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Qin Y, Lu S, Wen Y, Li S, Gao S, Zhang D, Li X, Yang J, Gu L, Li M, Wang F, Lu C. Genomic Analysis of a Novel Torradovirus "Rehmannia Torradovirus Virus": Two Distinct Variants Infecting Rehmannia glutinosa. Microorganisms 2024; 12:1643. [PMID: 39203485 PMCID: PMC11356386 DOI: 10.3390/microorganisms12081643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 08/08/2024] [Accepted: 08/09/2024] [Indexed: 09/03/2024] Open
Abstract
Rehmannia glutinosa, a crucial medicinal plant native to China, is extensively cultivated across East Asia. We used high-throughput sequencing to identify viruses infecting R. glutinosa with mosaic, leaf yellowing, and necrotic symptoms. A novel Torradovirus, which we tentatively named "Rehmannia torradovirus virus" (ReTV), was identified. The complete sequences were obtained through reverse-transcription polymerase chain reaction (RT-PCR), 5' and 3' rapid amplification of cDNA ends, and Sanger sequencing. The amino acid sequence alignment between the ReTV-52 isolate and known Torradovirus species in the Pro-Pol and coat protein regions were 51.3-73.3% and 37.1-68.1%, respectively. Meanwhile, the amino acid sequence alignment between the ReTV-8 isolate and known Torradovirus species in the Pro-Pol and coat protein regions were 52.7-72.8% and 36.8-67.5%, respectively. The sequence analysis classified ten ReTV strains into two variants. The ReTV-52 genome has two RNA segments of 6939 and 4569 nucleotides, while that of ReTV-8 consists of two RNA segments containing 6889 and 4662 nucleotides. Sequence comparisons and phylogenetic analysis showed ReTV strains clustered within the Torradovirus, exhibiting the closet relation to the squash chlorotic leaf spot virus. The RT-PCR results showed a 100% ReTV detection rate in all 60 R. glutinosa samples. Therefore, ReTV should be classified as a novel Torradovirus species. ReTV is potentially dangerous to R. glutinosa, and necessitating monitoring this virus in the field.
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Affiliation(s)
- Yanhong Qin
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Shuhao Lu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Yi Wen
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Shaojian Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Suxia Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Desheng Zhang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Xuemeng Li
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Jin Yang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Li Gu
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.G.); (M.L.)
| | - Mingjie Li
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (L.G.); (M.L.)
| | - Fei Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
| | - Chuantao Lu
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, No. 116, Huanyuan Road, Jinshui District, Zhengzhou 450002, China; (Y.Q.); (S.L.); (Y.W.); (S.L.); (S.G.); (D.Z.); (X.L.); (J.Y.); (F.W.)
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Alvarez-Quinto R, Amao M, Muller G, Fuentes S, Grinstead S, Fuentes-Bueno I, Roenhorst A, Westenberg M, Botermans M, Kreuze J, Mollov D. Evidence that an Unnamed Isometric Virus Associated with Potato Rugose Disease in Peru Is a New Species of Genus Torradovirus. PHYTOPATHOLOGY 2023; 113:1716-1728. [PMID: 37486151 DOI: 10.1094/phyto-11-22-0449-v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
A previously uncharacterized torradovirus species infecting potatoes was detected by high-throughput sequencing from field samples from Peru and in customs intercepts in potato tubers that originated from South America in the United States of America and the Netherlands. This new potato torradovirus showed high nucleotide sequence identity to an unidentified isometric virus (SB26/29), which was associated with a disease named potato rugose stunting in southern Peru characterized over two decades ago. Thus, this virus is tentatively named potato rugose stunting virus (PotRSV). The genome of PotRSV isolates sequenced in this study were composed of two polyadenylated RNA segments. RNA1 ranges from 7,086 to 7,089 nt and RNA2 from 5,228 to 5,230 nt. RNA1 encodes a polyprotein containing the replication block (helicase-protease-polymerase), whereas RNA2 encodes a polyprotein cleaved into a movement protein and the three capsid proteins (CPs). Pairwise comparison among PotRSV isolates revealed amino acid identity values greater than 86% in the protease-polymerase (Pro-Pol) region and greater than 82% for the combined CPs. The closest torradovirus species, squash chlorotic leaf spot virus, shares amino acid identities of ∼58 and ∼41% in the Pro-Pol and the combined CPs, respectively. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Robert Alvarez-Quinto
