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Moyo L, Raikhy G, Hamid A, Mallik I, Gudmestad NC, Gray S, Pappu HR. Phylogenetics of tobacco rattle virus isolates from potato (Solanum tuberosum L.) in the USA: a multi-gene approach to evolutionary lineage. Virus Genes 2022; 58:42-52. [PMID: 34671909 DOI: 10.1007/s11262-021-01875-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/05/2021] [Indexed: 01/22/2023]
Abstract
Tobacco rattle virus (TRV) is an important soil-borne virus of potato that is transmitted by stubby-root nematodes. TRV causes corky ringspot, a tuber disease of economic importance to potato production. Utilizing protein-coding regions of the whole genome and a range of computational tools, the genetic diversity, and population structure of TRV isolates from several potato-growing regions (Colorado, Idaho, Indiana, Minnesota, Nebraska, North Dakota, and Washington State) in the USA were determined. Phylogenetic analyses based on RNA2 nucleotide sequences, the coat protein (CP) and nematode transmission (2b) genes, showed geographical clustering of USA isolates with previously known American isolates, while European isolates grouped in a distinct cluster. This was corroborated by the observed genetic differentiation and infrequent gene flow between American and European isolates. Low genetic diversity was revealed among American isolates compared to European isolates. Phylogenetic clustering based on RNA1 genes (RdRp, RdRp-RT, and 1a) were all largely incongruent to that of 1b gene (virus suppressor of RNA silencing). This genetic incongruence suggested the influence of recombination. Furthermore, the RdRp, RdRp-RT, and 1a genes were predicted to be more conserved and under negative selection, while the 1b gene was less constrained. Different evolutionary lineages between TRV RNA1 and RNA2 genomic segments were revealed.
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Affiliation(s)
- Lindani Moyo
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA
- Department of Environmental Science and Health, National University of Science and Technology, PO Box AC939, Ascot, Bulawayo, Zimbabwe
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7600, South Africa
| | - Gaurav Raikhy
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Aflaq Hamid
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Ipsita Mallik
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Neil C Gudmestad
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Stewart Gray
- Section of Plant Pathology and Plant-Microbe Biology, School of Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Hanu R Pappu
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA.
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, WA, 99164, USA.
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Rahman J, Baldwin IT, Gase K. California TRV-based VIGS vectors mediate gene silencing at elevated temperatures but with greater growth stunting. BMC PLANT BIOLOGY 2021; 21:553. [PMID: 34809584 PMCID: PMC8607596 DOI: 10.1186/s12870-021-03324-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/08/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Tobacco rattle virus (TRV) based virus-induced gene silencing (VIGS), a widely used functional genomics tool, requires growth temperatures typically lower than those of the plant's native environment. Enabling VIGS under native conditions in the field according to applicable safety regulations could be a revolutionary advance for ecological research. RESULTS Here, we report the development of an enhanced thermal tolerant VIGS vector system based on a TRV California isolate. cDNA clones representing the whole viral genome were sequenced and used to construct separate binary plant transformation vectors for functional elements of RNA1 (6765 nt) and RNA2 (3682 nt). VIGS of target genes was induced by transient transformation of the host plant with both vectors or by treating the host plant with sap from already VIGS induced plants. In Nicotiana attenuata the silencing efficiency of the PDS (phytoene desaturase) gene was 90% at 28 °C and 78% at 30 °C. Silencing at these temperatures was more prominent and durable than silencing induced by the widely used TRV PpK20-based pBINTRA6/pTV00 system, but was associated with a viral phenotype. Differences in the suppressor protein and RNA dependent RNA polymerase sequences between the TRV California isolate and PpK20 may be the reason for their different thermal tolerance. CONCLUSIONS The new TRV California-based VIGS vectors induce gene silencing in Nicotiana attenuata at higher temperatures than the existing pBINTRA6/pTV00 vector system, but cause greater growth defects. The new vector system opens up an avenue to study genes functions in planta under field conditions.
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Affiliation(s)
- Jamilur Rahman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
- Present address: Department of Genetics and Plant Breeding, Sher-e-Bangla Agricultural University, Dhaka, 1207 Bangladesh
| | - Ian T. Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
| | - Klaus Gase
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knoell-Str. 8, 07745 Jena, Germany
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Batista ARS, Nicolini C, Rodrigues KB, Melo FL, Vasques RM, de Macêdo MA, Inoue-Nagata AK, Nagata T. Unique RNA 2 sequences of two Brazilian isolates of Pepper ringspot virus, a tobravirus. Virus Genes 2014; 49:169-73. [DOI: 10.1007/s11262-014-1066-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/01/2014] [Indexed: 10/25/2022]
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MacFarlane SA, Neilson R. Testing of transmission of tobraviruses by nematodes. CURRENT PROTOCOLS IN MICROBIOLOGY 2009; Chapter 16:Unit16B.5. [PMID: 19235148 DOI: 10.1002/9780471729259.mc16b05s12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Virus diseases often are spread between plants by vector organisms, some of which live below ground (e.g., fungi and nematodes) and feed on the plant root system. Tobraviruses are one of only two groups of plant viruses that have nematode vectors. They are primarily viruses of weed plants but can cause significant economic damage in a range of cultivated crops including potato, peas, beans, and many ornamental species. Identifying these viruses and their nematode vectors is a very important part of the struggle to combat disease in crop plants, and requires specialized techniques that will be discussed further in this unit.
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