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

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.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.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.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.The National Research Foundation of South Africahttps://link.springer.com/journal/106582022-09-14hj2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog