Novel viruses associated with plants of the family Amaryllidaceae in South Africa

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

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dc.contributor.author	Read, David Alan
dc.contributor.author	Roberts, Ronel
dc.contributor.author	Swanevelder, Dirk
dc.contributor.author	Pietersen, Gerhard
dc.contributor.author	Thompson, Genevieve D.
dc.date.accessioned	2022-03-04T04:41:09Z
dc.date.issued	2021-10
dc.description	SUPPLEMENTARY INFORMATION : Supplementary Fig. 1: Foliar symptoms associated with each plant sampled in this study. The unique sample accession number is shown in the bottom right-hand corner of each image. Images A to L show the Agapanthus cultivars sampled, M to Q the Clivia cultivars, R is a cultivar of Hippeastrum and S shows the single plant of Scadoxus puniceus that was sampled.	en_ZA
dc.description	Supplementary Fig. 2: Alignment of the minus-strand priming site of Agapanthus tungro virus (AgTV) with whole genome sequences of Rice tungro bacilliform virus (RTBV).	en_ZA
dc.description	Supplementary Figure 3.1: Maximum likelihood phylogeny based on the complete nucleotide sequences of Agapanthus tungro virus variants (sources from this study indicated by a solid circle marker) and selected members of the Caulimoviridae family. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the General Time Reversible 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 viral genus corresponding to each reference is shown in brackets, while the sample number is indicated for samples related to this study. Supplementary Figure 3.2: Maximum likelihood phylogeny based on the amino acid sequences of the heat shock protein homolog of Agapanthus velarivirus variants (sources from this study indicated by solid circle markers) and selected members of the Closteroviridae family. 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 viral genus corresponding to each reference is shown in brackets, while the sample number is indicated for samples related to this study. A heat shock protein 70 amino acid sequence of Arabidopsis thaliana was used as an outgroup. Supplementary Figure 3.3: Maximum likelihood phylogeny based on the amino acid sequences of the replicase gene of members of the Betaflexiviridae family found in this study (sources from this study indicated by solid circle markers) and selected members of the same family. These include the nerine latent virus, well as novel viruses, clivia carlavirus A and agapanthus virus A, as well as. 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). All positions containing gaps and missing data were eliminated (complete deletion option). 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 viral genus corresponding to each reference is shown in brackets, while the sample number is indicated for samples related to this study. Supplementary figure 3.4: Maximum likelihood phylogeny based on the amino acid sequences of the polyprotein of Hippeastrum mosaic virus and the novel clivia yellow stripe virus strains (sources from this study indicated by solid circle markers) and selected members of the Potyvirus genus. The phylogeny represents the tree with the highest log likelihood and was generated in MEGA X using the Le Gascuel model. All positions containing gaps and missing data were eliminated (complete deletion option). 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. Representatives from other genera of the Potyviridae family form the outgroup, with the genus name corresponding to each genus shown in brackets. Supplementary figure 3.5: Maximum likelihood phylogeny based on the amino acid sequences of the produ ct of the N gene of scadoxus chlorotic ringspot virus (sources from this study indicated by a solid circle marker) and selected members of the Orthotospovirus genus. 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). All positions were used in the analysis. 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.	en_ZA
dc.description	Supplementary table 1: The pre- and post-assembly read numbers associated with each sample. The number of contigs exceeding 1000bp, for both the CLC Genomics Workbench and metaSPAdes assemblies, are listed. The datasets are linked to sample specific NCBI Biosample accession numbers.	en_ZA
dc.description	Supplementary Table 2: Primers used in all PCR, RT-PCR and RACE assays. The genomic target region, melting temperature (Tm) and product size (RT-PCR) are listed. Key: CP – Coat protein; Pol – Polyprotein; AgTV – Agapanthus tungro virus; AgVV – Agapanthus velarivirus; AgVA – Agapanthus virus A; AgCVB – Agapanthus carlavirus B; ClCVA – Clivia carlavirus A; CYSV – Clivia yellow stripe virus, HiMV – Hippeastrum mosaic virus; NeLV – Nerine latent virus; ScSRV – Scadoxus chlorotic ringspot virus; GSP – Gene specific primer; -F – Forward; -R – Reverse.	en_ZA
dc.description	Supplementary Table 3: List of viruses from this study with their associated sample and NCBI GenBank accession numbers. Genome length, assembling software used for the specific genome’s assembly, the number of reads involved in the assembly, as well as the average coverage and the percentage of total reads, are also presented. AgTV – Agapanthus tungro virus; AgVV – Agapanthus velarivirus, AgVA – Agapanthus virus A, ClCVA – Clivia carlavirus A, NeLV – Nerine latent virus, HiMV – Hippeastrum mosaic virus, ScCRV – Scadoxus chlorotic ringspot virus.	en_ZA
dc.description.abstract	Nineteen samples from members of the plant genera Agapanthus, Clivia, Hippeastrum, and Scadoxus were collected from gardens in the Gauteng and Western Cape provinces of South Africa. The plants displayed highly variable symptoms of viral disease, including chlorosis, necrosis, streaking, and ringspot. RNAtag-seq was used to characterize the associated viral populations. Plants of the genus Agapanthus were found to be associated with three novel viruses from the families Caulimoviridae, Closteroviridae, and Betaflexiviridae; plants of the genus Clivia were associated with novel members of the families Potyviridae and Betaflexiviridae; and plants of the genus Scadoxus were associated with a novel member of the family Tospoviridae. Nerine latent virus was associated with plants of the genera Agapanthus, Clivia, and Hippeastrum, while hippeastrum mosaic virus was associated exclusively with a Hippeastrum cultivar.	en_ZA
dc.description.department	Forestry and Agricultural Biotechnology Institute (FABI)	en_ZA
dc.description.embargo	2022-07-19
dc.description.librarian	hj2022	en_ZA
dc.description.uri	http://link.springer.com/journal/705	en_ZA
dc.identifier.citation	Read, D.A., Roberts, R., Swanevelder, D. et al. Novel viruses associated with plants of the family Amaryllidaceae in South Africa. Archives of Virology 166, 2817–2823 (2021). https://doi.org/10.1007/s00705-021-05170-3.	en_ZA
dc.identifier.issn	0304-8608 (print)
dc.identifier.issn	1432-8798 (online)
dc.identifier.other	10.1007/s00705-021-05170-3
dc.identifier.uri	http://hdl.handle.net/2263/84331
dc.language.iso	en	en_ZA
dc.publisher	Springer	en_ZA
dc.rights	© 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature. The original publication is available at : http://link.springer.comjournal/705.	en_ZA
dc.subject	Novel viruses	en_ZA
dc.subject	Amaryllidaceae	en_ZA
dc.subject	South Africa (SA)	en_ZA
dc.subject	Agapanthus	en_ZA
dc.subject	Clivia	en_ZA
dc.subject	Hippeastrum	en_ZA
dc.title	Novel viruses associated with plants of the family Amaryllidaceae in South Africa	en_ZA
dc.type	Postprint Article	en_ZA