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Lameront P, Shabanian M, Currie LMJ, Fust C, Li C, Clews A, Meng B. Elucidating the Subcellular Localization of GLRaV-3 Proteins Encoded by the Unique Gene Block in N. benthamiana Suggests Implications on Plant Host Suppression. Biomolecules 2024; 14:977. [PMID: 39199365 PMCID: PMC11352578 DOI: 10.3390/biom14080977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 09/01/2024] Open
Abstract
Grapevine leafroll-associated virus 3 (GLRaV-3) is a formidable threat to the stability of the global grape and wine industries. It is the primary etiological agent of grapevine leafroll disease (GLD) and significantly impairs vine health, fruit quality, and yield. GLRaV-3 is a member of the genus Ampelovirus, Closteroviridae family. Viral genes within the 3' proximal unique gene blocks (UGB) remain highly variable and poorly understood. The UGBs of Closteroviridae viruses include diverse open reading frames (ORFs) that have been shown to contribute to viral functions such as the suppression of the host RNA silencing defense response and systemic viral spread. This study investigates the role of GLRaV-3 ORF8, ORF9, and ORF10, which encode the proteins p21, p20A, and p20B, respectively. These genes represent largely unexplored facets of the GLRaV-3 genome. Here, we visualize the subcellular localization of wildtype and mutagenized GLRaV-3 ORFs 8, 9, and 10, transiently expressed in Nicotiana benthamiana. Our results indicate that p21 localizes to the cytosol, p20A associates with microtubules, and p20B is trafficked into the nucleus to carry out the suppression of host RNA silencing. The findings presented herein provide a foundation for future research aimed at the characterization of the functions of these ORFs. In the long run, it would also facilitate the development of innovative strategies to understand GLRaV-3, mitigate its spread, and impacts on grapevines and the global wine industry.
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Affiliation(s)
- Patrick Lameront
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.S.); (L.M.J.C.); (C.F.); (C.L.); (A.C.); (B.M.)
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Rahman MM, Jarugula S, Bagewadi B, Fayad A, Karasev AV, Naidu RA. Characterization of a New, Country Bean ( Lablab purpureus) Lineage of Bean Common Mosaic Necrosis Virus. PLANT DISEASE 2024; 108:434-441. [PMID: 37709726 DOI: 10.1094/pdis-04-23-0822-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: 09/16/2023]
Abstract
Country bean (Lablab purpureus, family Fabaceae) is grown in subsistence agriculture in Bangladesh as a multipurpose crop for food, animal feed, and green manure. This study was undertaken to investigate the genetic diversity of bean common mosaic necrosis virus (BCMNV, genus Potyvirus, family Potyviridae) in country beans. Leaf samples from country beans showing yellowing, vein banding, and mosaic symptoms were collected during field surveys between 2015 and 2019 cropping seasons from farmers' fields in different geographic regions. These samples were tested by serological and molecular diagnostic assays for the presence of BCMNV. Virus-positive samples were subjected to high-throughput Illumina sequencing to generate near-complete genomes of BCMNV isolates. In pairwise comparisons, the polyprotein sequences of BCMNV isolates from Bangladesh showed greater than 98% identities among themselves and shared less than 84% sequence identity at the nucleotide level with virus isolates reported from other countries. In the phylogenetic analysis, BCMNV isolates from Bangladeshi country beans formed a separate clade from virus isolates reported from common beans in other countries in the Americas, Africa, Europe, and from East Timor. Grow-out studies showed seed-to-seedling transmission of BCMNV, implying a possible seedborne nature of the virus in country beans.