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97333, U.S.A
| | - Melody Amao
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Giovanna Muller
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Segundo Fuentes
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Samuel Grinstead
- U.S. Department of Agriculture-Agricultural Research Service, National Germplasm Resources Laboratory, Beltsville, MD 20705, U.S.A
| | - Irazema Fuentes-Bueno
- U.S. Department of Agriculture-Agricultural Research Service, National Germplasm Resources Laboratory, Beltsville, MD 20705, U.S.A
| | - Annelien Roenhorst
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Marcel Westenberg
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), National Plant Protection Organization, Geertjesweg 15, 6706EA Wageningen, The Netherlands
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center, La Molina, Lima 15023, Peru
| | - Dimitre Mollov
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97330, U.S.A
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Kim MH, Byun HS, Kwak HR, Kwon SJ, Seo JK. First report of citrus leaf blotch virus infecting Viburnum lentago in South Korea. PLANT DISEASE 2023; 107:2568. [PMID: 36734939 DOI: 10.1094/pdis-11-22-2640-pdn] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Viburnum lentago (family Adoxaceae) is a perennial plant species native to northeastern United States and southern Canada. Globally, V. lentago is a popular garden plant due to its abundant flowers and beautiful autumnal color. V. lentago is also commercially cultivated for medicinal purposes because its roots and fruits can be used in herbal preparations (Jiao et al. 2021). In June 2022, virus-like symptoms of vein chlorosis and yellowing were observed in the leaves of many V. lentago trees planted in a public park in Wonju, South Korea. Leaf samples were collected from five symptomatic V. lentago trees. To identify the causal agent(s) of the virus-like symptoms, total RNA was isolated from one sample using PureLink® RNA Mini Kit (Invitrogen, USA) and subjected to library construction using Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, Inc., USA). RNA-Seq was performed using an Illumina NovaSeq 6000 system (Macrogen, Korea). De novo assembly of 118,878,556 quality-filtered reads was performed using the Trinity pipeline (Kwon et al. 2018), yielding 296,109 contigs. BLASTn and BLASTx analyses of the contigs against the GenBank viral reference database identified only one large contig (8,816 nt) containing a 26-nt poly(A) tail of viral origin. This contig had a maximum nucleotide identity of 85.53 % (with 99 % coverage) with isolate HZ (accession No. MH427034) of citrus leaf blotch virus (CLBV; genus Citrivirus, family Betaflexiviridae), suggesting that the collected sample was infected with CLBV. All collected V. lentago samples were tested using RT-PCR with CLBV-specific primers (CLBV-Det-Fw 5'-AACGAGGCCAATTCTGCTAT-3' and CLBV-Det-Rv 5'-GACTGCTTGACTAACAC-CCA-3'). All samples were positive for CLBV. For biological indexing, sap from the symptomatic V. lentago leaves was mechanically inoculated to indicator plants, including Nicotiana benthamiana, N. occidentalis, N. tabacum, Datura stramonium, Chenopodium quinoa, Vigna unguiculata, and V. lentago. Three months later, only V. lentago developed the same vein chlorosis symptoms observed in the collected samples, and no other tested plants exhibited obvious symptoms. Further, only V. lentago sample tested positive for CLBV using RT-PCR analysis. To determine the complete genome sequence of the CLBV V. lentago isolate, the contig sequence was confirmed by de novo sequencing of the RT-PCR products amplified using CLBV-specific primers. The 5' terminal sequence of the contig was determined using the 5' rapid amplification of cDNA ends method (Seo et al. 2015). The full-length sequence of CLBV isolated from V. lentago was 8,795 nt in length (excluding poly(A) tail), and deposited in GenBank under the accession number OP751940. Although numerous isolates of CLBV have been identified in various plant species, including citrus, kiwi, and lemon plants (Cao et al. 2017), the V. lentago isolate is likely a distinct variant because its CP gene has a maximum nucleotide identity of 85.53 % with that of a kiwi isolate (MH339916). With little information available on viral diseases infecting V. lentago, this is the first identified and completely sequenced CLBV infecting V. lentago. Significantly, V. lentago plants infected with CLBV did not flower throughout the summer period, reducing their value as an ornamental plant. Furthermore, V. lentago might have acted as an intermediate host to transfer CLBV to other crops such as citrus. To the best of our knowledge, this is the first report of CLBV infecting V. lentago in South Korea and the world.
