Table 2.
Begomovirus genomes identified in whiteflies.
| Library | Genome a (Accession) | Best match b (% Identity)/Accession Number |
|---|---|---|
| CA_S | VEM Squash leaf curl virus DNA-A * (KT099117) | SLCV, Imperial Valley, CA (99%)/DQ285016 |
| VEM Squash leaf curl virus DNA-B * (KT099159) | SLCV, Imperial Valley, CA (95%)/DQ285017 | |
| Guat_S | VEM Melon chlorotic leaf curl virus DNA-A * (KT099118) | MCLCuV, Guatemala (96%)/AF325497 |
| VEM Melon chlorotic leaf curl virus DNA-B * (KT099160) | MCLCuV, Guatemala (96%)/AF325498 | |
| VEM Tomato severe leaf curl virus DNA-A * (KT099119) | ToSLCV, Guatemala and Mexico (97%)/AF130415/DQ347947 | |
| VEM Sida golden mosaic Honduras virus 1a DNA-A (KT099120) | SiGMHV, Honduras (94%)/Y11097 | |
| VEM Sida golden mosaic Honduras virus 1b DNA-A (KT099121) | SiGMHV, Honduras (94%)/Y11098 | |
| VEM Sida golden mosaic Honduras virus 1 DNA-B (KT099161) | SiGMHV, Honduras (82%)/AJ250731 | |
| VEM begomovirus 1a DNA-A (KT099122) | BICV, Mexico (80%)/JX827487 | |
| VEM begomovirus 1b DNA-A (KT099123) | BICV, Mexico (80%)/JX827488 | |
| VEM begomovirus 1c DNA-A (KT099124) | BICV, Mexico (80%)/JX827489 | |
| VEM begomovirus 2 DNA-A (KT099125) | SiYMV, Cuba (84%)/JN411687 | |
| VEM begomovirus 3a DNA-A (KT099126) | CoYSV, Mexico (83%)/DQ875868 | |
| VEM begomovirus 3b DNA-A (KT099127) | CoYSV, Mexico (83%)/DQ875869 | |
| VEM begomovirus 3a DNA-B (KT099162) | SiGMV/SiYVV, Honduras (82%)/AJ250731/Y11100 | |
| VEM begomovirus 3b DNA-B (KT099163) | SiGMV/SiYVV, Honduras (82%)/AJ250731/Y11101 | |
| VEM begomovirus 4 DNA-A (KT099128) | JMV, Dominican Republic and Florida (85%)/KJ174330/KF998097 | |
| Guat_T2 | VEM Tomato severe leaf curl virus DNA-A * (KT099129) | ToSLCV, Mexico (99%)/DQ347947 |
| VEM Tomato mosaic Havana virus DNA-A * (KT099130) | ToMHV, Nicaragua (99%)/EF088197 | |
| VEM Tomato mosaic Havana virus DNA-B * (KT099164) | ToMHV, Cuba (92%)/Y14875 | |
| Israel_S | VEM Squash leaf curl virus DNA-A (KT099131) | SLCV, Israel (99%)/KM595109 |
| VEM Squash leaf curl v irus DNA-B * (KT099165) | SLCV, Palestine (99%)/KC441466 | |
| VEM Cotton leaf curl Gezira virus DNA-A (KT099132) | CLCuGV, Egypt and Pakistan (94%)/AF155064/FR751146 | |
| PR_T1 | VEM Sweet potato leaf curl virus (KT099133) | SPLCV/SPLCLaV, Brazil and Spain (91%)/FJ969833/EU839579 |
| PR_T2 | VEM begomovirus 5a DNA-A (KT099134) | WfVEM1/SiGMLV, Florida and Jamaica (90%)/HM859902/HQ009522 |
| VEM begomovirus 5b DNA-A (KT099135) | WfVEM1/SiGMLV, Florida and Jamaica (90%)/HM859902/HQ009523 | |
| VEM begomovirus 5c DNA-A (KT099136) | WfVEM1/SiGMLV, Florida and Jamaica (90%)/HM859902/HQ009524 | |
| VEM begomovirus 5d DNA-A (KT099137) | WfVEM1/SiGMLV, Florida and Jamaica (90%)/HM859902/HQ009525 | |
| VEM begomovirus 5e DNA-A (KT099138) | WfVEM1/SiGMLV, Florida and Jamaica (90%)/HM859902/HQ009526 | |
| VEM begomovirus 5 DNA-B (KT099166) | SiYVV, Cuba (79%)/HE806449 | |