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Affiliation(s)
- Mohammad M Rahman
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
| | - Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
| | - Basavaraj Bagewadi
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Amer Fayad
- Center for International Research, Education, and Development, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID, U.S.A
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
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Li S, Anane RF, Chen Z, Duan C, Wang Z, Gao L, Yu D, Chu B, Yang Z, Wen G, Zhao M. Complete genome sequence of a novel closterovirus isolated from Dregea volubilis. Arch Virol 2023; 168:154. [PMID: 37145182 DOI: 10.1007/s00705-023-05775-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/01/2023] [Indexed: 05/06/2023]
Abstract
The complete genome sequence of a putative novel closterovirus, tentatively named "Dregea volubilis closterovirus 1" (DvCV1, GenBank accession no. MZ779122), infecting Dregea volubilis in China was determined using high-throughput sequencing (HTS). The complete genome sequence of DvCV1 consists of 16,165 nucleotides (nt) and contains nine ORFs. The genome structure of DvCV1 is typical of members of the genus Closterovirus. Complete genome sequence analysis showed that DvCV1 shares 41.4-48.4% nucleotide sequence identity with other known closteroviruses. The putative RNA-dependent RNA polymerase (RdRp), heat shock protein 70-like protein (HSP70h), and coat protein (CP) of DvCV1 share 46.80-62.65%, 31.06-51.80%, and 28.34-37.37% amino acid sequence identity, respectively, with the RdRp, HSP70h and CP of other closteroviruses. Phylogenetic analysis based on HSP70h aa sequences placed DvCV1 alongside other members of the genus Closterovirus in the family Closteroviridae. These results suggest that DvCV1 is a new member of the genus Closterovirus. This is the first report of a closterovirus infecting D. volubilis.
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Affiliation(s)
- Shangyun Li
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China
| | - Rex Frimpong Anane
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, 23 Innovation Walk, Clayton, VIC, 3800, Australia
| | - Zeli Chen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China
| | - Chunfang Duan
- Tropical and Subtropical Cash Crops Research Institute, Yunnan Academy of Agricultural Sciences, Baoshan, 678000, China
| | - Zhe Wang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China
| | - Like Gao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China
| | - Daihong Yu
- Plant Protection and Quarantine Station of Yuanjiang County, Yuxi, Yunnan, 653300, China
| | - Bifan Chu
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China
| | - Zefen Yang
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China
| | - Guosong Wen
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China
| | - Mingfu Zhao
- Key Laboratory for Agricultural Biodiversity for Pest Management of China, Ministry of Education, Yunnan Agricultural University, No. 95, Jinhei Road, Panlong District, Kunming, Yunnan, 650201, China.
- Research and Development Center for Health Product, College of Agronomy and Biotechnology, Yunnan Agricultural University, No. 95, Jinhei Road, Kunming, Yunnan, 650201, China.
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Morán F, Olmos A, Glasa M, Silva MBD, Maliogka V, Wetzel T, Ruiz-García AB. A Novel and Highly Inclusive Quantitative Real-Time RT-PCR Method for the Broad and Efficient Detection of Grapevine Leafroll-Associated Virus 1. PLANTS (BASEL, SWITZERLAND) 2023; 12:876. [PMID: 36840223 PMCID: PMC9962094 DOI: 10.3390/plants12040876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis vinifera L.) is one of the most important crops in the world due to its economic and social impact. Like many other crops, grapevine is susceptible to different types of diseases caused by pathogenic microorganisms. Grapevine leafroll-associated virus 1 (GLRaV-1) is a virus associated with grapevine leafroll disease and it is considered at the national and European level as a pathogen that must be absent in propagative plant material. For this reason, the availability of specific, sensitive and reliable detection techniques to ascertain the sanitary status of the plants is of great importance. The objective of this research was the development of a new GLRaV-1 detection method based on a TaqMan quantitative real-time RT-PCR targeted to the coat protein genomic region and including a host internal control in a duplex reaction. To this end, three new GLRaV-1 full genomes were recovered by HTS and aligned with all sequences available in the databases. The method has been validated following EPPO standards and applied for the diagnosis of field plant material and transmission vectors. The new protocol designed has turned out to be highly sensitive as well as much more specific than the current available methods for the detection and absolute quantitation of GLRaV-1 viral titer.
