Table 1.
Trees sequenced in this study.
Table 2.
Number of reads and contigs obtained from sequencing and bioinformatics analysis.
Table 3.
Summary of known viruses present in trees symptomatic and asymptomatic for apple declinea.
Table 4.
Putative novel viruses detected in apple samples.
Fig 1.
Detection of novel viruses by RT-PCR.
Detection of A) Apple ilarvirus 1 in 5R, B) Apple narna-like virus 2 in 3R, C) Apple ourmia-like virus 1 in 3L, D) Apple ourmia-like virus 2 in 5R, E) Apple ourmia-like virus 3 in 3R and 6R, F) Apple partiti-like virus 1 in 1R and 2R, G) Apple partiti-like virus 2 in 1R and 2R, H) Apple partiti-like virus 3 in 2R, I) Apple tombus-like virus 2 in 6R, J) Apple virus A in 3R, K) Apple virus B in 5R, L) Apple virus C in 1R, and M) Apple virus D in 2R. Sizes for the ladder are, in descending order, 1.5 kb, 1 kb, 900 bp, 800 bp, 700 bp, 600 bp, 500 bp, 400 bp, 300 bp, 200 bp, and 100 bp.
Fig 2.
A) RNA2 and RNA3 for Apple ilarvirus 1. The predicted open reading frames for the replicase in RNA2 and the coat and movement proteins in RNA 3 are shown. B) The protein phylogenetic tree for the replicase, C) movement protein, and D) coat protein. Accession numbers for nucleotide and protein sequences are provided in S4 Table.
Fig 3.
Apple tombus-like viruses 1 and 2.
A) Partial genomes showing the open reading frames for ORF1, RdRp, and the capsid. B) Phylogenetic tree for the RdRp amino acid sequence, C) ORF1, and D) the capsid. Accession numbers are provided in S4 Table.
Fig 4.
A) Genome showing five open reading frames, including two capsid proteins and a polyprotein. B) Phylogenetic tree of the polyprotein amino acid sequence. C) Phylogenetic tree of the capsid (ORF4) protein. Accession numbers are provided in S4 Table.
Fig 5.
A) Genome showing four open reading frames, including a peptidase and RdRp. B) Phylogenetic tree of the RdRp and C) the peptidase. Accession numbers are provided in S4 Table.
Fig 6.
Apple narna-like, ourmia-like, and partiti-like viruses.
A) Genomes showing the RdRp for Apple narna-like viruses 1 and 2, Apple ourmia-like viruses 1, 2, and 3, and Apple partiti-like viruses 1, 2, and 3. B) Phylogenetic tree of the RdRp for Apple narna-like viruses 1 and 2. C) Phylogenetic tree of the RdRp for Apple ourmia-like viruses 1, 2, and 3. D) Phylogenetic tree of the RdRp of Apple partiti-like viruses 1, 2, and 3. Accession numbers are provided in S4 Table.
Fig 7.
A) Genome of Apple virus C showing predicted open reading frames for the RdRp and capsid. B) Phylogenetic tree of the RdRp. C) Phylogenetic tree of the capsid. Accession numbers are provided in S4 Table.
Fig 8.
Apple viruses A, B, and D. A) Genomes showing predicted open reading frames for Apple virus A, B, and D. B) Phylogenetic tree of polyprotein for Apple virus A, C) Apple virus B, and D) Apple virus D. Accession numbers are provided in S4 Table.