Table 3.
Putative recombination events detected using the RDP4.1 program among begomoviruses and betasatellites associated with PaLCD, based on provided datasets from India; 44 DNA-A sequence and 26 associated betasatellite.
| Event no. | Breakpoints | Recombinant | Parents | Methods | p valve | ||
|---|---|---|---|---|---|---|---|
| DNA-A | Begin | End | Major | Minor | |||
| 1 | 2,330 | 2,680 | MH765693_ChiLCV | MH807200_PaLCr | Unknown (KP725057_AgEV) | R,G,M,C,S,3S | 8.36E-49 |
| 2 | 458 | 1,186 | MH807205_PaLCV | KX302713_PaLCV | Unknown (KX302707_CLCuB) | R,G,B,M,C,S,3S | 1.91E-44 |
| 3 | 431 | 1,256 | KX302707_CLCuBV | Unknown(MH765696_CrYVM) | KX302713_PaLCV | R,G,M,C,S,3S | 8.12E-44 |
| 4 | 988 | 1,373 | DQ989325_ToLCNDV | MH105055_ToLCV | KX302713_PaLCV | R,G,M,C,S,3S | 2.84E-35 |
| 5 | 2,335 | 2,679 | MH988458_PaLCV | KP725057_AgEV | Unknown (MH807200_PaLCr) | R,G,M,C,S,3S | 7.60E-34 |
| 6 | 500 | 1,050 | MH765696_CrYVMV | MH765693_ChiLC | Unknown (KX353622_PaYLC) | R,G,M,C,S,3S | 4.27E-26 |
| 7 | 2,312 | 2,656 | MH807200_PaLCrV | MH807202_DLCV | KP725057_AgEV | R,G,M,C,S,3S | 3.01E-25 |
| 8 | 136 | 446 | KX302713_PaLCV | KP725055_ToLCV | Unknown (MH988458_PaLCV) | R,G,B,M,C,S,3S | 4.46E-24 |
| 9 | 1,292 | 1,365 | HM140367_PaLCrV | HM140369_PaLCr | KF307208_PaLCV | R,G,M,C,3S | 1.38E-21 |
| 10 | 334 | 1,274 | MG757245_ToLCGV | KX353622_PaYLC | Unknown (MH807202_DLCV) | R,G,M,C,S,3S | 3.02E-22 |
| 11 | 2,032 | 2,326 | MH807204_PaYLCV | Unknown (MH765693_ChiLC) | HM140368_PaLCr | R,G,M,C,S,3S | 6.75E-20 |
| 12 | 441 | 959 | KX353622_PaYLCV | MN529626_PaLCV | HM140368_PaLCr | R,G,B,M,C,S,3S | 3.06E-19 |
| 13 | 159 | 430 | KX302707_CLCuBV | JN558352_CLCuM | MH988458_PaLCV | R,G,C,3S | 3.60E-19 |
| 14 | 2,663 | 121 | MH105055_ToLCV | Unknown (MH807202_DLCV) | MH807200_PaLCr | R,G,M,C,S,3S | 1.03E-16 |
| 15 | 2,680 | 256 | KF307208_PaLCV | MH765696_CrYVM | MH765693_ChiLC | R,G,M,S,3S | 1.52E-15 |
| 16 | 2,110 | 2,325 | MG757245_ToLCGV | MN529626_PaLCV | Unknown (MH765693_ChiLC) | R,G,M,C,S,3S | 1.71E-14 |
| 17 | 2,109 | 2,328 | HM140364_ChiLCV | MN529626_PaLCV | Unknown (MH765693_ChiLC) | R,G,M,C,S | 9.38E-16 |
| 18 | 2,657 | 744 | MH807200_PaLCrV | MH807202_DLCV | HM140369_PaLCr | R,G,M,S | 9.21E-16 |
