | T | ||
| PI 157033 (G1) | IND2 (G3) × BAR-YL1 (G1) | 5001 | 5238 | ++ | ++ | ++ | ++ | ++ | − | ++ |
| Sorg1_1 (G3) | FL86 (G1) × FL84 (G3) | 624 | 728 | ++ | ++ | ++ | ++ | ++ | − | ++ |
| MU-AB193 (G2) | CHN-GD-ZJ4 (G1) × MU-AB197 (G2) | 2579 | 4506 | ++ | ++ | ++ | ++ | ++ | ++ | ++ |
| Sorg3_3 (G3) | SCYLV (G1) × ZJWL003 (G3) | 4503 | 5001 | ++ | ++ | ++ | ++ | ++ | ++ | ++ |
| MU-SC1233 (G2) | CHN-YN-KY2 (G1) × MU-AB193 (G2) | 4507* | 5214 | ++ | ++ | ++ | ++ | ++ | ++ | ++ |
| MU-AB193 (G2) | PI 157033 (G1) × REU-YL2 (G2) | 1093 | 1463 | ++ | ++ | ++ | ++ | ++ | ++ | ++ |
| MU-SC1233 (G2) | CHN-GD-ZJ15 (G1) × MU-AB197 (G2) | 2556 | 4506* | ++ | + | − | + | + | ++ | ++ |
| GZ-GZ18 (G1) | CHN-GD-WY19 (G1) × FL86 (G1) | 4437 | 5468 | ++ | ++ | ++ | ++ | ++ | ++ | + |
| Sorg2_2 (G3) | FL86 (G1) × IND2 (G3) | 4976 | 5178 | ++ | + | ++ | + | ++ | ++ | ++ |
| Sorg3_3 (G3) | SCYLV (G1) × FL180 (G3) | 387 | 521 | ++ | ++ | − | ++ | ++ | − | + |
| Sorg1_1 (G3) | PI 157033 (G1) × Sorg3_3 (G3) | 4257 | 4343* | ++ | + | + | − | + | − | + |
| IND2 (G3) | FL180 (G3) × CBLK97154 (G3) | 5026 | 5237 | ++ | ++ | ++ | + | + | + | + |
aPhylogroups are shown in brackets.
bActual breakpoint position undetermined (it was most likely overprinted by a subsequent one) shown as an asterisk (*).
cSeven algorithms implemented in RDP4 software were used, including RDP (R), GENECONV (G), BootScan (B), Maximum Chisquare (M), Chimaera (C), Sister Scan (S), and 3Seq (T). Symbols are showed for recombination signals at different statistical significance levels: ++, P ≤ 10–6; +, 10–6 < P ≤ 0.05; −, P > 0.05 (not significant).