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Affiliation(s)
- Félix Morán
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská Cesta 9, 84505 Bratislava, Slovakia
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Nám. J. Herdu 2, 91701 Trnava, Slovakia
| | - Marilia Bueno Da Silva
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
| | - Varvara Maliogka
- Plant Pathology Laboratory, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Breitenweg, 71, 67435 Neustadt an der Weinstrasse, Germany
| | - Ana Belén Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, Moncada, 46113 Valencia, Spain
- Departamento de Microbiología y Ecología, C/Doctor Moliner 50, Burjasot, 46100 Valencia, Spain
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Song Y, Hanner RH, Meng B. Probing into the Effects of Grapevine Leafroll-Associated Viruses on the Physiology, Fruit Quality and Gene Expression of Grapes. Viruses 2021; 13:v13040593. [PMID: 33807294 PMCID: PMC8066071 DOI: 10.3390/v13040593] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/19/2022] Open
Abstract
Grapevine leafroll is one of the most widespread and highly destructive grapevine diseases that is responsible for great economic losses to the grape and wine industries throughout the world. Six distinct viruses have been implicated in this disease complex. They belong to three genera, all in the family Closteroviridae. For the sake of convenience, these viruses are named as grapevine leafroll-associated viruses (GLRaV-1, -2, -3, -4, -7, and -13). However, their etiological role in the disease has yet to be established. Furthermore, how infections with each GLRaV induce the characteristic disease symptoms remains unresolved. Here, we first provide a brief overview on each of these GLRaVs with a focus on genome structure, expression strategies and gene functions, where available. We then provide a review on the effects of GLRaV infection on the physiology, fruit quality, fruit chemical composition, and gene expression of grapevine based on the limited information so far reported in the literature. We outline key methodologies that have been used to study how GLRaV infections alter gene expression in the grapevine host at the transcriptomic level. Finally, we present a working model as an initial attempt to explain how infections with GLRaVs lead to the characteristic symptoms of grapevine leafroll disease: leaf discoloration and downward rolling. It is our hope that this review will serve as a starting point for grapevine virology and the related research community to tackle this vastly important and yet virtually uncharted territory in virus-host interactions involving woody and perennial fruit crops.
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Affiliation(s)
- Yashu Song
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Robert H. Hanner
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 53876)
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Wang Y, Song Y, Wang Y, Cao M, Hu T, Zhou X. Discovery and Characterization of a Novel Ampelovirus on Firespike. Viruses 2020; 12:E1452. [PMID: 33339381 PMCID: PMC7766885 DOI: 10.3390/v12121452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/09/2020] [Accepted: 12/09/2020] [Indexed: 11/17/2022] Open
Abstract
A novel RNA virus was identified in firespike (Odontonema tubaeforme) plants exhibiting leaf curling and chlorosis. The molecular features of the viral genomic RNA and proteins resemble those of ampeloviruses. Based on sequence comparisons and phylogenetic analysis, we propose a new species in the genus Ampelovirus, which we have tentatively named Firespike leafroll-associated virus (FLRaV). Bioassays showed that the virus is mechanically transmissible to Nicotiana benthamiana. In addition, a full-length cDNA clone of FLRaV could successfully infect N. benthamiana via agroinfiltration.
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Affiliation(s)
- Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
| | - Yu Song
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
| | - Yongzhi Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing 400712, China;
| | - Tao Hu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.W.); (Y.S.); (Y.W.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Wen S, Wang G, Yang Z, Wang Y, Rao M, Lu Q, Hong N. Next-Generation Sequencing Combined With Conventional Sanger Sequencing Reveals High Molecular Diversity in Actinidia Virus 1 Populations From Kiwifruit Grown in China. Front Microbiol 2020; 11:602039. [PMID: 33391218 PMCID: PMC7774462 DOI: 10.3389/fmicb.2020.602039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/11/2020] [Indexed: 01/04/2023] Open
Abstract
Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in the six libraries. Two full-length and two near-full genome sequences of AcV-1 variants were determined by Sanger sequencing. The genome structure of these Chinese AcV-1 variants was identical to that of isolate K75 and consisted of 12 open reading frames (ORFs). Analyses of these sequences together with the NGS-derived contig sequences revealed high molecular diversity in AcV-1 populations, with the highest sequence variation occurring at ORF1a, ORF2, and ORF3, and the available variants clustered into three phylogenetic clades. For the first time, our study revealed different domain compositions in the viral ORF1a and molecular recombination events among AcV-1 variants. Specific reverse transcriptase–polymerase chain reaction assays disclosed the presence of AcV-1 in plants of four kiwifruit species and unknown Actinidia spp. in seven provinces and one city.
