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Kwon JA, Kim SE, Igori D, Ahn JK, Seo HK, Park YC, Moon JS. Complete genome sequence of a new putative member of the genus Pelarspovirus that infects Quercus aliena Blume in South Korea. Arch Virol 2024; 169:24. [PMID: 38206482 DOI: 10.1007/s00705-023-05921-4] [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: 09/26/2023] [Accepted: 10/24/2023] [Indexed: 01/12/2024]
Abstract
The complete nucleotide sequence of a newly discovered virus infecting Quercus aliena Blume, tentatively named "quercus leafroll virus" (QLRV), was determined through high-throughput and Sanger sequencing. The sequence comprises 3,940 nucleotides, has five open reading frames, and has a typical pelarspovirus genome organization, with neither 3' polyadenylation nor a 5' cap. The proteins encoded by QLRV share 17.9 to 44.2% amino acid sequence identity with known pelarspovirus proteins. The highest amino acid sequence identity values for the RNA-dependent RNA polymerase (RdRp) and coat protein were 67.5% and 55.2%, respectively, which are below the current thresholds for pelarspovirus species demarcation. On the basis of these results, we propose classifying QLRV as a new member of the genus Pelarspovirus, family Tombusviridae.
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Affiliation(s)
- Jeong A Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Se Eun Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Davaajargal Igori
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Jun Ki Ahn
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, 15588, Korea
| | - Han Kyu Seo
- HK Genomics, Inc., Daejeon, Republic of Korea
| | | | - Jae Sun Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea.
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Salamon P, Nagyne-Galbacs Z, Demian E, Achs A, Alaxin P, Predajňa L, Agyemang ED, Desiderio F, Takacs AP, Menzel W, Škorić D, Glasa M, Varallyay E. Clematis vitalba Is a Natural Host of the Novel Ilarvirus, Prunus Virus I. Viruses 2023; 15:1964. [PMID: 37766370 PMCID: PMC10536899 DOI: 10.3390/v15091964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Clematis vitalba L. is a climbing shrub and a pioneer plant in abandoned orchards or vineyards that are widespread in temperate climate zones. In past years, several viruses infecting the Clematis species have been identified, including different ilarviruses. Prunus virus I (PrVI) is a recently described ilarvirus, which has been shown to infect sweet cherries and peaches in Greece. Moreover, its presence has been detected in ornamental Clematis in Russia. In the present work, we analyzed the virome of wildly growing C. vitalba plants from Hungary, Slovakia and Croatia showing different kinds of symptoms using high-throughput sequencing (HTS) of small RNAs or ribodepleted RNAs. Applying HTS enabled us to identify the presence of PrVI in C. vitalba, and the bioinformatic analyses were further validated with RT-PCR using PrVI-specific primers and Sanger dideoxy sequencing. Nearly full genome sequences of all three viral RNAs of one Hungarian, two Slovak and one Croatian isolate were determined. Their phylogenetic analysis showed high similarity to each other and to other PrVI isolates described from Central Europe. As the sampled plants were co-infected with other viruses, it is not possible to determine a direct correlation between the infection with PrVI and the observed symptoms. Analyses of different Prunus species in stock collection showed infection of several peach and sweet cherry varieties in Hungary. Our results expand the knowledge on the natural host range of PrVI and highlight the necessity to evaluate alternative plant hosts (even non-Prunus) of PrVI and the role of the virus in the etiology of the potential diseases.
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Affiliation(s)
- Pal Salamon
- Applied Plant Genomics Group, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary;
| | - Zsuzsanna Nagyne-Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
| | - Emese Demian
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
| | - Adam Achs
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
| | - Peter Alaxin
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
| | - Evans Duah Agyemang
- Department of Plant Protection, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Deák Ferenc Street 17, 8360 Keszthely, Hungary; (E.D.A.); (A.P.T.)
| | - Francesco Desiderio
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
| | - Andras Peter Takacs
- Department of Plant Protection, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Deák Ferenc Street 17, 8360 Keszthely, Hungary; (E.D.A.); (A.P.T.)
| | - Wulf Menzel
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany;
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, 10000 Zagreb, Croatia;
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences, Dúbravská Cesta 9, 84505 Bratislava, Slovakia; (A.A.); (P.A.); (L.P.); (M.G.)
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia
| | - Eva Varallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Godollo, Hungary; (Z.N.-G.); (E.D.); (F.D.)
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Dey KK, Leite M, Hu JS, Jordan R, Melzer MJ. Detection of Jasmine virus H and characterization of a second pelarspovirus infecting star jasmine (Jasminum multiflorum) and angelwing jasmine (J. nitidum) plants displaying virus-like symptoms. Arch Virol 2018; 163:3051-3058. [PMID: 30069855 DOI: 10.1007/s00705-018-3947-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 05/10/2018] [Indexed: 11/26/2022]
Abstract
Star jasmine (Jasminum multiflorum) plants growing in Hawaii expressing a diverse array of virus-like foliar symptoms were examined for the presence of a causal agent. Symptomatic tissues collected from three locations on the island of Oahu, Hawaii consistently harbored double-stranded (ds)RNAs approximately 4.2 and 1.7 kbp in size. Sanger and high-throughput sequencing approaches revealed these dsRNAs were from two distinct virus species co-infecting the same host plant. One of these two viruses was the recently characterized Jasmine virus H (JaVH), and the second we designated as Jasmine mosaic-associated virus (JMaV). Both viruses were subsequently found, by high-throughput sequencing, in a single angelwing jasmine (J. nitidum) plant exhibiting similar ringspot symptoms and growing at the U.S. National Arboretum in Washington, DC. Phylogenetic placement, genome organization, and sequence comparisons indicate these two viruses are classifiable as members of the genus Pelarspovirus (family Tombusviridae). To determine if either of these viruses were associated with the observed symptoms, a PCR-based detection assay was developed to detect and distinguish these two viruses in several Hawaii-grown plants. All 32 samples collected from four Oahu locations displayed symptoms. All 32 samples were positive for JaVH, and 16 were positive for JMaV. An asymptomatic star jasmine plant from the island of Hawaii was negative for both JaVH and JMaV. Both viruses were also found in a symptomatic J. sambac sample from Maryland while only JMaV was detected in a symptomatic Jasminum sp. sample from California.
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Affiliation(s)
- Kishore K Dey
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL, 32614, USA
| | - Milena Leite
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
- Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - John S Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Ramon Jordan
- Floral and Nursery Plants Research Unit, US National Arboretum, USDA-ARS, Beltsville, MD, 20705, USA
| | - Michael J Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA.
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Complete nucleotide sequence of jasmine virus H, a new member of the family Tombusviridae. Arch Virol 2017; 163:731-735. [PMID: 29214362 DOI: 10.1007/s00705-017-3663-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022]
Abstract
Jasmine virus H (JaVH) is a novel virus associated with symptoms of yellow mosaic on jasmine. The JaVH genome is 3,867 nt in length with five open reading frames (ORFs) encoding a 27-kDa protein (ORF 1), an 87-kDa replicase protein (ORF 2), two centrally located movement proteins (ORF 3 and 4), and a 37-kDa capsid protein (ORF 5). Based on genomic and phylogenetic analysis, JaVH is predicted to be a member of the genus Pelarspovirus in the family Tombusviridae.
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