Table 3.
Recombination crossover sites in Turnip mosaic virus genome detected by recombination detecting programs
| Gene/region and crossover site* | Recombination detecting program† | P‐value‡ | Z‐value§ | Parental‐like lineage | Reference isolate¶ |
|---|---|---|---|---|---|
| P1 | |||||
| Nt 401 | RGBMCSRSSP | 8.5 × 10−42 | 4.46 | World‐B × Asian‐BR | MD49J |
| Nt 680 | RGBSRSSP | 6.4 × 10−13−1.0 × 10−16 | 4.30–5.82 | World‐B × World‐B | 2J, DMJ |
| Nt 727 | RGBMCSRSSP | 1.1 × 10−24−3.0 × 10−36 | 3.33–5.55 | World‐B × Asian‐BR | MD47J, MN978J, NDJ, SN4J |
| Nt 752 | RGBMCSRSSP | 5.7 × 10−21−8.9 × 10−37 | 3.74–5.40 | World‐B × Asian‐BR | 59J, FD27J, KGD54J, MD974J |
| Nt 932 | RGBMCSRSSP | 2.8 × 10−22 | 4.94 | Asian‐BR × World‐B | FD27J |
| Nt 947 | RGBMCSRSSP | 9.4 × 10−28 | 4.38 | Asian‐BR × World‐B | 1J |
| Between P1 and Ct‐CI | RGBMCSRSSP | 1.2 × 10−10−2.1 × 10−53 | 3.21–6.76 | Asian‐BR × World‐B | ND10J (SGD311J) |
| GBMCSRSSP | 8.1 × 10−19 | 5.21 | World‐B × Asian‐BR | FD27J | |
| RGBMCSRSSP | 7.2 × 10−15 | 5.45 | Asian‐BR × Basal‐BR | RHS1 | |
| Ct‐CI | None | ||||
| 6K2 | |||||
| Nt 5765 | RGBMCSRP | 1.5 × 10−16−2.1 × 10−53 | 2.97–2.99 | World‐B × Asian‐BR | (HOD517J) (SGD311J) |
| Nt 5894 | RGBMCSRSSP | 9.0 × 10−9−6.4 × 10−20 | 4.75–6.79 | Basal‐BR × Asian‐BR | CHL13, CHL14, RHS1 |
| VPg | |||||
| Nt 6035 | RGBMCSRSSP | 1.2 × 10−9−3.9 × 10−21 | 3.47–5.48 | World‐B × Asian‐BR | KGD54J, ND10J |
| Nt 6121 | RGMCSRSSP | 3.1 × 10−22 | 3.16 | Asian‐BR × World‐B | HOD517J |
| RGBMCSRSSP | 6.5 × 10−24−2.1 × 10−27 | 4.83–4.94 | Asian‐BR × Asian‐BR | FD27J, SD3J | |
| Nt 6300 | RGBMCSR | 3.4 × 10−4−7.2 × 10−10 | 2.28–4.32 | World‐B × World‐B | 2J, C1, CHN5, CHN12 |
| NIa‐Pro | |||||
| Nt 6539 | GBMCSRSSP | 2.4 × 10−21 | 3.76 | Asian‐BR × World‐B | NDJ |
| NIb | None | ||||
| CP | |||||
| Nt 8904 | RGMCSRSSP | 6.7 × 10−29 | 4.04 | Asian‐BR × World‐B | CHN1 |
Approximately estimated recombination crossover sites detected in the Turnip mosaic virus concat aligned sequences by the recombination detecting programs. Crossover site shows locations of individual genes/regions in 1J genome (Ohshima et al. 1996).
Recombinant isolates identified by the recombination detecting programs; R (rdp), G (geneconv), B (bootscan), M (maxchi), C (chimaera) and SR (siscan) programs in rdp2, and SS (siscan synonymous site analysis) in siscan version 2 and P (phylpro) programs. The analysis was carried out with default settings for the different detection methods and a Bonferroni‐corrected P values cutoff of 0.01. Typical pattern for the detected recombinants is listed.
The reported P‐value is for the program in bold type in RDP2 and is the greatest P‐value among the isolates calculated for the region in question.
One of the parents of recombinants showed Z‐values greater than 3 in (on analysis of all nucleotide‐sites in SR of rdp2 program; thus, lower Z‐values of one of the parents identified in SS of siscan version 2 program is shown.
For all isolates, see Fig. 2. Recombination crossover sites of the isolates (in parentheses) were detected by the programs using 40 entire genomic sequences available from the international gene sequence data bases. For details of the genogroups, basal‐BR, Asian‐BR and world‐B, see Ohshima et al. (2002).