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Detection and identification of viruses and viroids in nuclear grapevine material in South Africa
Thesis (PhDAgric)--Stellenbosch University, 2024.
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Stellenbosch : Stellenbosch University
2025
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| _version_ | 1867613848768348160 |
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| access_status_str | Open Access |
| author | Morgan, Seamus William |
| author2 | Burger, Johan T. |
| author_browse | Burger, Johan T. Morgan, Seamus William |
| author_facet | Burger, Johan T. Morgan, Seamus William |
| author_sort | Morgan, Seamus William |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhDAgric)--Stellenbosch University, 2024. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/131844 |
| institution | Stellenbosch University (South Africa) |
| last_indexed | 2026-06-10T12:42:40.195Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/131844 Detection and identification of viruses and viroids in nuclear grapevine material in South Africa Morgan, Seamus William Burger, Johan T. Pietersen, Gerhard Stellenbosch University. Faculty of AgriSciences. Dept. of Genetics. Grapevine (Vitis spp.) -- Yields Grapevine leafroll virus -- Genetics Grapes -- Breeding -- South Africa Viroids Viroid diseases of plants Grapes -- Diseases and pests -- Genetic aspects Nucleotide sequence UCTD Thesis (PhDAgric)--Stellenbosch University, 2024. ENGLISH ABSTRACT: Grapevine (Vitis spp.) is one of the most widely cultivated crops and one in which several viral diseases exist, many of which can severely impact crop yield and grapevine health. It is therefore necessary for the grapevine industry to be supplied with healthy and virus-free plant material. This generally starts with virus-tested nuclear plants from which the entire industry’s material is propagated. Over three years, 97 of these nuclear Vitis accessions were subjected to next generation RNA sequencing for the identification of virus and virus-like agents present in these. Five viruses were observed in six nuclear accessions and four viroids were identified and found to be prevalent in the accessions. The viruses found were grapevine Rupestris stem pitting-associated virus, grapevine fleck virus, grapevine Syrah virus, grapevine leafroll-associated virus 4, grapevine Rupestris vein feathering virus, while the viroids hop stunt viroid (HSVd), grapevine yellow speckle viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), and Australian grapevine viroid (AGVd) were identified. In addition, grapevine hammerhead viroid-like RNA (GHVd) was also detected, which is currently only considered a putative viroid species. The occurrence of grapevine fleck virus (GFkV) as a single infection in accession BA8 of the nuclear material provided the opportunity to obtain more definitive sequence data for this understudied virus. Fortuitously, a second GFkV positive sample (I4233) was obtained in a parallel study and was therefore also subjected to NGS analysis along with the isolate BA8. From these two RNA sequence datasets, two genomes of GFkV were generated. For GFkV BA8, 77% of the putative whole genome was assembled from NGS data, and PCR amplification, and Sanger sequencing of amplicons obtained using primers designed to fill the gaps in the genome. A genome of 90% coverage was assembled for sample I4233. Analysis revealed regions of high variability and high cytosine content. This study has extended the sequence information available for this poorly characterised virus. Given the presence of viroids in many of the nuclear accessions, and the availability of NGS datasets from the South African Vitis germplasm collection, the viroid presence of the collection was assessed. This is the first study on the diversity of grapevine infecting viroids in South Africa, which apart from identifying five grapevine infecting viroids also provides only the second report of Japanese grapevine viroid (JGVd) internationally and the first report of it outside of Japan. AFRIKAANSE OPSOMMING: Wingerd (Vitis spp.) is een van die gewasse wat die meeste gekweek word en een waarin verskeie virussiektes voorkom, waarvan verskeie