| 19 | 2,066 | 2,326 | MH765695_PeLCV | MH988458_PaLCV | Unknown (KF307208_PaLCV) | R,G,B,M,C,3S | 3.22E-12 |
| 20 | 2,326 | 144 | MG757245_ToLCGV | MH765695_PeLCV | KP725055_ToLCV | R,G,M,C,S,3S | 6.02E-27 |
| 21 | 223 | 615 | HM140366_ChiLCV | MF574143_ChiLC | Unknown (HM140369_PaLCr) | R,G,M,C | 3.81E-12 |
| 22 | 962 | 1,539 | MH765697_ChiLCV | MH765693_ChiLC | MH765698_ChiLC | R,G,M,C,S,3S | 4.78E-12 |
| 23 | 1,074 | 1,555 | MH807202_DLCV | MH988458_PaLCV | MH807200_PaLCr | R,G,B,M,C,S,3S | 5.22E-12 |
| 24 | 438 | 606 | MN529626_PaLCV | Y15934_PaLCV-I | Unknown (HM140367_PaLCr) | R,G,B,M,C,S,3S | 5.33E-11 |
| 25 | 2,312 | 2,669 | KP725057_AgEV | MH807202_DLCV | JN558352_CLCuM | R,G,M,C,3S | 9.13E-13 |
| 26 | 1,246 | 1807 | KX302710_PaLCrV | MH674437_PaLCr | Unknown (MH807203_PaLCr) | R,G,M,C,S,3S | 5.17E-15 |
| 27 | 1,063 | 1,153 | HM140368_PaLCrV | MH765698_ChiLC | Unknown (MH807205_PaLCV) | R,G,M,3S | 8.02E-11 |
| 28 | 1,554 | 1785 | MH988458_PaLCV | KX302713_PaLCV | MH807202_DLCV | R,G,C,S,3S | 3.10E-09 |
| 29 | 750 | 962 | MH988458_PaLCV | KX302707_CLCuB | MH765693_ChiLC | R,M,C,3S | 1.27E-08 |
| 30 | 2,117 | 2,673 | HM140368_PaLCrV | MH807202_DLCV- | Unknown (MH765698_ChiLC) | R,G,C,S,S | 3.82E-11 |
| 31 | 434 | 1,072 | MN529626_PaLCV | KX302713_PaLCV | KY800906_PaLCV | R,G,B,M,S,3S | 5.53E-07 |
| 32 | 1,892 | 2031 | KX302713_PaLCV | MN529626_PaLCV | MH807200_PaLCr | R,G,M,C,3S | 4.97E-08 |
| 33 | 1,108 | 1,552 | HM140365_ChiLCV | Unknown (MH988458_PaLCV) | KX353622_PaYLC | R,G,M,C,S,3S | 1.27E-15 |
| 34 | 275 | 440 | GU136803_ChiLCV | HM140364_ChiLC | KX353622_PaYLC | R,G,S | 9.42E-11 |
| 35 | 2,687 | 26 | MH765695_PeLCV | MH765693_ChiLC | Unknown (JN558352_CLCuM) | R,G,S,3S | 7.35E-07 |
| 36 | 1,279 | 1,553 | MH988458_PaLCV | KX353622_PaYLC | MG757245_ToLCG | R,G,C,3S | 1.78E-08 |
| 37 | 2,127 | 2,299 | MH807200_PaLCrV | MH988457_PaLCV | KX302707_CLCuB | R,G,3S | 1.35E-04 |
| 38 | 137 | 506 | Y15934_PaLCV-I | Unknown (MH765698_ChiLC) | MH988458_PaLCV | R,G,S,3S | 7.21E-05 |
| 39 | 2,651 | 49 | JN558352_CLCuMV | MH765697_ChiLC | KP725057_AgEV | R,S,S | 1.21E-04 |
| 40 | 1,074 | 1,223 | KP725055_ToLCV | MN529626_PaLCV | Unknown (MH765698_ChiLC) | R,G,M,C | 6.30E-05 |
| 41 | 302 | 382 | MH988458_PaLCV | MH807205_PaLCV | MH105055_ToLCV | R,G,M,S | 2.03E-10 |
