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Donkey orchid symptomless virus: a viral 'platypus' from Australian terrestrial orchids.

Wylie SJ, Li H, Jones MG - PLoS ONE (2013)

Bottom Line: A 69-kDa protein (ORF1) that overlapped the replicase shared low identity with MPs of plant tymoviruses (Tymoviridae).The putative 25-kDa movement protein (MP) (ORF7) shared limited (27%) identity with 3A-like MPs of members of the plant-infecting Tombusviridae and Virgaviridae.Transmissibility was shown when DOSV systemically infected Nicotiana benthamiana plants.

View Article: PubMed Central - PubMed

Affiliation: Australian Plant Virology Laboratory, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Australia.

ABSTRACT
Complete and partial genome sequences of two isolates of an unusual new plant virus, designated Donkey orchid symptomless virus (DOSV) were identified using a high-throughput sequencing approach. The virus was identified from asymptomatic plants of Australian terrestrial orchid Diuris longifolia (Common donkey orchid) growing in a remnant forest patch near Perth, western Australia. DOSV was identified from two D. longifolia plants of 264 tested, and from at least one plant of 129 Caladenia latifolia (pink fairy orchid) plants tested. Phylogenetic analysis of the genome revealed open reading frames (ORF) encoding seven putative proteins of apparently disparate origins. A 69-kDa protein (ORF1) that overlapped the replicase shared low identity with MPs of plant tymoviruses (Tymoviridae). A 157-kDa replicase (ORF2) and 22-kDa coat protein (ORF4) shared 32% and 40% amino acid identity, respectively, with homologous proteins encoded by members of the plant virus family Alphaflexiviridae. A 44-kDa protein (ORF3) shared low identity with myosin and an autophagy protein from Squirrelpox virus. A 27-kDa protein (ORF5) shared no identity with described proteins. A 14-kDa protein (ORF6) shared limited sequence identity (26%) over a limited region of the envelope glycoprotein precursor of mammal-infecting Crimea-Congo hemorrhagic fever virus (Bunyaviridae). The putative 25-kDa movement protein (MP) (ORF7) shared limited (27%) identity with 3A-like MPs of members of the plant-infecting Tombusviridae and Virgaviridae. Transmissibility was shown when DOSV systemically infected Nicotiana benthamiana plants. Structure and organization of the domains within the putative replicase of DOSV suggests a common evolutionary origin with 'potexvirus-like' replicases of viruses within the Alphaflexiviridae and Tymoviridae, and the CP appears to be ancestral to CPs of allexiviruses (Alphaflexiviridae). The MP shares an evolutionary history with MPs of dianthoviruses, but the other putative proteins are distant from plant viruses. DOSV is not readily classified in current lower order virus taxa.

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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) GarlicvirusA (family Alphaflexiviridae, genus Allexivirus) encodes a 40-kDa protein (P40) and nucleotide binding protein (NTBP), (c) Plantago asiaticamosaicvirus (Alphaflexiviridae, Potexvirus), (d) Tomato bushy stunt virus (TBSV) (Tombusviridae, Tombusvirus), (e) Sorghum chlorotic spot virus (SCSV) (Tombusviridae, Furovirus), and (f) Turnipyellowmosaicvirus (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.
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pone-0079587-g001: 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) GarlicvirusA (family Alphaflexiviridae, genus Allexivirus) encodes a 40-kDa protein (P40) and nucleotide binding protein (NTBP), (c) Plantago asiaticamosaicvirus (Alphaflexiviridae, Potexvirus), (d) Tomato bushy stunt virus (TBSV) (Tombusviridae, Tombusvirus), (e) Sorghum chlorotic spot virus (SCSV) (Tombusviridae, Furovirus), and (f) Turnipyellowmosaicvirus (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.

Mentions: The genomes of both isolates contained seven open reading frames (ORF) flanked by a 5’ untranslated region (UTR) and 3’ UTR (Figure 1), although this is assumed for isolate Mariginiup12 because the 5’ terminal region of the genome was not determined. A 3’ polyadenylation sequence was not detected for either genome. Neither the 5’UTR nor the 3’UTR shared identity with those of other viruses. The 3’UTR sequences of the two isolates were 146-147 nt in length and shared 91.8 % nt sequence identity.


Donkey orchid symptomless virus: a viral 'platypus' from Australian terrestrial orchids.

