Table 5. Recombination analysis of betasatellite and alphasatellite molecules using Recombination Detection Program, version 4.66.
| Satellite molecules | Associated with CLCuD sequence | Recombination site (region) | Event Number | Major parent x minor parent | Detected by methoda | Max. P valueb |
|---|---|---|---|---|---|---|
| Betasatellite | ||||||
| KT228325 (CLCuMB) | Ma-14-3 (CLCuMuV-Ra) | 17–762 (βC1) | 1 | ToYLCuB (NC019532) xCLCuMB (KT228326*) | R,B,3-S | 2.58x10-7 |
| 1160–1201 (upstream of SCR) | 2 | ToLCuB (NC 009570)/PLCuB (NC004706) x CLCuGzB(NC006935) | R,G, M | 3.12x10-3 | ||
| KM103522 (CLCuMB) | S-11 (CLCuMuV-Fai) | 129–870 (βC1) | 3 | LuLDB (JX315326)/ToLCuJVB (NC005497)/ CLCuMB (KT228326*) x CLCuMB/ CrYVMoB (HQ631430) | B, M, 3-S | 5.67x10-4 |
| 948–1028 (A-rich) | 4 | CLCuMB (IARI-30)/CLCuMB ((KT228326*)/CLCuMBxCrYVMoB (HQ631430)/ToLCuB (NC 009570)/ LuLDB (JX315326) | R, B, C | 1.38 x 10−3 | ||
| KT228326 (CLCuMB) | Si-14-1 (CLCuKoV-Bu) | 1–110 (SCR) | 5 | ALCB (NC012557) xCLCuMB | G,M | 1.14x10-9 |
| Alphasatellite | ||||||
| KM103525 (GDarSLA) | Rh-4 (CLCuMuV-Ra) | 1030–1111 (A-rich) | 1 | GDarSLA (FJ218493) xMaYA (NC008561)/CLCuMuA (NC018082) /CLCuBuA (FR772090) | R,M,C | 1.7x10-9 |
| KM103523 (GDarSLA) | Hi-3 (CLCuMuV-PK) | 1–996 (Rep) | 6 | AYVSA (FJ956707)/OkVA (FN658718)/TLCuNA (JQ041697) xGDarSLA (KM103525ψ)/ GDarSLA (KM103526ω) | B,G,3-S | 5.01x10-8 |
| KT228319 (GDarSLA) | Ma-14-3 (CLCuMuV-Ra) | 1–1025 (Rep) | 4 | TLCuNA (JQ041697)/GDarSLA (KM103525 ψ) /MaYA (NC008561) x GDarSLA (KT228320*) | G,B,3-S | 2.76x10-10 |
| 1028–1086 (A-rich) | 5 | GDarSLA (KT228320*) xMaYA (NC008561)/CLCuBuA (FR772090) | R,M,C | 4.72x10-16 | ||
| KM103526 (GDarSLA) | Sa-3 (CLCuMuV-Ra) | 64–639 (Rep) | 2 | CLCuBuA (IARI-45-2)/CLCuBuA (FR772090)/CLCuGVA (HM446369) xGDarSLA (FJ218493)/ GDarSLA (KM103523π) | R,G,3-S | 2.1x10-2 |
| 1185–1263 (A-rich) | 3 | GDarSLA (FJ218493)/ GDarSLA (KM103523π) xCLCuMuA (NC018082) | B,M,C | 5.9x10-4 | ||
a:B Bootscan, C Chimera, G Geneconv, M Maxchi, R RDP, S Siscan and 3-S 3SEQ implemented in the RDP4,
b: highest acceptable P-value cut-off of 0.05 detected evidences of recombination events among the sequences; CLCuD-begomovirus represented by special character superscript to the Accession no’s. of associated betasatellite and alphasatellite molecule; Si-14-1 (CLCuKoV-Bu) by *, Hi-3 (CLCuMuV-PK) by π, Rh-4 (CLCuMuV-Ra) by ψ and Sa-3 (CLCuMuV-Ra) by ω; Tomato yellow leaf curl betasatellite (ToYLCuB), Tomato leaf curl betasatellite (ToLCuB), Papaya leaf curl betasatellite (PLCuB), Cotton leaf curl Gezira betasatellite (CLCuGzB), luffa leaf distortionbetasatellite (LuLDB), Tomato leaf curl Joydebpur virus (ToLCuJVB), Croton yellow vein mosaic betasatellite (CrYVMoB), Ageratum leaf curl betasatellite (ALCB), Malvastrum yellow mosaic alphasatellite (MaYA), Cotton leaf curl Gezira alphasatellite (CLCuGVA), Tomato leaf curl New Delhi alphasatellite (TLCuNA), Ageratum yellow vein Singapore alphasatellite (AYVSA),Okra virus alphasatellite (OkVA)