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Abrahamian P, Grinstead S, Kinard GR, Goenaga R, Rott P, Mollov D. Complete sequence and genome characterization of miscanthus virus M, a new betaflexivirus from Miscanthus sp. Arch Virol 2024; 169:27. [PMID: 38214767 DOI: 10.1007/s00705-024-05966-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/21/2023] [Indexed: 01/13/2024]
Abstract
A novel betaflexivirus, tentatively named "miscanthus virus M" (MiVM), was isolated from Miscanthus sp. The complete genome of MiVM is 7,388 nt in length (excluding the poly(A) tail). It contains five open reading frames and has a genome organization similar to those of members of the families Alphaflexiviridae and Betaflexiviridae (subfamily Quinvirinae). The amino acid sequences of both the replicase and coat protein shared less than 45% identity with the corresponding sequences of members of either family. Phylogenetic analysis confirmed that MiVM belongs to the family Betaflexiviridae and subfamily Quinvirinae but it was too distantly related to be included in any currently recognized genus in this family. We therefore propose that miscanthus virus M represents a new species and a new genus in the family Betaflexiviridae.
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Affiliation(s)
- Peter Abrahamian
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, USA.
| | - Samuel Grinstead
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, USA
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, MD, USA
| | - Gary R Kinard
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, USA
| | - Ricardo Goenaga
- USDA-ARS Tropical Agriculture Research Station, Mayaguez, PR, USA
| | - Philippe Rott
- CIRAD, UMR PHIM, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Dimitre Mollov
- USDA-ARS National Germplasm Resources Laboratory, Beltsville, MD, USA.
- USDA-ARS Horticultural Crops Research Unit, Corvallis, OR, 97330, USA.
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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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Lelwala RV, LeBlanc Z, Gauthier MEA, Elliott CE, Constable FE, Murphy G, Tyle C, Dinsdale A, Whattam M, Pattemore J, Barrero RA. Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants. Viruses 2022; 14:v14071480. [PMID: 35891459 PMCID: PMC9317486 DOI: 10.3390/v14071480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21–22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ.
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Affiliation(s)
- Ruvini V. Lelwala
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Zacharie LeBlanc
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Marie-Emilie A. Gauthier
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Greg Murphy
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Callum Tyle
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Adrian Dinsdale
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Mark Whattam
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Roberto A. Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Correspondence:
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