Table 1.
Summary of unique recombination breakpoints in the RNA segments of PPSMV-1 and PPSMV-2 isolates as detected by the Recombination Detection Program v.4.16 (RDP4), using seven different methods RDP, GENECONV, BOOTSCAN, MAXIMUM CHISQUARE, CHIMAERA, SISCAN, 3 SEQ. The p-values of all the seven methods are given; Non-Significant p-values are indicated as NS. Parents of the interspecies recombinations are marked in bold fonts with red colour.
| PPSMV Genomic Segment | RNA 1 | RNA 2 | RNA 4 | RNA 5 | ||
|---|---|---|---|---|---|---|
| Recombinant Isolate | PPSMV-1 Bihar | PPSMV-1 Pune | PPSMV-1 Mahagaon | PPSMV-2 Patancheru | PPSMV-1 Bihar | |
| Recombination Breakpoint | 5403–5495 nt | 554–1550 nt | 862–1178 nt | 1228–1398 nt | 453–688 nt | |
| Parent Isolates | Major | PPSMV-1 Mahagaon | PPSMV-1 Patancheru | PPSMV-1 Kalaburagi | PPSMV-1 Kalaburagi | PPSMV-2 Bihar |
| Minor | PPSMV-2 Patancheru | PPSMV-1 Kalaburagi | PPSMV-1 Delhi.1 | PPSMV-1 Patancheru | PPSMV-1 Kalaburagi | |
| p-values for 7 recombination detection methods of RDP4 | RDP | 8.710 × 10−07 | NS | 4.794 × 10−08 | 1.432 × 10−10 | NS |
| GENECONV | 3.152 × 10−07 | 1.811 × 10−02 | NS | 1.820 × 10−09 | 1.877 × 10−05 | |
| BOOTSCAN | NS | 6.993 × 10−03 | 4.917 × 10−02 | 1.134 × 10−10 | 1.748 × 10−06 | |
| MAXI CHISQUARE | NS | 6.874 × 10−04 | 2.057 ×10−02 | 1.043 ×10−03 | 1.556 × 10−04 | |
| CHIMAERA | NS | 2.252 × 10−04 | NS | 9.874×10−04 | 6.743 × 10−03 | |
| SISCAN | 2.912 × 10−08 | 2.404 × 10−06 | 3.634× 10−06 | 3.692 ×10−06 | 1.886 × 10−10 | |
| 3SEQ | 1.454 × 10−09 | 5.609 × 10−06 | 3.969 × 10−02 | NS | 2.209 × 10−04 | |