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Affiliation(s)
- Myung-Hwi Kim
- Seoul National University, 26725, Seoul, Korea (the Republic of);
| | - Hee-Seong Byun
- National Institute of Agricultural Sciences, 230986, Crop Protection Division, 166, Nongsaengmyeong-ro, Iseo-myeon, Wanju, Korea (the Republic of), 55365;
| | - Hae-Ryun Kwak
- Rural Development Administration, 54670, Crop protection, National Institute of Agricultural Sciences, 166,Nongsaengmyeong-ro, Iseo-myeon, Jeonju, Korea (the Republic of), 54875
- United States;
| | - Sun-Jung Kwon
- Seoul National University, 26725, Institutes of Green Bio Science and Technology, Gwanak-gu, Seoul, Korea (the Republic of);
| | - Jang-Kyun Seo
- Seoul National University, Graduate School of International Agricultural Technology, 1447-1 Pyeongchang-ro, Pyeongchang city, Gangwon-do, Korea (the Republic of), 25354;
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Carvajal-Yepes M, Jimenez J, Belalcazar J, Cuasquer JB, Lozano I, Olaya CA, Cuellar WJ. Genome Analysis and Pathobiology of Cassava-Infecting Torradoviruses Containing a Putative Maf/HAM1 Pyrophosphatase Domain. PLANT DISEASE 2022; 106:2808-2816. [PMID: 35471077 DOI: 10.1094/pdis-11-21-2520-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Next generation sequencing has been used to identify and characterize the full genome sequence of a cassava-infecting torradovirus, revealing the presence of a Maf/HAM1 domain downstream of the RNA-dependent RNA-polymerase (RdRp) domain in RNA1 in all isolates sequenced. A similar domain is also found in unrelated potyvirids infecting Euphorbiaceae hosts in the Americas and cassava in Africa. Even though cassava torrado-like virus (CsTLV) could not be mechanically transmitted to a series of herbaceous hosts, it can be efficiently transmitted by bud graft-inoculation to different cassava landraces. Our bioassays show that CsTLV has a narrow host range. Crystal-like structures of isometric virus-like particles were observed in cells of plants with single infection by CsTLV, and consistently induced chlorotic leaf spots and affected root yields significantly. Moreover, CsTLV infection induces changes in the accumulation of total sugars in storage roots. Field surveys indicated the presence of CsTLV in the main cassava growing regions of Colombia, and the occurrence of two different cassava-infecting torradovirus species. Profiles of small RNAs of 21 to 24 nucleotides in length, derived from CsTLV RNAs targeted by cassava RNA silencing defense mechanisms, are also reported.
