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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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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, Applechloroticleafspotvirus; ALV, Apricotlatentvirus; APLV, Andeanpotatolatentvirus; ASGV, Applestemgroovingvirus; ASPV, Applestempittingvirus; BVF, Botrytis virusF; BVX, Botrytis virusX; CLBV, Citrus leafblotchvirus; CMLV, Cherrymottleleafvirus; CVA, CherryvirusA; GarVA, GarlicvirusA; GarVC, GarlicvirusC; GarVE, GarlicvirusE; GCLV, Garliccommonlatentvirus; GFkV, Grapevinefleckvirus; GVA, GrapevinevirusA; GVB, GrapevinevirusB; ICRSV, Indiancitrusringspotvirus; LoLV, Lolium latentvirus; MRFV, Maizerayadofinovirus; OVX, Opuntia virusX; PepMV, Pepinomosaicvirus; PlAMV, Plantago asiaticamosaicvirus; PVT, PotatovirusT; PVX, PotatovirusX; SLV, Shallotlatentvirus; SMYEV, Strawberrymildyellowedgevirus; SsDRV, Sclerotinia sclerotiorumdebilitation-associatedRNAvirus; SWMV, Switchgrassmosaicvirus; TYMV, Turnipyellowmosaicvirus; WClMV, Whiteclovermosaicvirus. 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.
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pone-0079587-g002: 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, Applechloroticleafspotvirus; ALV, Apricotlatentvirus; APLV, Andeanpotatolatentvirus; ASGV, Applestemgroovingvirus; ASPV, Applestempittingvirus; BVF, Botrytis virusF; BVX, Botrytis virusX; CLBV, Citrus leafblotchvirus; CMLV, Cherrymottleleafvirus; CVA, CherryvirusA; GarVA, GarlicvirusA; GarVC, GarlicvirusC; GarVE, GarlicvirusE; GCLV, Garliccommonlatentvirus; GFkV, Grapevinefleckvirus; GVA, GrapevinevirusA; GVB, GrapevinevirusB; ICRSV, Indiancitrusringspotvirus; LoLV, Lolium latentvirus; MRFV, Maizerayadofinovirus; OVX, Opuntia virusX; PepMV, Pepinomosaicvirus; PlAMV, Plantago asiaticamosaicvirus; PVT, PotatovirusT; PVX, PotatovirusX; SLV, Shallotlatentvirus; SMYEV, Strawberrymildyellowedgevirus; SsDRV, Sclerotinia sclerotiorumdebilitation-associatedRNAvirus; SWMV, Switchgrassmosaicvirus; TYMV, Turnipyellowmosaicvirus; WClMV, Whiteclovermosaicvirus. 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.

Mentions: The complete putative viral replicase from isolate Mariginiup11 was 4188 nt in length, and is calculated to encode a protein of 157.6-kDa. The N-terminus of the replicase was not obtained for isolate Mariginiup12. Aligned, the replicases of the two isolates shared 95.5 % amino acid (91.5 % nt) identity over the common region. The complete amino acid sequence of the replicase of isolate Mariginiup11 shared highest identity (31-32 %) with replicase sequences of members of the family Alphaflexiviridae (Table 1). Its sequence fits with high confidence between members of the Alphaflexiviridae and a group formed by members of the Gammaflexiviridae and the Tymoviridae (Figure 2a). CDD and InterProScan [18 predicted the presence of three active domains within the replicase: a viral methyltransferase (Met), a helicase, and an RNA-dependent RNA polymerase (RdRp), typical of some flexivirus genomes (Figure 1). The putative Met domain was approximately 1659 nt in length. The conserved Met motif DEAD [19] was present at its C-terminal region from nt 1944-1955. A helicase domain estimated to be 613 nt long contained conserved motifs A (GKS) and B (DE) [20], which were identified from nt positions 2040-2048 and 2217–2222, respectively. The putative RdRp domain estimated to be 696 nt in length contained the conserved core motif S/TG (X3)T(X3)NS/T(X22)GDD (where X is any amino acid residue) [21] at nt 3690-3797.


