dc.contributor.author |
Morgan, Seamus W.
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dc.contributor.author |
Read, David Alan
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|
dc.contributor.author |
Burger, Johan
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dc.contributor.author |
Pietersen, Gerhard
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dc.date.accessioned |
2024-05-09T08:36:20Z |
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dc.date.available |
2024-05-09T08:36:20Z |
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dc.date.issued |
2023-04 |
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dc.description |
DATA AVAILABILITY : All sequence data generated or analysed during this study have been Submitted to Genbank under Accession numbers provided in the supplementary information files (Table 6). |
en_US |
dc.description.abstract |
Seven viroid species and one putative viroid species have been reported to infect grapevine namely, hop stunt viroid (HSVd), grapevine yellow speckle viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), Australian grapevine viroid (AGVd), Japanese grapevine viroid (JGVd), grapevine latent viroid (GLVd), and citrus exocortis viroid (CEVd), as well as a grapevine hammerhead viroid-like RNA (GHVd), so far. In this study, RNA sequence (RNA-Seq) data, from 229 Vitis accessions from the field-maintained vineyard of the South African Vitis germplasm collection, were analysed to determine the diversity of the viroids present. Five of the seven known grapevine-infecting viroids and one putative grapevine-infecting viroid species were very commonly found, with 214 of the 229 samples containing at least one viroid species. HSVd, GYSVd-1, GYSVd-2, AGVd, and JGVd, as well as GHVd, were identified in the RNA-Seq data of the samples and confirmed using RT-PCR and Sanger sequencing. The HSVd sequences indicated the presence of two variants, with one showing multiple nucleotide insertions. AGVd and GYSVd-2 did not display significant sequence diversity, confirming past international studies. GYSVd-1 occurs as four major variants worldwide and representatives of all four variants were identified in this vineyard. This is the first report on the diversity of viroids infecting grapevine in South Africa and the first report of JGVd outside of Japan and GHVd in South Africa. Further studies are needed to fully assess the population and to identify potentially new viroid species. |
en_US |
dc.description.department |
Forestry and Agricultural Biotechnology Institute (FABI) |
en_US |
dc.description.librarian |
hj2024 |
en_US |
dc.description.sdg |
SDG-02:Zero Hunger |
en_US |
dc.description.uri |
http://link.springer.com/journal/11262 |
en_US |
dc.identifier.citation |
Morgan, S.W., Read, D.A., Burger, J.T. et al. Diversity of viroids infecting grapevines in the South African Vitis germplasm collection. Virus Genes 59, 244–253 (2023). https://doi.org/10.1007/s11262-023-01971-7. |
en_US |
dc.identifier.issn |
0920-8569 (print) |
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dc.identifier.issn |
1572-994X (online) |
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dc.identifier.other |
10.1007/s11262-023-01971-7 |
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dc.identifier.uri |
http://hdl.handle.net/2263/95864 |
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dc.language.iso |
en |
en_US |
dc.publisher |
Springer |
en_US |
dc.rights |
© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2023. The original publication is available at : http://link.springer.comjournal/11262. |
en_US |
dc.subject |
Hop stunt viroid (HSVd) |
en_US |
dc.subject |
Grapevine hammerhead viroid-like RNA (GHVd) |
en_US |
dc.subject |
Citrus exocortis viroid (CEVd) |
en_US |
dc.subject |
Grapevine latent viroid (GLVd) |
en_US |
dc.subject |
Grapevine yellow speckle viroid 2 (GYSVd-2) |
en_US |
dc.subject |
Australian grapevine viroid (AGVd) |
en_US |
dc.subject |
Japanese grapevine viroid (JGVd) |
en_US |
dc.subject |
Viroids |
en_US |
dc.subject |
Grapevine |
en_US |
dc.subject |
Next-generation sequencing (NGS) |
en_US |
dc.subject |
Diversity |
en_US |
dc.subject |
Reverse transcription polymerase chain reaction (RT-PCR) |
en_US |
dc.subject |
SDG-02: Zero hunger |
en_US |
dc.title |
Diversity of viroids infecting grapevines in the South African Vitis germplasm collection |
en_US |
dc.type |
Postprint Article |
en_US |