wingerdgesondheid en oesopbrengste nadelig kan beïnvloed. Dit is dus nodig dat die wingerdbedryf van gesonde en virusvrye plantmateriaal voorsien word. Dit begin gewoonlik met virus-getoetste kern-plante waarvan die hele bedryf se materiaal vermeerder word. Oor drie jaar is 97 van hierdie kern Vitis-inskrywings onderwerp aan volgende generasie RNA-volgordebepaling vir die identifikasie van virus- en virusagtige agente wat daarin teenwoordig is. Vyf virusse is in ses kern-inskrywings waargeneem en vier viroïede is geïdentifiseer en gevind dat dit algemeen voorkom in die inskrywings. Die virusse wat gevind was, is ‘grapevine Rupestris stem pitting-associated virus’, ‘grapevine fleck virus’, ‘grapevine Syrah virus’, ‘grapevine leafroll-associated virus 4’, ‘grapevine Rupestris vein feathering virus’, terwyl ‘hop stunt viroid (HSVd)’, ‘grapevine yellow speckle viroid 1 (GYSVd-1)’, ‘grapevine yellow speckle viroid 2 (GYSVd- 2)’, en ‘Australian grapevine viroid (AGVd)’ geïdentifiseer was. Verder is ‘grapevine hammerhead viroid-like RNA (GHVd)’ ook opgespoor, wat tans slegs as 'n moontlike viroïed spesie beskou word. Die voorkoms van ‘grapevine fleck virus (GFkV)’ as 'n enkel-infeksie in inskrywing BA8 van die kernmateriaal het die geleentheid gebied om meer definitiewe volgorde-data vir hierdie onder- bestudeerde virus te verkry. Toevallig is 'n tweede GFkV positiewe monster (I4233) in 'n parallelle studie opgespoor en is dus ook aan NGS analise onderwerp saam met die isolaat BA8. Uit hierdie twee RNA-volgordedatastelle is twee genome van GFkV gegenereer. Vir GFkV BA8 is 77% van die vermeende heel-genoom saamgestel uit NGS-data, asook PCR-amplifisering, en Sanger- volgordebepaling van fragmente verkry met behulp van inleiers wat ontwerp is om die gapings in die genoom te vul. 'n Genoom van 90% dekking is vir monster I4233 saamgestel. Ontleding het gebiede van hoë variasie en hoë sitosien-inhoud aangetoon. Hierdie studie het die volgorde-inligting wat beskikbaar is vir hierdie swak gekarakteriseerde virus verbeter. Gegewe die teenwoordigheid van viroïede in baie van die kern-inskrywings, en die beskikbaarheid van NGS-datastelle van die Suid- Afrikaanse Vitis kiemplasmaversameling, is die viroïed teenwoordigheid van die versameling geassesseer. Hierdie is die eerste studie oor die diversiteit van wingerd-infekterende viroïede in Suid-Afrika, wat afgesien van die identifisering van vyf wingerd-infekterende viroïede, ook slegs die tweede internasionale rapportering is van ‘Japanese grapevine viroid (JGVd)’, en die eerste rapportering daarvan buite Japan. Doctoral 2025-04-02T13:49:55Z 2025-04-02T13:49:55Z 2024-12 Thesis https://scholar.sun.ac.za/handle/10019.1/131844 Stellenbosch University 165 pages : illustrations (some color) application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Grapevine (Vitis spp.) -- Yields Grapevine leafroll virus -- Genetics Grapes -- Breeding -- South Africa Viroids Viroid diseases of plants Grapes -- Diseases and pests -- Genetic aspects Nucleotide sequence UCTD Morgan, Seamus William Detection and identification of viruses and viroids in nuclear grapevine material in South Africa |
| title | Detection and identification of viruses and viroids in nuclear grapevine material in South Africa |
| title_full | Detection and identification of viruses and viroids in nuclear grapevine material in South Africa |
| title_fullStr | Detection and identification of viruses and viroids in nuclear grapevine material in South Africa |
| title_full_unstemmed | Detection and identification of viruses and viroids in nuclear grapevine material in South Africa |
| title_short | Detection and identification of viruses and viroids in nuclear grapevine material in South Africa |
| title_sort | detection and identification of viruses and viroids in nuclear grapevine material in south africa |
| topic | Grapevine (Vitis spp.) -- Yields Grapevine leafroll virus -- Genetics Grapes -- Breeding -- South Africa Viroids Viroid diseases of plants Grapes -- Diseases and pests -- Genetic aspects Nucleotide sequence UCTD |
| url | https://scholar.sun.ac.za/handle/10019.1/131844 |
| work_keys_str_mv | AT morganseamuswilliam detectionandidentificationofvirusesandviroidsinnucleargrapevinematerialinsouthafrica |