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Table 2 List of recombination events detected in CMG DNA-A and DNA-B sequences

From: Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar

  Event number Recombinant Region Minor parent Major parent Methods P-value
  Begin End     
DNA-A 1 EACMMV/SACMV 1685 1974 EACMKV Unknown RGBMCST 5.5 × 10−16
2 SACMV 131 448 ACMV SACMV RGBMCST 4.1 × 10−70
3 SACMV 502 907 EACMV-like SACMV RGBMCST 6.1 × 10−60
4 SACMV 177 388 ACMV SACMV RGBMCST 3.4 × 10−39
5 SACMV 2093 32 EACMKV SACMV RGBMCST 1.2 × 10−30
6 SACMV 340 449 ACMV SACMV RGBMCST 4.5 × 10−16
7 SACMV 163 195 Unknown SACMV RGB 4.5 × 10−06
8 SACMV 440 479 ACMV SACMV RGBS 3.6 × 10−13
9 SACMV 580 615 ACMV SACMV RGB 4.8 × 10−10
10 EACMMV 1996 2804 EACMV SACMV RGBMCST 2.2 × 10−29
11 EACMMV 54 1052 Unknown EACMV RGBMCS 5.0 × 10−30
12 EACMZV 93 1924 EACMV-like Unknown RGBMCSt 2.5 × 10−67
13 EACMZV a1928 2077 Unknown EACMZV RGBcST 3.6 × 10−10
14 EACMCV 1131 1790 Unknown EACMV-like RGBMCST 7.8 × 10−14
15 EACMCV 1836 2800 EACMV Unknown RGBMcSt 1.4 × 10−39
16 EACMCV 543 1103 EACMV-like EACMCV RGBMCST 2.4 × 10−42
17 EACMCV 623 669 ACMV EACMCV RGBS 3.8 × 10−12
18 EACMCV 1847 a1968 EACMV EACMCV RGBST 5.7 × 10−06
19 EACMCV 1468 1505 ACMV EACMCV RGs 3.4 × 10−03
20 EACMCV 1910 2061 EACMV EACMCV RGBS 2.0 × 10−05
21 EACMCV 185 1079 EACMKV EACMCV RGBMCST 1.7 × 10−25
22 EACMCV 33 a171 Unknown EACMCV RGBMCST 1.3 × 10−24
23 EACMCV 10 1054 EACMV-like EACMCV RGBMCST 3.6 × 10−21
24 EACMCV 509 1089 EACMKV EACMCV RGBMCST 4.0 × 10−26
25 EACMCV 1835 42 EACMV EACMCV RGBMCST 1.3 × 10−11
26 EACMCV 654 698 ACMV EACMCV RGBsT 1.9 × 10−05
27 EACMV-UG 549 1007 ACMV EACMV RGBMCST 1.2 × 10−62
28 EACMV a1710 2084 EACMZV EACMV RGBMCST 1.3 × 10−22
29 EACMV 1680 1902 SACMV EACMV rgbMCST 8.9 × 10−04
30 EACMV 1309 1988 EACMKV EACMV RGBMCST 3.0 × 10−12
31 EACMV 1956 2798 EACMV EACMKV RGBMCST 1.2 × 10−31
32 EACMKV 1 815 EACMV-like SACMV RGBMCST 4.0 × 10−45
33 EACMKV 1 759 EACMV-like SACMV RGBMCST 2.9 × 10−56
34 EACMKV 141 570 EACMV-like SACMV RGBMCST 6.3 × 10−59
35 EACMKV 32 a128 EACMV SACMV RGBST 2.4 × 10−10
36 EACMKV 1739 2006 Unknown Unknown RBM 8.2 × 10−04
37 EACMKV 1884 2014 EACMCV EACMKV RGBMCST 9.1 × 10−19
38 EACMKV 1090 1788 EACMCV EACMKV RGBMCST 9.9 × 10−78
39 EACMKV 1865 2798 SACMV EACMKV RGBMCST 4.6 × 10−72
40 EACMKV 549 1160 SACMV EACMKV RGBMCST 7.9 × 10−46
41 EACMKV 570 1154 Unknown EACMKV rGBMC 1.7 × 10−15
42 EACMKV 1804 2796 SACMV EACMKV RGBMCST 1.0 × 10−43
43 EACMKV 759 a1182 SACMV EACMKV RGBMCST 1.9 × 10−21
44 EACMKV 35 1056 EACMKV SACMV RGBMCST 4.6 × 10−35
45 EACMKV 1510 a1872 SACMV EACMKV RGBMCST 4.4 × 10−14
DNA-B 1 EACMCV 2541 53 EACMV-like EACMCV RGBMCST 7.6 × 10−35
2 EACMV-like 1124 1461 EACMCV EACMV-like RGBMCST 1.2 × 10−49
3 CMMGV 1569 2697 Unknown EACMV-like RGBMCST 5.0 × 10−66
4 EACMV-like 2227 2287 Unknown EACMV-like RGBMCS 9.7 × 10−23
5 SLCMV 2595 2712 Unknown SLCMV RGBMCST 6.7 × 10−17
6 EACMV-like 2668 2780 EACMCV EACMV-like RGBMCST 4.3 × 10−16
7 EACMCV 1495 2585 EACMV-like Unkown RGBmC 1.4 × 10−07
8 EACMV-like 854 1120 Unknown EACMV-like RGBMCST 3.1 × 10−09
9 EACMV-like 2345 2756 Unknown EACMV-like RGBMCST 1.9 × 10−15
10 EACMV-like 2119 2752 EACMV-like EACMV-like RBGMCS 2.9 × 10−16
11 EACMV-like 2638 2699 Unknown EACMV-like RGBS 3.0 × 10−05
12 EACMV-like 869 1597 EACMV-like EACMV-like rMCsT 8.1 × 10−04
  1. For each event, the species of the recombinants and inferred parents, the recombinant region breakpoints and the list of methods which detected the event are indicated (R: RDP; G: GENECONV; B: BOOTSCAN; M: MAXCHI; C: CHIMAERA; S: SISCAN; T: 3SEQ). The reported p-values are for the methods in bold type and are the smallest p-values calculated for the region in question. Whereas upper-case letters imply that a method detected recombination with a multiple comparison corrected p-value <0.05, lower-case letters imply that the method detected recombination with a multiple comparison corrected p-value >0.05
  2. aBreakpoints not inferred by RDP