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Affiliation(s)
| | - Jenyfer Jimenez
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia (UNAL), Palmira, Colombia
| | - John Belalcazar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Juan B Cuasquer
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Ivan Lozano
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Cristian A Olaya
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
| | - Wilmer J Cuellar
- International Center for Tropical Agriculture (CIAT), AA 6713, Cali, Colombia
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Ferriol INMACULADA, Vallino MARTA, Ciuffo MARINA, Nigg JAREDC, Zamora‐Macorra ERIKAJ, Falk BRYCEW, Turina M. The Torradovirus-specific RNA2-ORF1 protein is necessary for plant systemic infection. MOLECULAR PLANT PATHOLOGY 2018; 19:1319-1331. [PMID: 28940803 PMCID: PMC6638011 DOI: 10.1111/mpp.12615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 06/07/2023]
Abstract
Tomato apex necrosis virus (ToANV, species Tomato marchitez virus, genus Torradovirus, family Secoviridae) causes a severe tomato disease in Mexico. One distinctive feature of torradoviruses compared with other members of the family Secoviridae is the presence of an additional open reading frame (ORF) in genomic RNA2 (denominated RNA2-ORF1), located upstream of ORF2. RNA2-ORF2 encodes a polyprotein that is processed into a putative movement protein and three capsid proteins (CPs). The RNA2-ORF1 protein has homologues only amongst other torradoviruses and, so far, no function has been associated with it. We used recombinant and mutant ToANV clones to investigate the role of the RNA2-ORF1 protein in various aspects of the virus infection cycle. The lack of a functional RNA2-ORF1 resulted in an inability to systemically infect Nicotiana benthamiana and tomato plants, but both positive- and negative-strand RNA1 and RNA2 accumulated locally in agroinfiltrated areas in N. benthamiana plants, indicating that the RNA2-ORF1 mutants were replication competent. Furthermore, a mutant with a deletion in RNA2-ORF1 was competent for virion formation and cell-to-cell movement in the cells immediately surrounding the initial infection site. However, immunological detection of the ToANV CPs in the agroinfiltrated areas showed that this mutant was not detected in the sieve elements even if the surrounding parenchymatic cells were ToANV positive, suggesting a role for the RNA2-ORF1 protein in processes occurring prior to phloem uploading, including efficient spread in inoculated leaves.
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Affiliation(s)
| | - MARTA Vallino
- Institute for Sustainable Plant Protection, CNRTurin10135Italy
| | - MARINA Ciuffo
- Institute for Sustainable Plant Protection, CNRTurin10135Italy
| | - JARED C. Nigg
- Department of Plant PathologyUC‐DavisDavisCA 95616USA
| | | | - BRYCE W. Falk
- Department of Plant PathologyUC‐DavisDavisCA 95616USA
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNRTurin10135Italy
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Verbeek M, Dullemans AM, van der Vlugt RAA. Aphid transmission of Lettuce necrotic leaf curl virus, a member of a tentative new subgroup within the genus Torradovirus. Virus Res 2017; 241:125-130. [PMID: 28223184 DOI: 10.1016/j.virusres.2017.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 11/24/2022]
Abstract
Lettuce necrotic leaf curl virus (LNLCV) was described as the first non-tomato-infecting member of the genus Torradovirus. Until today, the virus was found only in The Netherlands in two different areas in open field crops of lettuce. In 2015, LNLCV was accepted by the ICTV as a new member of the genus Torradovirus. The tomato-infecting (TI) torradoviruses Tomato torrado virus (ToTV), Tomato marchitez virus (ToMarV) and Tomato chocolàte virus (ToChV) are transmitted by at least three whitefly species in a semi-persistent and stylet-borne manner. As LNLCV was transmitted in open fields in The Netherlands, where whiteflies are present only in low incidence, transmission studies were set up to identify the natural vector of LNLCV. Whitefly species which survive Dutch open field conditions during summer, as well as lettuce colonizing aphid species, were tested for their ability to transmit LNLCV. Lengths of acquisition and inoculation periods were chosen in accordance with the conditions for TI torradoviruses. Transmission experiments involving whiteflies were never successful. Transmission with aphids was only successful in case of the lettuce-currant aphid, Nasonovia ribisnigri. Localization of LNLCV virions in N. ribisnigri with a nested RT-PCR indicated the stylets as possible retention sites. The willow-carrot aphid Cavariella aegopodii did not transmit LNLCV in our transmission experiment but the virus could be detected in the stylets of this aphid, leaving C. aegopodii as a possible vector for LNLCV.
