Table 4.
Putative recombination events detected using the RDP4.1 program among genes of begomoviruses associated with PaLCD, based on provided datasets from India; six genes/ORF’s of 44 DNA-A sequences.
| Event no. | Breakpoints | Recombinant | Parents | Methods | p valve | ||
|---|---|---|---|---|---|---|---|
| Begin | End | Major | Minor | ||||
| AV2 (Pre-CP) | |||||||
| 1 | 363 | 85 | MN529626_PaLCV | Y15934_PaLCV-I | Unknown (KX302713_PaLCV) | R,G,B,M,C,S,3S | 9.95E-13 |
| AV1(CP) | |||||||
| 1 | 442 | 767 | MH988458_PaLCV | KX302707_CLCuBV | MH765693_ChiLC | R,G,M,C,S,3S | 7.37E-13 |
| 2 | 1 | 138 | KX302713_PaLCV | KX302707_CLCuBV | Unknown (KF307208_PaLCV) | R,G,B,M,C,3S | 5.62E-12 |
| 3 | 136 | 294 | MN529626_PaLCV | KY800906_PaLCV | Unknown (JN558352_CLCuM) | R,B,M,C,3S | 1.04E-06 |
| 4 | 178 | 310 | HM140366_ChiLC | GU136803_ChiLC | MH674437_PaLCr | R,G,M,3S | 6.67E-06 |
| 5 | 244 | 320 | MH988458_PaLCV | MH988457_PaLCV | MH765696_CrYVM | R,G,M,3S | 7.82E-05 |
| 6 | 446 | 165 | MH765693_ChiLC | HM140368_PaLCr | MH765695_PeLCV | R,M,C,3S | 1.91E-09 |
| AC3 (Ren) | |||||||
| 1 | 87 | 177 | HM140367_PaLCr | MH807203_PaLCr | KF307208_PaLCV | R,G,M,C,S,3S | 1.88E-11 |
| 2 | 55 | 151 | KX302707_CLCuB | KF307208_PaLCV | JN558352_CLCuM | R,G,M,C,3S | 8.48E-09 |
| 3 | 403 | 92 | DQ989325_ToLCNDV | MH765697_ChiLC | MH105055_ToLCV | R,G,M,C,3S | 2.11E-04 |
| AC2(TrAP) | |||||||
| 1 | 235 | 309 | HM140367_PaLCr | HM140369_PaLCr | KF307208_PaLCV | R,G,M,C,S,3S | 2.18E-15 |
| 2 | 408 | 217 | MH765698_ChiLC | DQ989325_ToLCN | Unknown(MH105055_ToLCV) | R,G,M,C,S,3S | 1.51E-14 |
| 3 | 215 | 405 | DQ989325_ToLCNDV | MH105055_ToLCV | KY800906_PaLCV | R,G,M,C,S,3S | 5.83E-15 |
| 4 | 205 | 405 | MG757245_ToLCG | HM140369_PaLCr | KY800906_PaLCV | R,M,C,S,3S | 1.95E-10 |
| 5 | 52 | 97 | MH807200_PaLCr | MG757245_ToLCG | MH765698_ChiLC | R,M,3S | 1.52E-03 |
| AC1(Rep) | |||||||
| 1 | 1,072 | 278 | MH988458_PaLCV2 | MH807200_PaLCr | Unknown (KP725057_AgEV-) | R,G,M,C,S,3S | 7.45E-25 |
| 2 | 1,059 | 283 | MH765693_ChiLC2 | MH807200_PaLCr | Unknown (KP725057_AgEV) | R,G,M,C,S,3S | 1.57E-21 |
| 3 | 1,065 | 276 | MH807202_DLCV 1 | MH807200_PaLCr | Unknown (KP725057_AgEV) | R,G,M,C,S,3S | 3.16E-13 |
| 4 | 284 | 493 | MH765693_ChiLC | MG757245_ToLCG | MN529626_PaLCV | R,G,M,C,S,3S | 2.15E-12 |
| 5 | 274 | 579 | MH807204_PaYLC 1 | Unknown (MH807202_DLCV) | HM140368_PaLCr | R,G,M,S,3S | 1.84E-10 |
| 6 | 279 | 455 | KP725055_ToLCV1 | KX353622_PaYLC | Unknown (JN558352_CLCuM) | R,G,M,C,3S | 9.28E-15 |
| 7 | 680 | 783 | KX302713_PaLCV1 | MN529626_PaLCV | MH807200_PaLCr | R,G,M,C,S,3S | 1.18E-16 |
| 8 | 34 | 203 | JN558352_CLCuM2 | KX302707_CLCuB | HM140368_PaLCr | R,M,C,3S | 3.58E-10 |
| 9 | 271 | 494 | JN558352_CLCuM | Unknown (MH807202_DLCV) | MH807203_PaLCr | R,M,3S | 3.34E-08 |
| 10 | 1,072 | 271 | KP725057_AgEV2 | Unknown(MH765695_PeLCV) | MH807200_PaLCr | R,G,M,C,S,3S | 1.35E-06 |
| 11 | 281 | 520 | KX353622_PaYLC1 | MN529626_PaLCV | Unknown (MH765698_ChiLC) | R,G,M,3S | 1.69E-10 |
| 12 | 15 | 278 | HM140371_ChiLC1 | KX353622_PaYLC | Unknown(DQ989325_ToLCNDV) | R,M,C,3S | 1.20E-10 |
| 13 | 1,065 | 286 | MH807201_PaLCr1 | HM140367_PaLCr | Unknown (MH807200_PaLCr) | R,G,M,C,3S | 2.81E-05 |
| 14 | 730 | 1,082 | MG757245_ToLCG 1 | KP725055_ToLCV | MH765695_PeLCV | R,G,M,C,3S | 2.22E-07 |
| 15 | 397 | 473 | DQ989325_ToLCNDV 1 | Unknown (MH807202_DLCV) | HM140367_PaLCr | R,M,C | 1.67E-03 |
| 16 | 279 | 625 | MH807203_PaLCr 1 | MH807202_DLCV | MH765695_PeLCV | R,M,C,3S | 1.35E-04 |
| 17 | 751 | 971 | MH988458_PaLCV | MH988457_PaLCV | MH765695_PeLCV | R,G,M,C,3S | 4.99E-06 |
| 18 | 371 | 601 | MH765695_PeLCV1 | MH988457_PaLCV | Unknown(MN529626_PaLCV) | R,M,3S | 4.63E-04 |
| 19 | 578 | 785 | KP725057_AgEV | HM140365_ChiLC | Unknown (MH765698_ChiLC) | R,M,C,S,3S | 3.67E-03 |
| AC4 | |||||||
| 1 | 127 | 226 | KF307208_PaLCV | Unknown (KP725055_ToLCV) | MH765695_PeLCV | R,M,C,S,3S | 1.13E-05 |
R, RDP; G, Geneconv; B, Bootscan; M, MaxChi; C, Chimarea; S, SiScan; 3Seq, Sequence Triplets; and @The lowest p value calculated for the underline and bold method are given in the column.