| VEM begomovirus 6b DNA-B (KT099167) | SiGMFV, Florida (78%)/HE806443 | |
| PR_P | VEM begomovirus 6 DNA-A (KT099139) | SiYMV, Cuba (88%)/HQ822123 |
| VEM begomovirus 6a DNA-B (KT099168) | SiGMFV, Florida (78%)/HE806443 | |
| VEM Sweet potato leaf curl virus (KT099140) | SPLCV, Puerto Rico (93%)/DQ644563 | |
| VEM Macroptilium mosaic Puerto Rico virus DNA-A* (KT099141) | MaMPRV, Puerto Rico (99%)/AF449192 | |
| VEM Macroptilium mosaic Puerto Rico virus DNA-B* (KT099169) | MaMPRV, Puerto Rico (98%)/AY044134 | |
| PR_E | VEM begomovirus 5f DNA-A (KT099142) | WfVEM1/SiGMLV, Florida and Jamaica (90%)/HM859902/HQ009522 |
| VEM Sweet potato leaf curl virus (KT099143) | SPLCV/SPLCLaV, Brazil, Puerto Rico and Spain (91%)/FJ969833/DQ644563/EU839579 | |
| Spain_B | VEM Sweet potato leaf curl virus 1 (KT099144) | SPLCV, Spain (97%)/EU856364 |
| Spain_S | VEM Sweet potato leaf curl virus 2 (KT099145) | SPLCESV, Spain (94%)/EF456743 |
| Spain_T | VEM begomovirus 7a (KT099146) | ToLCNamV, Madagascar (81%)/AM701764 |
| VEM begomovirus 7b (KT099147) | ToLCNamV, Madagascar (81%)/AM701765 | |
| VEM begomovirus 7c (KT099148) | ToLCNamV, Madagascar (81%)/AM701766 | |
| VEM begomovirus 7d (KT099149) | ToLCNamV, Madagascar (81%)/AM701767 | |
| VEM begomovirus 7e (KT099150) | ToLCNamV, Madagascar (81%)/AM701768 | |
| VEM begomovirus 7f (KT099151) | ToLCKMV, Comoros (82%)/AM701759 | |
| VEM begomovirus 7g (KT099152) | ToLCKMV, Comoros (81%)/AM701759 | |
| Spain_W1 | VEM begomovirus 7h (KT099153) | ToLCNamV, Madagascar (81%)/AM701764 |
| VEM begomovirus 7i (KT099154) | ToLCNamV, Madagascar (81%)/AM701765 | |
| VEM begomovirus 7j (KT099155) | ToLCNamV, Madagascar (81%)/AM701766 | |
| VEM begomovirus 7k (KT099156) | ToLCNamV, Madagascar (81%)/AM701767 | |
| VEM Tomato yellow leaf curl virus-[Almeria] 1 * (KT099157) | TYLCV, Spain (99%)/AJ489258 | |
| Spain_W2 | VEM Tomato yellow leaf curl virus-[Almeria] 1a* (KT099158) | TYLCV, Spain (99%)/AJ489258 |
a Genomes detected in whiteflies were identified as “VEM” followed by the virus name with the best match in the database. However, genomes from novel species that shared <91% pairwise identity with sequences found in GenBank were named as “VEM begomovirus #”. Percent nucleotide identities were calculated across entire genomes only. Genomes that were not PCR-verified are highlighted with an asterisk (*); b Virus names for best matches in GenBank are abbreviated according to underlined letters in the “Genomes” column. Best matches for novel species identified in this study include Blechum interveinal chlorosis virus (BICV), Sida yellow mottle virus (SiYMV), Corchorus yellow spot virus (CoYSV), Sida golden mosiac virus (SiGMV), Sida yellow vein virus (SiYVV), Jatropha mosaic virus (JMV), Whitefly VEM 1 begomovirus (WfVEM1), Sida golden mosaic Liguanea virus (SiGMLV), Sida golden mosaic Florida virus (SiGMFV), Tomato leaf curl Namakely virus (ToLCNamV), and Tomato leaf curl Comoros virus (ToLCKMV).