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Affiliation(s)
- Martin Verbeek
- Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Annette M Dullemans
- Wageningen University and Research, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
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Seo JK, Kim MK, Kwak HR, Kim JS, Choi HS. Complete genome sequence of longan witches' broom-associated virus, a novel member of the family Potyviridae. Arch Virol 2017; 162:2885-2889. [PMID: 28501954 DOI: 10.1007/s00705-017-3405-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
The complete genome sequence of a new virus isolated from a longan (Dimocarpus longan Lour.) plant showing witches' broom syndrome was determined. The viral genome is composed of a monopartite single-stranded RNA of 9,428 nucleotides excluding the 3' poly(A) tail and contains one large single open reading frame encoding a polyprotein of 3086 amino acids. BLAST searches of protein databases showed that the encoded polyprotein has a maximum amino acid sequence identity of 35% (with 85% coverage) to that of the isolate Minnesota of rose yellow mosaic virus (RoYMV; family Potyviridae; genus not assigned). Molecular and phylogenetic analysis of the genome and encoded protein sequences showed that the identified virus has the general features that are characteristic of members of the family Potyviridae although it has extremely low sequence similarity to known members of the family Potyviridae. The name longan witches' broom-associated virus (LWBaV) is proposed for this new virus, which may be considered a member of a new genus in the family Potyviridae.
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Affiliation(s)
- Jang-Kyun Seo
- Department of International Agricultural Technology and Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea.
| | - Mi-Kyeong Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jeong-Soo Kim
- Department of Plant Medicals, Andong National University, Andong, 36729, Republic of Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, 55365, Republic of Korea.
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The complete genome sequence of a novel virus, bellflower veinal mottle virus, suggests the existence of a new genus within the family Potyviridae. Arch Virol 2017; 162:2457-2461. [DOI: 10.1007/s00705-017-3374-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/05/2017] [Indexed: 10/19/2022]
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Ferriol I, Silva Junior D, Nigg J, Zamora-Macorra E, Falk B. Identification of the cleavage sites of the RNA2-encoded polyproteins for two members of the genus Torradovirus by N-terminal sequencing of the virion capsid proteins. Virology 2016; 498:109-115. [DOI: 10.1016/j.virol.2016.08.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/15/2016] [Accepted: 08/17/2016] [Indexed: 11/16/2022]
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Rozado-Aguirre Z, Adams I, Collins L, Fox A, Dickinson M, Boonham N. Detection and transmission of Carrot torrado virus, a novel putative member of the Torradovirus genus. J Virol Methods 2016; 235:119-124. [PMID: 27260658 DOI: 10.1016/j.jviromet.2016.05.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/06/2016] [Accepted: 05/29/2016] [Indexed: 11/28/2022]
Abstract
A new Torradovirus tentatively named Carrot torrado virus (CaTV) was an incidental finding following a next generation sequencing study investigating internal vascular necrosis in carrot. The closest related viruses are Lettuce necrotic leaf curl virus (LNLCV) found in the Netherlands in 2011 and Motherwort yellow mottle virus (MYMoV) found in Korea in 2014. Primers for reverse transcriptase-PCR (RT-PCR) and RT-qPCR were designed with the aim of testing for the presence of virus in plant samples collected from the field. Both methods successfully amplified the target from infected samples but not from healthy control samples. The specificity of the CaTV assay was also checked against other known carrot viruses and no cross-reaction was seen. A comparative study between methods showed RT-qPCR was the most reliable method, giving positive results in samples where RT-PCR fails. Evaluation of the Ct values following RT-qPCR and a direct comparison demonstrated this was due to improved sensitivity. The previous published Torradovirus genus specific RT-PCR primers were tested and shown to detect CaTV. Also, virus transmission experiments carried out suggest that unlike other species of the same genus, Carrot torrado virus could be aphid-transmitted.
