Table 2.
Endogenous badnavirus‐related sequences obtained in this study
| Sequence name | Accession number | Amplification method | Primers | Size (bp) | Plant of origin (yam species) | Also present in: (yam species) | Related RT‐RNaseH partb | eDBV groupc |
|---|---|---|---|---|---|---|---|---|
| G1Dr | KF830002 | Outward facing primers PCR |
49‐R2 63‐F2 |
5253 | GN155 (D. rotundata) | NDa | BN4Dr (95%–99%) | eDBV9a |
| S3G1Dr | KF830010 | Direct PCR |
verifG1F verifG1R |
3595 | Sd3 (D. rotundata) | Sd2 (D. rotundata) | NDa | |
| G2G1aDr | KF830003 | Direct PCR |
verifG1F verifG1R |
348 | GN290 (D. rotundata) | GP425, CRB146, CRB152 (D. cayenensis) | NDa | |
| G2G1bDr | KF830004 | Direct PCR |
verifG1F verifG1R |
624 | GN290 (D. rotundata) | GP425, CRB146, CRB152 (D. cayenensis) | NDa | |
| G2G1cDr | KF830005 | Direct PCR |
verifG1F verifG1R |
1285 | GN290 (D. rotundata) | GP425, CRB146, CRB152 (D. cayenensis) | NDa | |
| G2G1dDr | KF830006 | Direct PCR |
verifG1F verifG1R |
1499 | GN290 (D. rotundata) | GP425, CRB146, CRB152 (D. cayenensis) | BN4Dr (100%) | eDBV9a |
| H2Dc | KF830007 | Outward facing primers PCR |
B389‐1F B389‐3R |
514 | HT1 (D. cayenensis) | GP425, CRB146, CRB152 (D. cayenensis) | FJ60a_Dr (100%) | eDBV9b |
| S1H3Dr | KF830008 | Direct PCR |
B389‐2F B389‐3R |
2160 | Sd1 (D. rotundata) | GN290 (D. rotundata) | FJ60a_Dr (100%) | eDBV9b |
| S1H4Dr | KF830009 | Direct PCR |
B389‐2F B389‐4R |
405 | Sd1 (D. rotundata) | GP425, CRB146, CRB152 (D. cayenensis); GN290 (D. rotundata) | FJ60a_Dr (100%) | eDBV9b |
eDBV, endogenous Dioscorea bacilliform viruses.
a
Not determined.
b
Most closely related badnavirus RT‐RNaseH sequence available in GenBank and its percentage of nucleotide identity to the sequence from this study.
c
Association of eDBV group and subgroup is based on the phylogenetic analysis shown in Fig. 5.