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Affiliation(s)
- Shaohua Wen
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanxiang Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Rao
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qian Lu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan, China
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Adiputra J, Jarugula S, Naidu RA. Intra-species recombination among strains of the ampelovirus Grapevine leafroll-associated virus 4. Virol J 2019; 16:139. [PMID: 31744534 PMCID: PMC6862812 DOI: 10.1186/s12985-019-1243-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/15/2019] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Grapevine leafroll disease is one of the most economically important viral diseases affecting grape production worldwide. Grapevine leafroll-associated virus 4 (GLRaV-4, genus Ampelovirus, family Closteroviridae) is one of the six GLRaV species documented in grapevines (Vitis spp.). GLRaV-4 is made up of several distinct strains that were previously considered as putative species. Currently known strains of GLRaV-4 stand apart from other GLRaV species in lacking the minor coat protein. METHODS In this study, the complete genome sequence of three strains of GLRaV-4 from Washington State vineyards was determined using a combination of high-throughput sequencing, Sanger sequencing and RACE. The genome sequence of these three strains was compared with corresponding sequences of GLRaV-4 strains reported from other grapevine-growing regions. Phylogenetic analysis and SimPlot and Recombination Detection Program (RDP) were used to identify putative recombination events among GLRaV-4 strains. RESULTS The genome size of GLRaV-4 strain 4 (isolate WAMR-4), strain 5 (isolate WASB-5) and strain 9 (isolate WALA-9) from Washington State vineyards was determined to be 13,824 nucleotides (nt), 13,820 nt, and 13,850 nt, respectively. Multiple sequence alignments showed that a 11-nt sequence (5'-GTAATCTTTTG-3') towards 5' terminus of the 5' non-translated region (NTR) and a 10-nt sequence (5'-ATCCAGGACC-3') towards 3' end of the 3' NTR are conserved among the currently known GLRaV-4 strains. LR-106 isolate of strain 4 and Estellat isolate of strain 6 were identified as recombinants due to putative recombination events involving divergent sequences in the ORF1a from strain 5 and strain Pr. CONCLUSION Genome-wide analyses showed for the first time that recombinantion can occur between distinct strains of GLRaV-4 resulting in the emergence of genetically stable and biologically successful chimeric viruses. Although the origin of recombinant strains of GLRaV-4 remains elusive, intra-species recombination could be playing an important role in shaping genetic diversity and evolution of the virus and modulating the biology and epidemiology of GLRaV-4 strains.
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Affiliation(s)
- Jati Adiputra
- Department of Plant Pathology, Irrigated Agriculture Research and Extension center, Washington State University, Prosser, Washington, 99350, USA.,Present address, Center for Diagnostic Standards of Agricultural Quarantine, Ministry of Agriculture, Indonesia Agricultural Quarantine Agency, Jakarta, Indonesia
| | - Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extension center, Washington State University, Prosser, Washington, 99350, USA
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension center, Washington State University, Prosser, Washington, 99350, USA.
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Xiao H, Li C, Al Rwahnih M, Dolja V, Meng B. Metagenomic Analysis of Riesling Grapevine Reveals a Complex Virome Including Two New and Divergent Variants of Grapevine leafroll-associated virus 3. PLANT DISEASE 2019; 103:1275-1285. [PMID: 30932733 DOI: 10.1094/pdis-09-18-1503-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The virome of a major white wine grape of cultivar Riesling showing decline and leafroll disease symptoms was analyzed through high-throughput sequencing (HTS) using total RNAs as templates and the Illumina HiSeq 2500 platform. Analysis of HTS data revealed the presence of five viruses and three viroids in the infected vine. These viruses are Grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-3 (genus Ampelovirus, family Closteroviridae) and three viruses of the family Betaflexiviridae (namely, Grapevine virus A [GVA], Grapevine virus B, and Grapevine rupestris stem pitting-associated virus [GRSPaV]). We also show that multiple distinct strains of three viruses (GLRaV-3, GVA, and GRSPaV) were present in this diseased grapevine. The complete genomes of two novel and highly divergent isolates of GLRaV-3 were determined using the draft genomes derived from HTS data and two independent rapid amplification of cDNA ends (RACE) strategies to obtain sequences at both the 5' and the 3' termini of the viral genomes. Questionable genome regions of both isolates were also verified through cloning of reverse transcription polymerase chain reaction products and Sanger sequencing. These two isolates are vastly divergent from all other isolates of GLRaV-3 whose genome sequences are available in GenBank. Isolate ON8415A has up to 76% nucleotide sequence identities to other isolates representing existing variant groups. We also revealed high degrees of variation in both length and sequence in the terminal untranslated regions (UTRs) of GLRaV-3 variants. The 5'-UTR of most GLRaV-3 isolates whose complete genomes have been sequenced contain tandem repeats of 65 nucleotides, a highly unusual feature rarely observed in (+)single-stranded RNA viruses. Mechanisms for the biogenesis of these tandem repeats and their function in virus replication and pathogenesis require investigation. Findings of this research add to the genetic diversity, evolutionary biology, and diagnostics of GLRaV-3 that afflicts the global grape wine industry.