| 42 | 498 | 626 | MH988458_PaLCV | KX302713_PaLCV | MH807205_PaLCV | R,G,M,C,3S | 7.02E-04 |
| 43 | 1,390 | 1,553 | MH765698_ChiLCV | MH765695_PeLCV | MH807202_DLCV | R,G,C,3S | 2.85E-06 |
| 44 | 1,553 | 1,611 | HM140370_ChiLCV | KY800906_PaLCV | Y15934_PaLCV-I | R,G,B | 2.67E-03 |
| 45 | 1,958 | 2,051 | MH988458_PaLCV | MN529626_PaLCV | MH765697_ChiLC | R,M,C,3S | 3.69E-03 |
| 46 | 435 | 959 | MH765698_ChiLCV | HM140370_ChiLC | HM140368_PaLCr | R,G,S,3S | 1.05E-11 |
| 47 | 616 | 2,106 | HM140366_ChiLCV | KY800906_PaLCV | Unknown (MF574143_ChiLC) | R,M,S,3S | 4.61E-06 |
| 48 | 2,526 | 2,679 | MH988458_PaLCV | Unknown (MH765697_ChiLC) | MH765696_CrYVM | R,C,S,3S | 5.31E-04 |
| Betasatellite | |||||||
| 1 | 1,053 | 1,250 | MN529627_MM1B | KP725056_CB1/T | MH825686_PSBB3 | R,G,M,C | 2.18E-13 |
| 2 | 580 | 747 | HM143909_Naj1 | HM143911_Naj2 | Unknown (KX302714_Hajip) | R,M,C | 8.19E-09 |
| 3 | 1,054 | 1,159 | MH825686_PSBB3 | Unknown (KX302716_Guntu) | MH825690_PSBB6 | R,M,C,S | 2.38E-08 |
| 4 | 1,059 | 213 | KX302714_Hajip | MH825689_PSBB6 | Unknown (MH825684_PSBB2) | R,C,M,S | 9.11E-11 |
| 5 | 1,252 | 170 | MH825686_PSBB3 | MH825683_PSBB1 | Unknown (MH825684_PSBB2) | R,G,M,C | 8.15E-07 |
| 6 | 576 | 646 | MN529627_MM1B | KP725056_CB1/T | Unknown (MH825691_PSBB6) | R,M,C | 1.86E-06 |
| 7 | 746 | 832 | KP725056_CB1/T | HM143901_Pani1 | Unknown (KX302719_Bhopa) | R,M,C | 4.74E-06 |
| 8 | 1,090 | 1,110 | KX302716_Guntu | HM143901_Pani1 | Unknown (MH825685_PSBB3) | R,G,M | 6.46E-06 |
| 9 | 27 | 106 | HM143908_PSB8 | MH825683_PSBB1 | Unknown (KX353620_DP2/T) | R,G,M,C | 3.07E-05 |
| 10 | 1,157 | 1,243 | KX353620_DP2/T | Unknown (MH825689_PSBB6) | MH825683_PSBB1 | R,M,C,S,3S | 4.32E-05 |
| 11 | 995 | 1,133 | MH825684_PSBB2 | KX302717__Moha | MH825685_PSBB3 | R,G,M,C,S,3S | 5.28E-07 |
| 12 | 1,081 | 1,109 | KX353620_DP2/T | Unknown (MH825688_PSBB5) | KP725056_CB1/T | R,M,C,S,3S | 2.09E-04 |
| 13 | 891 | 143 | KX302717__Moha | MH825689_PSBB6 | HM143911_Naj2 | R,B,M,C | 1.82E-06 |
| 14 | 973 | 1,053 | MH825686_PSBB3 | MH825689_PSBB6 | MH825691_PSBB6 | R,G,S,3S | 1.21E-07 |
| 15 | 1,217 | 1,259 | MH825683_PSBB1 | HM143909_Naj1 | MH825691_PSBB6 | R,G,S,3S | 1.81E-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.