Detection and diversity of grapevine virus L from a Vitis cultivar collection in Stellenbosch, South Africa

Read, David Alan; Thompson, Genevieve D.; Swanevelder, Dirk; Pietersen, Gerhard

Detection and diversity of grapevine virus L from a Vitis cultivar collection in Stellenbosch, South Africa

dc.contributor.author	Read, David Alan
dc.contributor.author	Thompson, Genevieve D.
dc.contributor.author	Swanevelder, Dirk
dc.contributor.author	Pietersen, Gerhard
dc.contributor.email	david.read@fabi.up.ac.za	en_ZA
dc.date.accessioned	2022-02-25T13:02:45Z
dc.date.issued	2021-12
dc.description	Supplementary Figure 1. Maximum likelihood phylogeny based on the amino acid sequences derived from ORF 1 of grapevine virus L (GVL) from this study and references derived from extant GVL genomes (references indicated by a solid circle marker). The cognate sequence from grapevine virus E (GVE) was used as an outgroup. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the Le Gascuel model with gamma distribution (n=5). Bootstrapping was applied (1000 replicates) and the percentage of trees in which the associated taxa clustered together is shown next to the branches. Bootstrap percentages lower than 50 are not shown. The identity of each phylogroup is shown alongside the phylogeny.	en_ZA
dc.description	Supplementary figure 2. Illustration from the RDP4 program showing the potential parents of the single recombination event that appears to have led to the establishment of recombinant variants of grapevine virus L, associated with phylogroup IV.	en_ZA
dc.description	Supplementary Table 1. Details of the grapevine virus L genomes from this study, which includes the Vitis species or cultivar (of V. vinifera) that was sampled. “H” indicates an interspecific hybrid/cultivar. The number of reps indicates how many replicate plants were associated with each species/cultivar.	en_ZA
dc.description.abstract	A total of 229 Vitis cultivars were sampled from a collection in Stellenbosch, Western Cape, South Africa and subjected to an RNAtag-seq workflow and Illumina HiSeq 2500 sequencing. Following de novo assembly and initial BLASTn analysis of the resulting reads showed that 85 cultivars were infected with grapevine virus L (GVL), with a total of 96 complete/near complete genomes. This is the first time that GVL has been detected in South Africa. Phylogenetic analyses of the amino acid sequences of ORF1 showed that GVL from this study is diverse, grouping with references from Croatia, USA and China, as well as forming a unique South African phylogroup.	en_ZA
dc.description.department	Biochemistry	en_ZA
dc.description.department	Forestry and Agricultural Biotechnology Institute (FABI)	en_ZA
dc.description.department	Genetics	en_ZA
dc.description.department	Microbiology and Plant Pathology	en_ZA
dc.description.embargo	2022-09-14
dc.description.librarian	hj2022	en_ZA
dc.description.sponsorship	The National Research Foundation of South Africa	en_ZA
dc.description.uri	https://link.springer.com/journal/10658	en_ZA
dc.identifier.citation	Read, D.A., Thompson, G.D., Swanevelder, D. et al. Detection and diversity of grapevine virus L from a Vitis cultivar collection in Stellenbosch, South Africa. European Journal of Plant Pathology 161, 1007–1011 (2021). https://doi.org/10.1007/s10658-021-02380-y.	en_ZA
dc.identifier.issn	0929-1873 (print)
dc.identifier.issn	1573-8469 (online)
dc.identifier.other	10.1007/s10658-021-02380-y
dc.identifier.uri	http://hdl.handle.net/2263/84241
dc.language.iso	en	en_ZA
dc.publisher	Springer	en_ZA
dc.rights	© Koninklijke Nederlandse Planteziektenkundige Vereniging 2021. The original publication is available at : https://link.springer.com/journal/10658.	en_ZA
dc.subject	South Africa (SA)	en_ZA
dc.subject	RNAtag-seq	en_ZA
dc.subject	Grapevine virus L (GVL)	en_ZA
dc.title	Detection and diversity of grapevine virus L from a Vitis cultivar collection in Stellenbosch, South Africa	en_ZA
dc.type	Postprint Article	en_ZA