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Gauthier MEA, Abeynayake SW, Lelwala RV, McMaster CA, Eichner R, Morrison J, Elliott CE, Fiorito S, Dinsdale A, Pattemore J, Barrero RA. First detection and complete genome sequence of a new potexvirus naturally infecting Adenium obesum. Arch Virol 2023; 168:244. [PMID: 37676508 PMCID: PMC10484807 DOI: 10.1007/s00705-023-05871-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/06/2023] [Indexed: 09/08/2023]
Abstract
Here, we report the detection and complete genome sequence of a novel potexvirus, tentatively named "Adenium obesum virus X" (AobVX), isolated from Adenium obesum, that was sent for virus screening at Australian Government post-entry quarantine (PEQ) facilities after being imported into Australia from China. The AobVX genome is 6781 nucleotides in length excluding the poly(A) tail and is predicted to encode conserved potexvirus proteins and sequence motifs across five open reading frames. The RNA-dependent RNA polymerase of this virus shares the highest amino acid sequence similarity with that of nerine potexvirus 1 (58.7% identity) and nerine virus X (58.58% identity). This is the first report of a positive-sense single-stranded RNA virus in A. obesum related to members of the genus Potexvirus in the family Alphaflexiviridae.
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Affiliation(s)
- Marie-Emilie A Gauthier
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Shamila W Abeynayake
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
- Department of Animal, Plant and Soil Sciences, Centre for AgriBiosciences, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Ruvini V Lelwala
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Cassie A McMaster
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Robin Eichner
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Jennifer Morrison
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Candace E Elliott
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Sonia Fiorito
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Adrian Dinsdale
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Julie Pattemore
- Department of Agriculture, Forestry and Fisheries, PO Box 858, Canberra, ACT, 2061, Australia
| | - Roberto A Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD, 4000, Australia
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Quintanilha-Peixoto G, Fonseca PLC, Raya FT, Marone MP, Bortolini DE, Mieczkowski P, Olmo RP, Carazzolle MF, Voigt CA, Soares ACF, Pereira GAG, Góes-Neto A, Aguiar ERGR. The Sisal Virome: Uncovering the Viral Diversity of Agave Varieties Reveals New and Organ-Specific Viruses. Microorganisms 2021; 9:microorganisms9081704. [PMID: 34442783 PMCID: PMC8400513 DOI: 10.3390/microorganisms9081704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/29/2022] Open
Abstract
Sisal is a common name for different plant varieties in the genus Agave (especially Agave sisalana) used for high-quality natural leaf fiber extraction. Despite the economic value of these plants, we still lack information about the diversity of viruses (virome) in non-tequilana species from the genus Agave. In this work, by associating RNA and DNA deep sequencing we were able to identify 25 putative viral species infecting A. sisalana, A. fourcroydes, and Agave hybrid 11648, including one strain of Cowpea Mild Mottle Virus (CPMMV) and 24 elements likely representing new viruses. Phylogenetic analysis indicated they belong to at least six viral families: Alphaflexiviridae, Betaflexiviridae, Botourmiaviridae, Closteroviridae, Partitiviridae, Virgaviridae, and three distinct unclassified groups. We observed higher viral taxa richness in roots when compared to leaves and stems. Furthermore, leaves and stems are very similar diversity-wise, with a lower number of taxa and dominance of a single viral species. Finally, approximately 50% of the identified viruses were found in all Agave organs investigated, which suggests that they likely produce a systemic infection. This is the first metatranscriptomics study focused on viral identification in species from the genus Agave. Despite having analyzed symptomless individuals, we identified several viruses supposedly infecting Agave species, including organ-specific and systemic species. Surprisingly, some of these putative viruses are probably infecting microorganisms composing the plant microbiota. Altogether, our results reinforce the importance of unbiased strategies for the identification and monitoring of viruses in plant species, including those with asymptomatic phenotypes.
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Affiliation(s)
- Gabriel Quintanilha-Peixoto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Paula Luize Camargos Fonseca
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Fábio Trigo Raya
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Marina Pupke Marone
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Dener Eduardo Bortolini
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
| | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA;
| | - Roenick Proveti Olmo
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- CNRS UPR9022, INSERM U1257, Université de Strasbourg, 67084 Strasbourg, France
| | - Marcelo Falsarella Carazzolle
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | | | - Ana Cristina Fermino Soares
- Center of Agricultural, Environmental and Biological Sciences, Universidade Federal do Recôncavo da Bahia, Cruz das Almas 44380-000, Brazil;
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics and Evolution, Institute of Biology, Universidade Estadual de Campinas, Campinas 13083-872, Brazil; (F.T.R.); (M.P.M.); (M.F.C.); (G.A.G.P.)
| | - Aristóteles Góes-Neto
- Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (G.Q.-P.); (P.L.C.F.); (D.E.B.); (R.P.O.)