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Affiliation(s)
- Zuriñe Rozado-Aguirre
- Plant Protection Programme, Fera, Sand Hutton, York YO41 1LZ, United Kingdom; University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom.
| | - Ian Adams
- Plant Protection Programme, Fera, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Larissa Collins
- Plant Protection Programme, Fera, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Adrian Fox
- Plant Protection Programme, Fera, Sand Hutton, York YO41 1LZ, United Kingdom
| | - Matthew Dickinson
- University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Neil Boonham
- Plant Protection Programme, Fera, Sand Hutton, York YO41 1LZ, United Kingdom
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Blouin AG, Ross HA, Hobson-Peters J, O'Brien CA, Warren B, MacDiarmid R. A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies. Mol Ecol Resour 2016; 16:1255-63. [PMID: 26990372 DOI: 10.1111/1755-0998.12525] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 11/30/2022]
Abstract
Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase-polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Māori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31-74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.
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Affiliation(s)
- Arnaud G Blouin
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
| | - Howard A Ross
- School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
| | - Jody Hobson-Peters
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Caitlin A O'Brien
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Qld, 4072, Australia
| | - Ben Warren
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Robin MacDiarmid
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, P.O. Box 92019, Auckland, New Zealand
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12
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Wieczorek P, Obrępalska-Stęplowska A. A single amino acid substitution in movement protein of tomato torrado virus influences ToTV infectivity in Solanum lycopersicum. Virus Res 2016; 213:32-36. [PMID: 26562559 DOI: 10.1016/j.virusres.2015.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/04/2015] [Accepted: 11/04/2015] [Indexed: 10/22/2022]
Abstract
Tomato torrado virus (ToTV), which is a tomato-infecting member of the genus Torradovirus, induces severe systemic necrosis in Solanum lycopersicum cv. Beta Lux as well as leaf malformation and chlorosis in Nicotiana benthamiana. To date, neither the tomato gene conferring resistance to the pathogen nor the ToTV-encoded necrosis determinant have been characterized. We herein revealed that the phenylalanine 210 residue in the movement protein domain encoded by ToTV RNA2 is a necrosis-inducing pathogenicity determinant during tomato infection. Using a ToTV infectious RNA2 clone, we performed site-directed mutagenesis of the phenylalanine 210 residue, confirming its importance during ToTV infection and symptom manifestation in S. lycopersicum cv. Beta Lux, but not in N. benthamiana.
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Affiliation(s)
- Przemysław Wieczorek
- Interdepartmental Laboratory of Molecular Biology-National Research Institute, 20 WładysławaWęgorka St, Poznań 60-318, Poland
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13
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Kwon SJ, Choi GS, Yoon JY, Seo JK, Choi HS. Identification of Leonurus sibiricus as a Weed Reservoir for Three Pepper-Infecting Viruses. THE PLANT PATHOLOGY JOURNAL 2016; 32:65-9. [PMID: 26889117 PMCID: PMC4755677 DOI: 10.5423/ppj.nt.07.2015.0138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/30/2015] [Accepted: 08/30/2015] [Indexed: 06/05/2023]
Abstract
In plant virus ecology, weeds are regarded as wild reservoirs of viruses and as potential sources for insect-mediated transmission of viruses. During field surveys in 2013-2014, three Leonurus sibiricus plants showing virus-like symptoms were collected from pepper fields in Daegu, Seosan, and Danyang in Korea. Molecular diagnosis assays showed that the collected L. sibiricus samples were infected with either Tomato spotted wilt virus (TSWV), Pepper mild mottle virus (PMMoV), or Beet western yellow virus (BWYV), respectively. Since this is the first identification of TSWV, PMMoV, and BWYV from L. sibiricus, complete genome sequences of three virus isolates were determined to examine their phylogenetic relationships with the previously reported strains and isolates. Phylogenetic analyses performed using full genome sequences of the viruses showed the isolates of TSWV and PMMoV obtained from L. sibiricus are closely related to the pepper isolates of the corresponding viruses. Our results suggest that L. sibiricus could act an alternative host and reservoir of viruses that cause damages in pepper fields.