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

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

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, Applechloroticleafspotvirus; ALV, Apricotlatentvirus; APLV, Andeanpotatolatentvirus; ASGV, Applestemgroovingvirus; ASPV, Applestempittingvirus; BVF, Botrytis virusF; BVX, Botrytis virusX; CLBV, Citrus leafblotchvirus; CMLV, Cherrymottleleafvirus; CVA, CherryvirusA; GarVA, GarlicvirusA; GarVC, GarlicvirusC; GarVE, GarlicvirusE; GCLV, Garliccommonlatentvirus; GFkV, Grapevinefleckvirus; GVA, GrapevinevirusA; GVB, GrapevinevirusB; ICRSV, Indiancitrusringspotvirus; LoLV, Lolium latentvirus; MRFV, Maizerayadofinovirus; OVX, Opuntia virusX; PepMV, Pepinomosaicvirus; PlAMV, Plantago asiaticamosaicvirus; PVT, PotatovirusT; PVX, PotatovirusX; SLV, Shallotlatentvirus; SMYEV, Strawberrymildyellowedgevirus; SsDRV, Sclerotinia sclerotiorumdebilitation-associatedRNAvirus; SWMV, Switchgrassmosaicvirus; TYMV, Turnipyellowmosaicvirus; WClMV, Whiteclovermosaicvirus. 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.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0079587-g002: 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, Applechloroticleafspotvirus; ALV, Apricotlatentvirus; APLV, Andeanpotatolatentvirus; ASGV, Applestemgroovingvirus; ASPV, Applestempittingvirus; BVF, Botrytis virusF; BVX, Botrytis virusX; CLBV, Citrus leafblotchvirus; CMLV, Cherrymottleleafvirus; CVA, CherryvirusA; GarVA, GarlicvirusA; GarVC, GarlicvirusC; GarVE, GarlicvirusE; GCLV, Garliccommonlatentvirus; GFkV, Grapevinefleckvirus; GVA, GrapevinevirusA; GVB, GrapevinevirusB; ICRSV, Indiancitrusringspotvirus; LoLV, Lolium latentvirus; MRFV, Maizerayadofinovirus; OVX, Opuntia virusX; PepMV, Pepinomosaicvirus; PlAMV, Plantago asiaticamosaicvirus; PVT, PotatovirusT; PVX, PotatovirusX; SLV, Shallotlatentvirus; SMYEV, Strawberrymildyellowedgevirus; SsDRV, Sclerotinia sclerotiorumdebilitation-associatedRNAvirus; SWMV, Switchgrassmosaicvirus; TYMV, Turnipyellowmosaicvirus; WClMV, Whiteclovermosaicvirus. 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.
Mentions: The complete putative viral replicase from isolate Mariginiup11 was 4188 nt in length, and is calculated to encode a protein of 157.6-kDa. The N-terminus of the replicase was not obtained for isolate Mariginiup12. Aligned, the replicases of the two isolates shared 95.5 % amino acid (91.5 % nt) identity over the common region. The complete amino acid sequence of the replicase of isolate Mariginiup11 shared highest identity (31-32 %) with replicase sequences of members of the family Alphaflexiviridae (Table 1). Its sequence fits with high confidence between members of the Alphaflexiviridae and a group formed by members of the Gammaflexiviridae and the Tymoviridae (Figure 2a). CDD and InterProScan [18 predicted the presence of three active domains within the replicase: a viral methyltransferase (Met), a helicase, and an RNA-dependent RNA polymerase (RdRp), typical of some flexivirus genomes (Figure 1). The putative Met domain was approximately 1659 nt in length. The conserved Met motif DEAD [19] was present at its C-terminal region from nt 1944-1955. A helicase domain estimated to be 613 nt long contained conserved motifs A (GKS) and B (DE) [20], which were identified from nt positions 2040-2048 and 2217–2222, respectively. The putative RdRp domain estimated to be 696 nt in length contained the conserved core motif S/TG (X3)T(X3)NS/T(X22)GDD (where X is any amino acid residue) [21] at nt 3690-3797.

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