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
| | - Eric Roberto Guimarães Rocha Aguiar
- Center of Biotechnology and Genetics, Department of Biological Science, Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Brazil
- Correspondence: (A.G.-N.); (E.R.G.R.A.)
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Honma H, Tsushima D, Kawakami H, Fujihara N, Tsusaka T, Kawashimo M, Nishimura T, Fuji S. Complete nucleotide sequence of a new potexvirus, 'Cnidium virus X', isolated from Cnidium officinale in Japan. Arch Virol 2019; 164:1931-1935. [PMID: 31011816 DOI: 10.1007/s00705-019-04261-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
A flexuous virus was detected in a Cnidium officinale plant in Japan showing mosaic symptoms. The virus was assigned to the genus Potexvirus based on analysis of its complete nucleotide sequence. The genomic RNA of the virus was 5,964 nucleotides in length, excluding the 3'-terminal poly(A) tail. It contained five open reading frames (ORFs), consistent with other members of Potexvirus. The ORF sequences differ from those of previously reported potexviruses. Phylogenetic analysis indicated that the polymerase of the virus is closely related to that of strawberry mild yellow edge virus; and the CP, to those of both yam virus X and vanilla virus X. We propose that this virus be designated as "cnidium virus X" (CnVX).
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Affiliation(s)
- H Honma
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - D Tsushima
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan.
| | - H Kawakami
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - N Fujihara
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - T Tsusaka
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - M Kawashimo
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - T Nishimura
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - S Fuji
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
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Choi SH, Park MH, Ryu KH. Phylogeny, coat protein genetic variability, and transmission via seeds of Hosta Virus X. ACTA BIOLOGICA HUNGARICA 2012; 63:151-61. [PMID: 22453807 DOI: 10.1556/abiol.63.2012.1.12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The complete genome of Hosta Virus X (HVX), which is thought to be a distinct species of Potexvirus, was sequenced. Nucleotide sequences of HVX were compared with those of other members of the genus Potexvirus and phylogenetic tree was constructed. The range of identities of viral replicase open reading frame 1 (ORF1) between HVX and other potexviruses were 43.1%-55.1% and 35.9%-46.6% at the nucleotide and amino acid levels, respectively. Phylogenetic analysis was performed according to the amino acid sequence of the replicase to determine the position of HVX in the genus Potexvirus. Results from the phylogenetic analysis demonstrated that HVX was in the same group as Cassava common mosaic virus (CsCMV), Plantago asiatica mosaic virus (PlAMV), Tulip virus X (TVX), and Hydrangea ring spot virus (HdRSV). In particular, coat protein (CP) sequences among viruses from different Hosta cultivars were revealed to be less variable than those from different isolates of Potato virus X (PVX), a Potexvirus type species. In the present study, HVX was transmissible by seeds of the Hosta "Blue Cadet" cultivar. Moreover, HVX was detected in the embryo but not in the seed coat or endosperm of the seed.
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Affiliation(s)
- Sun H Choi
- Department of Horticulture, Biotechnology and Landscape Architecture, Seoul Women's University, Korea
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Complete nucleotide sequence of a new potexvirus, "Phaius virus X", isolated from Phaius flavus Lindl. Arch Virol 2007; 153:527-31. [PMID: 18183350 DOI: 10.1007/s00705-007-0010-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2007] [Accepted: 12/03/2007] [Indexed: 10/22/2022]
Abstract
A flexuous virus was isolated from cultivated Phaius flavus Lindl. plants in Japan with a latent infection. The virus was assigned to the genus Potexvirus based on morphology and analysis of its complete nucleotide sequence. The genome is 5,816 nucleotides in length, excluding the 3'-terminal poly (A) tail, and contains five open reading frames (ORFs), which is consistent with other members of the genus Potexvirus. The ORF nucleotide sequences differ from those of previously reported potexviruses, but the newly isolated virus is closely related to lily virus X and mint virus X. We propose that this virus should be designated as Phaius virus X (PhaVX).
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