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.
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).
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.
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.
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.
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.