Figure 1.
Genome organization of Donkey orchid symptomless virus.
Genome organization of Donkey orchid symptomless virus isolate Mariginiup11 (a), showing the nucleotide positions of open reading frames (ORF) including putative coat protein (CP), movement protein (MP), and untranslated regions (UTR), and calculated sizes of putative proteins. Open reading frames were designated with respect to the replicase (ORF1). Diagrams of genome organization of (b) Garlic virus A (family Alphaflexiviridae, genus Allexivirus) encodes a 40-kDa protein (P40) and nucleotide binding protein (NTBP), (c) Plantago asiatica mosaic virus (Alphaflexiviridae, Potexvirus), (d) Tomato bushy stunt virus (TBSV) (Tombusviridae, Tombusvirus), (e) Sorghum chlorotic spot virus (SCSV) (Tombusviridae, Furovirus), and (f) Turnip yellow mosaic virus (Tymoviridae, Tymovirus) are shown (not drawn to scale). Within the replicase, the papain-like protease (P), methyltransferase (M), helicase (H), and RNA-dependent RNA polymerase (RdRp) domains are indicated where present. In TBSV and SCSV, read-through opal stop codons are indicated by a dotted line, R-T = read-through region, and C-R = cysteine-rich protein.
Figure 2.
Evolutionary relationships of Donkey orchid symptomless virus replicase and coat protein.
Donkey orchid symptomless virus (DOSV) (represented with a black dot) replicase (a), and coat protein (b) using a General Reverse Transcription model with homologous proteins of representative viruses within the order Tymovirales. Relationships were inferred for amino acid sequences using the Maximum Likelihood method. The abbreviated names of the viruses used and their GenBank accession codes are shown. Genus names are given on the right. Genus names are colored according to family classification. Orange represents the Alphaflexiviridae, red represents the Gammaflexiviridae, green represents the Tymoviridae, and blue represents the Betaflexiviridae. The position of DOSV isolates are shown as black dots. ACLSV, Apple chlorotic leaf spot virus; ALV, Apricot latent virus; APLV, Andean potato latent virus; ASGV, Apple stem grooving virus; ASPV, Apple stem pitting virus; BVF, Botrytis virus F; BVX, Botrytis virus X; CLBV, Citrus leaf blotch virus; CMLV, Cherry mottle leaf virus; CVA, Cherry virus A; GarVA, Garlic virus A; GarVC, Garlic virus C; GarVE, Garlic virus E; GCLV, Garlic common latent virus; GFkV, Grapevine fleck virus; GVA, Grapevine virus A; GVB, Grapevine virus B; ICRSV, Indian citrus ringspot virus; LoLV, Lolium latent virus; MRFV, Maize rayado fino virus; OVX, Opuntia virus X; PepMV, Pepino mosaic virus; PlAMV, Plantago asiatica mosaic virus; PVT, Potato virus T; PVX, Potato virus X; SLV, Shallot latent virus; SMYEV, Strawberry mild yellow edge virus; SsDRV, Sclerotinia sclerotiorum debilitation-associated RNA virus; SWMV, Switchgrass mosaic virus; TYMV, Turnip yellow mosaic virus; WClMV, White clover mosaic virus. The percentage of replicate trees above 60 % in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Units are amino acid substitutions per site.
Figure 3.
Evolutionary relationships of Donkey orchid symptomless virus movement protein.
The movement protein of Donkey orchid symptomless virus (DOSV) isolates (represented by black dots) compared with representative viruses that have a 3A-like movement protein. Phylogeny is inferred with the Maximum Likelihood method using a General Reverse Transcription model. Abbreviated virus names and their GenBank accession codes are shown. Genus names are given on the right. Blue represents the family Bromoviridae, purple represents the genus Umbravirus (family unassigned), brown represents the Virgaviridae, and pink represents the Tombusviridae. TAV, Tomato aspermy virus; PSV, Peanut stunt virus; CMV, Cucumber mosaic virus; MYFV, Melandrium yellow fleck virus; BMV, Brome mosaic virus; SBLV, Spring beauty latent virus; CCMV, Cowpea chlorotic mottle virus; TBTV, Tobacco bushy top virus; PEMV-2, Pea enation mosaic virus-2; CMoV, Carrot mottle virus; SbWMV, Soil-borne wheat mosaic virus; SCSV, Sorghum chlorotic spot virus; PZSV, Pelargonium zonate spot virus; CRSV, Carnation ringspot virus. The percentage of replicate trees above 60 % in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches. Units are amino acid substitutions per site.