Table 2.
Putative recombination events detected among the tomato- and noncultivated host-infecting begomoviruses from Rio de Janeiro and Minas Gerais states, Brazil, based on a data set including only begomoviruses from Brazil
| Virus (recombinant isolate)a | Recombination breakpointb |
Parentc |
Methodsd | P valuee | ||
|---|---|---|---|---|---|---|
| Initial | Final | Major | Minor | |||
| EuYMV (Flo166:08) | 1547 | 2537 | ClLCV | Unknown | RGBMCS | 9.3 × 10−18 |
| SiCmMV (Coi4:07) | 1333 | 2285 | OMoV | Unknown | RGBMCS3 | 8.2 × 10−15 |
| SiCmMV (Coi4:07) | 1929 | (?) | Unknown | NDNV | RGBMCS3 | 3.3 × 10−07 |
| SimMV (Pda37:05) | 1619 | 2606 | OMoV | Unknown | RBMCS3 | 3.2 × 10−21 |
| SimMV (Pda37:05) | 1915 | (?) | Unknown | NDNV | RGBMCS | 3.3 × 10−07 |
| SiYLCV (Coi3:07) | 66 | 1997 | EuYMV | SiMoV | RGBMCS3 | 4.5 × 10−21 |
| ToCmMV (Coi22:07) | 35 | 1856 | EuYMV | SiMoV | RGBMCS3 | 4.5 × 10−21 |
| ToCmMV (Coi22:07) | 1917 | 2516 | Unknown | ToMlMV | RGBMCS | 9.3 × 10−18 |
| ToLDV (Pda4:05) | (?) | 921 | AbMBV | SimMV | RGBMC3 | 1.7 × 10−07 |
| ToLDV (Pda4:05) | 1582 | 2231 | OMoV | Unknown | RGBMCS3 | 8.2 × 10−15 |
| ToMlMV (Pda58:05) | 1935 | 2635 | ToCMoV | Unknown | RGBMCS | 5.2 × 10−05 |
| TMoLCV (Jai13:08) | (?) | 1159 | SiMoV | ToSRV | RBMCS | 6.2 × 10−04 |
| TMoLCV (Jai13:08) | 1945 | 2330 | Unknown | ToCMoV | RGBMCS | 5.2 × 10−15 |
| ToSRV (Flo165:08) | 1860 | 2179 | ToCMoV | SimMV | RGBMCS3 | 1.7 × 10−14 |
| ToYSV (Jai56.1:08) | 1898 | 2422 | ToCMoV | Unknown | RGBMCS | 5.2 × 10−05 |
| ToYVSV (Pda3:05) | 831 | 1046 | Unknown | ToSRV | RBMCS | 1.3 × 10−06 |
For simplicity, only one isolate of each species is listed for each recombination event. See Table S1 in the supplemental material for full virus names.
Numbering starts at the first nucleotide after the cleavage site at the origin of replication and increases clockwise. (?), breakpoint could not be precisely pinpointed.
Tomato virus designations are underlined; designations of viruses from noncultivated hosts are indicated in italics.
R, RDP; G, GeneConv; B, Bootscan; M, MaxChi; C, Chimera; S, SisScan; 3, 3SEQ.
The reported P values are for the programs indicated in bold, underlined type in column 6 and are the lowest P values calculated for the region in question.