Wylie SJ, Li H, Jones MG - PLoS ONE (2013)

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) GarlicvirusA (family Alphaflexiviridae, genus Allexivirus) encodes a 40-kDa protein (P40) and nucleotide binding protein (NTBP), (c) Plantago asiaticamosaicvirus (Alphaflexiviridae, Potexvirus), (d) Tomato bushy stunt virus (TBSV) (Tombusviridae, Tombusvirus), (e) Sorghum chlorotic spot virus (SCSV) (Tombusviridae, Furovirus), and (f) Turnipyellowmosaicvirus (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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3818234&req=5

pone-0079587-g001: 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) GarlicvirusA (family Alphaflexiviridae, genus Allexivirus) encodes a 40-kDa protein (P40) and nucleotide binding protein (NTBP), (c) Plantago asiaticamosaicvirus (Alphaflexiviridae, Potexvirus), (d) Tomato bushy stunt virus (TBSV) (Tombusviridae, Tombusvirus), (e) Sorghum chlorotic spot virus (SCSV) (Tombusviridae, Furovirus), and (f) Turnipyellowmosaicvirus (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.
Mentions: The genomes of both isolates contained seven open reading frames (ORF) flanked by a 5’ untranslated region (UTR) and 3’ UTR (Figure 1), although this is assumed for isolate Mariginiup12 because the 5’ terminal region of the genome was not determined. A 3’ polyadenylation sequence was not detected for either genome. Neither the 5’UTR nor the 3’UTR shared identity with those of other viruses. The 3’UTR sequences of the two isolates were 146-147 nt in length and shared 91.8 % nt sequence identity.

Bottom Line: A 69-kDa protein (ORF1) that overlapped the replicase shared low identity with MPs of plant tymoviruses (Tymoviridae).The putative 25-kDa movement protein (MP) (ORF7) shared limited (27%) identity with 3A-like MPs of members of the plant-infecting Tombusviridae and Virgaviridae.Transmissibility was shown when DOSV systemically infected Nicotiana benthamiana plants.

View Article: PubMed Central - PubMed

Affiliation: Australian Plant Virology Laboratory, Western Australian State Agricultural Biotechnology Centre, School of Veterinary and Life Sciences, Murdoch University, Perth, Australia.

ABSTRACT
Complete and partial genome sequences of two isolates of an unusual new plant virus, designated Donkey orchid symptomless virus (DOSV) were identified using a high-throughput sequencing approach. The virus was identified from asymptomatic plants of Australian terrestrial orchid Diuris longifolia (Common donkey orchid) growing in a remnant forest patch near Perth, western Australia. DOSV was identified from two D. longifolia plants of 264 tested, and from at least one plant of 129 Caladenia latifolia (pink fairy orchid) plants tested. Phylogenetic analysis of the genome revealed open reading frames (ORF) encoding seven putative proteins of apparently disparate origins. A 69-kDa protein (ORF1) that overlapped the replicase shared low identity with MPs of plant tymoviruses (Tymoviridae). A 157-kDa replicase (ORF2) and 22-kDa coat protein (ORF4) shared 32% and 40% amino acid identity, respectively, with homologous proteins encoded by members of the plant virus family Alphaflexiviridae. A 44-kDa protein (ORF3) shared low identity with myosin and an autophagy protein from Squirrelpox virus. A 27-kDa protein (ORF5) shared no identity with described proteins. A 14-kDa protein (ORF6) shared limited sequence identity (26%) over a limited region of the envelope glycoprotein precursor of mammal-infecting Crimea-Congo hemorrhagic fever virus (Bunyaviridae). The putative 25-kDa movement protein (MP) (ORF7) shared limited (27%) identity with 3A-like MPs of members of the plant-infecting Tombusviridae and Virgaviridae. Transmissibility was shown when DOSV systemically infected Nicotiana benthamiana plants. Structure and organization of the domains within the putative replicase of DOSV suggests a common evolutionary origin with 'potexvirus-like' replicases of viruses within the Alphaflexiviridae and Tymoviridae, and the CP appears to be ancestral to CPs of allexiviruses (Alphaflexiviridae). The MP shares an evolutionary history with MPs of dianthoviruses, but the other putative proteins are distant from plant viruses. DOSV is not readily classified in current lower order virus taxa.

Show MeSH
Related in: MedlinePlus