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Affiliation(s)
- Huogen Xiao
- 1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Caihong Li
- 1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Maher Al Rwahnih
- 2 Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A.; and
| | - Valerian Dolja
- 3 Department of Botany and Plant Pathology, Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Baozhong Meng
- 1 Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Adiputra J, Kesoju SR, Naidu RA. The Relative Occurrence of Grapevine leafroll-associated virus 3 and Grapevine red blotch virus in Washington State Vineyards. PLANT DISEASE 2018; 102:2129-2135. [PMID: 30226418 DOI: 10.1094/pdis-12-17-1962-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Vineyard surveys were conducted for three consecutive seasons in eastern Washington State, the major grapevine-growing region in the state, to document the occurrence of Grapevine leafroll-associated virus 3 (GLRaV-3) and Grapevine red blotch virus (GRBV). The majority of samples were collected from red-berried wine grape (Vitis vinifera) cultivars exhibiting symptoms of or suspected for grapevine leafroll (GLD) and red blotch (GRBD) diseases. A limited number of samples from white-berried cultivars were collected randomly due to the lack of visual symptoms. Samples were collected from a total of 2,063 grapevines from 18 red-berried cultivars and seven white-berried cultivars planted in eight American Viticultural Areas and tested for GLRaV-3 and GRBV using RT-PCR and PCR, respectively. The results showed 67.77% and 6.01% of total samples positive for GLRaV-3 and GRBV, respectively, and 9.06% of samples positive for both viruses. About 17% of samples tested negative for the two viruses, but some of these samples were positive for GLRaV-2 and GLRaV-4. Overall results indicated that GLRaV-3 was more common than GRBV, independent of cultivars and the geographic origin of samples. Due to variability in symptoms in red-berried cultivars, virus-specific diagnostic assays were deemed necessary for reliable identification of GLRaV-3 and GRBV and to differentiate GLD and GRBD symptoms from those induced by biotic and abiotic stresses in vineyards. A multiplex PCR protocol was developed for simultaneous detection of GLRaV-3 and GRBV in grapevine samples. A global phylogenetic analysis of GRBV genome sequences revealed segregation of virus isolates from Washington State vineyards into two distinct clades, with the majority of isolates belonging to clade II.
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Affiliation(s)
- Jati Adiputra
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350
| | - Sandya R Kesoju
- Department of Agriculture, Columbia Basin College, Pasco, WA 99301
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350
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Jarugula S, Gowda S, Dawson WO, Naidu RA. Development of infectious cDNA clones of Grapevine leafroll-associated virus 3 and analyses of the 5' non-translated region for replication and virion formation. Virology 2018; 523:89-99. [PMID: 30103103 DOI: 10.1016/j.virol.2018.07.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 01/28/2023]
Abstract
Infectious cDNA clones were developed for Grapevine leafroll-associated virus 3 (GLRaV-3, genus Ampelovirus, family Closteroviridae). In vitro RNA transcripts generated from cDNA clones showed replication via the production of 3'-coterminal subgenomic (sg) mRNAs in Nicotiana benthamiana protoplasts. The detection of sgRNAs and the recovery of progeny recombinant virions from N. benthamiana leaves agroinfiltrated with full-length cDNA clones confirmed RNA replication and virion formation. The 5' non-translated region (5' NTR) of GLRaV-3 was exchangeable between genetic variants and complement the corresponding cognate RNA functions in trans. Mutational analysis of the 5' NTR in minireplicon cDNA clones showed that the conserved 40 nucleotides at the 5'-terminus were indispensable for replication, compared to downstream variable portion of the 5' NTR. Some of the functional mutations in the 5' NTR were tolerated in full-length cDNA clones and produced sgRNAs and virions in N. benthamiana leaves, whereas other mutations affected replication and virion formation.
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Affiliation(s)
- Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, WA 99350, United States
| | - Siddarame Gowda
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - William O Dawson
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, WA 99350, United States.
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