Table 4. Recombination analysis of CLCuD-begomovirus genomes using the Recombination Detection Program version 4.66.
| CLCuD sequence | Recombination site (region) | Length (nt) | Event number | Major parent x minor parent | Detected by methoda | Max. P valueb |
|---|---|---|---|---|---|---|
| Faz-14 (CLCuMuV-Ra) | 64–901 (IR,V1,V2) | 838 | 7 | CLCuBaV/MeYVMVxCLCuMuV-Ra | R,M,B,G,Si | 2.72x 10−9 |
| 975–1001 (V1) | 27 | 8 | CLCoKoV-Bu/CLCuKoV-Lu xCLCuMuV-Ra | G,R,M | 8.05 x 10−3 | |
| Rh-4 (CLCuMuV-Ra) | 900–1002 (V1) | 103 | 3 | CLCuMuV-Ra xCLCuBaV | 3-S,B,C,M,R | 1.72 x 10−9 |
| 2632–2714 (IR) | 83 | 4 | CLCuMuV-Ra x CLCuMuV-Ra/CLCuKoV-Bu | C,M,R,G | 4.66 x 10−5 | |
| S-9 (CLCuMuV-Ra) | 16–63 (IR) | 48 | 1 | CLCuMuV-Ra xCLCuMuV- PK/Hib | R,G,3-S | 7.35 x 10−4 |
| 1595–2610 (C1, C4) | 1016 | 2 | CLCuMuV-Ra x CLCuMuV-Ra | 3-S,C,Si | 1.2 x 10−2 | |
| Sa-3 (CLCuMuV-Ra) | 62–1596 (IR,V1,V2,C1, C2, C3) | 1535 | 5 | CLCuKoV-La xCLCuMuV-Fai | 3-S,C,M | 9.8 x 10−15 |
| 2586–2723 (IR, C1, C4) | 141 | 6 | CLCuMuV-Fai xCLCoKoV-Bu | C,M,G | 2.1 X 10−7 | |
| Si-17 (CLCuMuV-Ra) | 900–1002 (V1) | 103 | 3 | CLCuMuV-Ra x CLCuBaV | C,3-S,R | 1.71 x 10−9 |
| 2642–2752 (IR) | 111 | 4 | CLCuMuV-Ra xCLCuMuV-Ra | G,M,R | 2.8 x 10−15 | |
| S-11(CLCuMuV-Fai) | 1774–2442 (C1, C4) | 669 | 9 | CLCuMuV-His xCLCuAlV-Al/CLCoKoV-Bu | Si,M,C | 9.1 x 10−41 |
| 2623–2749 (IR) | 127 | 10 | CLCuMuV-His xCLCoKoV-Bu | C,R,G | 1.53 x 10−15 | |
| Hi -14 (CLCuKoV-Bu) | 1–76 (IR) | 76 | 11 | ToLCuNDV/CLCuMuV-Ra xCLCuBaV/ CYVMV | R,B,G | 2.78x10-3 |
| Si-14-1 (CLCuKoV-Bu) | 11–75 (IR) | 65 | 12 | ToLCuNDV/CYVMV/CLCuKoV-La xCLCuMuV-Ra | B,C,G,R | 2.78 x 10−3 |
| Hmg-14 (CLCuKoV-Bu) | 1–76 (IR) | 76 | 11 | ToLCuNDV/CLCuBaV/ CLCuMuV-Ra xCLCuBaV/CLCuMuV-Ra/CYVMV | R,B,G | 2.78x10-3 |
a: B Bootscan, C Chimera, G Geneconv, M Maxchi, R RDP, Si Siscan and 3-S 3SEQ implemented in the RDP4,
b: highest acceptable P-value cut-off of 0.05 detected the evidences of recombination events among the sequences; Croton yellow vein mosaic virus, CYVMV (JN817516), Cotton leaf curl Bangalore virus, CLCuBaV (AY705380), Mesta yellow vein mosaic virus, MeYVMV (FJ159262) and Tomato leaf curl New Delhi virus, ToLCuNDV (KC545812)