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Affiliation(s)
- Sun-Jung Kwon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-862,
Korea
| | - Gug-Seoun Choi
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-862,
Korea
| | - Ju-Yeon Yoon
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju 565-862,
Korea
| | - Jang-Kyun Seo
- Crop Protection Division, National Academy of Agricultural Science, RDA, Wanju 565-851,
Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Academy of Agricultural Science, RDA, Wanju 565-851,
Korea
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14
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Gilbertson RL, Batuman O, Webster CG, Adkins S. Role of the Insect SupervectorsBemisia tabaciandFrankliniella occidentalisin the Emergence and Global Spread of Plant Viruses. Annu Rev Virol 2015; 2:67-93. [DOI: 10.1146/annurev-virology-031413-085410] [Citation(s) in RCA: 247] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert L. Gilbertson
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Ozgur Batuman
- Department of Plant Pathology, University of California, Davis, California 95616; ,
| | - Craig G. Webster
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
| | - Scott Adkins
- US Horticultural Research Laboratory, Agricultural Research Service, US Department of Agriculture, Fort Pierce, Florida 34945; ,
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15
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Seo JK, Kwak HR, Lee YJ, Kim J, Kim MK, Kim CS, Choi HS. Complete genome sequence of bellflower vein chlorosis virus, a novel putative member of the genus Waikavirus. Arch Virol 2015; 160:3139-42. [PMID: 26370789 DOI: 10.1007/s00705-015-2606-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/07/2015] [Indexed: 11/28/2022]
Abstract
The complete genome sequence of a new virus isolated from a bellflower (Campanula takesimana) plant was determined. The genome of this virus is composed of monopartite single-stranded RNA of 11,649 nucleotides in length. BLAST searches of protein databases showed that the encoded polyprotein has a maximum amino acid sequence identity of 42% (with 99% coverage) to the polyprotein of the isolate Orissa of rice tungro spherical virus (RTSV; genus Waikavirus). Phylogenetic analysis strongly supports that the identified virus is a member of a new species of the genus Waikavirus. The name bellflower vein chlorosis virus (BVCV) is proposed for this new virus.
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Affiliation(s)
- Jang-Kyun Seo
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Republic of Korea.
| | - Hae-Ryun Kwak
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Republic of Korea
| | - Ye-ji Lee
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Republic of Korea
| | - Jaedeok Kim
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Republic of Korea
| | - Mi-Kyeong Kim
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Republic of Korea
| | - Chang-Seok Kim
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Republic of Korea
| | - Hong-Soo Choi
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, 565-851, Republic of Korea.
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16
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van der Vlugt RAA, Verbeek M, Dullemans AM, Wintermantel WM, Cuellar WJ, Fox A, Thompson JR. Torradoviruses. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:485-512. [PMID: 26047567 DOI: 10.1146/annurev-phyto-080614-120021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Torradoviruses are an example of a group of recently discovered plant viruses. The first description of Tomato torrado virus, now the type member of the newly established genus Torradovirus within the family Secoviridae, was published in 2007 and was quickly followed by findings of other torradoviruses, initially all on tomato. Their characterization led to the development of tools that allowed recognition of still other torradoviruses, only very recently found on non-tomato crops, which indicates these viruses have a much wider host range and diversity than previously believed. This review describes the characteristics of this newly emerged group of plant viruses. It looks in detail at taxonomic relationships and specific characteristics in their genomes and encoded proteins. Furthermore, it discusses their epidemiology, including host range, semipersistent transmission by whitefly vectors, and impact on diverse cropping systems.
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