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Martínez-Fajardo C, Navarro-Simarro P, Morote L, Rubio-Moraga Á, Mondéjar-López M, Niza E, Argandoña J, Ahrazem O, Gómez-Gómez L, López-Jiménez AJ. Exploring the viral landscape of saffron through metatranscriptomic analysis. Virus Res 2024; 345:199389. [PMID: 38714217 PMCID: PMC11101869 DOI: 10.1016/j.virusres.2024.199389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/09/2024]
Abstract
Saffron (Crocus sativus L.), a historically significant crop valued for its nutraceutical properties, has been poorly explored from a phytosanitary perspective. This study conducted a thorough examination of viruses affecting saffron samples from Spanish cultivars, using high-throughput sequencing alongside a systematic survey of transcriptomic datasets from Crocus sativus at the Sequence Read Archive. Our analysis unveiled a broad diversity and abundance, identifying 17 viruses across the 52 analyzed libraries, some of which were highly prevalent. This includes known saffron-infecting viruses and previously unreported ones. In addition, we discovered 7 novel viruses from the Alphaflexiviridae, Betaflexiviridae, Potyviridae, Solemoviridae, and Geminiviridae families, with some present in libraries from various locations. These findings indicate that the saffron-associated virome is more complex than previously reported, emphasizing the potential of phytosanitary analysis to enhance saffron productivity.
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Affiliation(s)
- Cristian Martínez-Fajardo
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Pablo Navarro-Simarro
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Lucía Morote
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Ángela Rubio-Moraga
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain
| | - María Mondéjar-López
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Enrique Niza
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Facultad de Farmacia. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Javier Argandoña
- Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain
| | - Oussama Ahrazem
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain
| | - Lourdes Gómez-Gómez
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Facultad de Farmacia. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain
| | - Alberto José López-Jiménez
- Instituto Botánico. Universidad de Castilla-La Mancha, Campus Universitario s/n, Albacete 02071, Spain; Escuela Técnica Superior de Ingeniería Agronómica y de Montes y Biotecnología. Departamento de Ciencia y Tecnología Agroforestal y Genética. Universidad de Castilla-La Mancha, Albacete, Spain.
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Gogile A, Knierim D, Margaria P, Menzel W, Abide M, Kebede M, Kidanemariam D, Abraham A. White yam (Dioscorea rotundata) plants exhibiting virus-like symptoms are co-infected with a new potyvirus and a new crinivirus in Ethiopia. Virus Genes 2024:10.1007/s11262-024-02077-4. [PMID: 38833150 DOI: 10.1007/s11262-024-02077-4] [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: 04/19/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
White yam (Dioscorea rotundata) plants collected from farmers' fields and planted at the Areka Agricultural Research Center, Southern Ethiopia, displayed mosaic, mottling, and chlorosis symptoms. To determine the presence of viral pathogens, an investigation for virome characterization was conducted by Illumina high-throughput sequencing. The bioinformatics analysis allowed the assembly of five viral genomes, which according to the ICTV criteria were assigned to a novel potyvirus (3 genome sequences) and a novel crinivirus (2 genome sequences). The potyvirus showed ~ 66% nucleotide (nt) identity in the polyprotein sequence to yam mosaic virus (NC004752), clearly below the demarcation criteria of 76% identity. For the crinivirus, the RNA 1 and RNA 2 shared the highest sequence identity to lettuce chlorosis virus, and alignment of the aa sequence of the RdRp, CP and HSP70h (~ 49%, 45% and 76% identity), considered for the demarcation criteria, revealed the finding of a novel virus species. The names Ethiopian yam virus (EYV) and Yam virus 1 (YV-1) are proposed for the two tentative new virus species.
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Affiliation(s)
- Ashebir Gogile
- Department of Biotechnology, College of Natural and Applied Science, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
- Department of Biology, College of Natural and Computational Sciences, Wolaita Sodo University, Wolaita Sodo, Ethiopia.
| | - Dennis Knierim
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124, Brunswick, Germany
| | - Paolo Margaria
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124, Brunswick, Germany
| | - Wulf Menzel
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124, Brunswick, Germany
| | - Mereme Abide
- Department of Biotechnology, College of Natural and Applied Science, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Misrak Kebede
- Department of Biotechnology, College of Natural and Applied Science, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
| | - Dawit Kidanemariam
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Adane Abraham
- Department of Biotechnology, College of Natural and Applied Science, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia.
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana.
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3
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Obonyo D, Ouma G, Ikawa R, Odeny DA. Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus. Virology 2024; 593:110011. [PMID: 38367474 DOI: 10.1016/j.virol.2024.110011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses. METHODS We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X. RESULTS Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported. CONCLUSION Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing.
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Affiliation(s)
- Dennis Obonyo
- Department of Biotechnology, University of Eldoret, Kenya, P.O Box 1125-30100, Eldoret, Kenya; Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - George Ouma
- Institute for Climate Change and Adaptation, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Rachel Ikawa
- Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Eastern and Southern Africa, P.O Box 39063-00623, Nairobi, Kenya.
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Belete MT, Kim SE, Gudeta WF, Igori D, Kwon JA, Lee SH, Moon JS. Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis. Virol J 2024; 21:86. [PMID: 38622686 PMCID: PMC11017662 DOI: 10.1186/s12985-024-02361-7] [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: 12/04/2023] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants. RESULTS An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination. CONCLUSIONS We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.
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Affiliation(s)
- Mesele Tilahun Belete
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Amhara Agricultural Research Institute, Plant Biotechnology Research Division, Bahir Dar, Ethiopia
| | - Se Eun Kim
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Workitu Firmosa Gudeta
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Davaajargal Igori
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
- Department of Biology, School of Mathematics and Natural Sciences, Mongolian National University of Education, Ulaanbaatar, Mongolia
| | - Jeong A Kwon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Su-Heon Lee
- School of Applied Bioscience, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 98411, Republic of Korea.
| | - Jae Sun Moon
- Biosystem and Bioengineering Program, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- Plant System Engineering Research Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.
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Wu J, Zhang Y, Li F, Zhang X, Ye J, Wei T, Li Z, Tao X, Cui F, Wang X, Zhang L, Yan F, Li S, Liu Y, Li D, Zhou X, Li Y. Plant virology in the 21st century in China: Recent advances and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:579-622. [PMID: 37924266 DOI: 10.1111/jipb.13580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.
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Affiliation(s)
- Jianguo Wu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongliang Zhang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoming Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Ye
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Taiyun Wei
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaorong Tao
- Department of Plant Pathology, The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xianbing Wang
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lili Zhang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Dawei Li
- State Key Laboratory of Plant Environmental Resilience and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yi Li
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
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Comont G, Faure C, Candresse T, Laurens M, Valière S, Lluch J, Lefebvre M, Gambier S, Jolivet J, Corio-Costet MF, Marais A. Characterization of the RNA Mycovirome Associated with Grapevine Fungal Pathogens: Analysis of Mycovirus Distribution and Their Genetic Variability within a Collection of Botryosphaeriaceae Isolates. Viruses 2024; 16:392. [PMID: 38543758 PMCID: PMC10975779 DOI: 10.3390/v16030392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 05/23/2024] Open
Abstract
Botryosphaeriaceae are fungi involved in the decay of various woody species, including the grapevine, leading to significant production losses. This fungal family is largely ubiquitous, and seven species of Botryosphaeriaceae have been identified in French vineyards, with variable levels of aggressiveness, both in vitro and in planta. Mycoviruses can impact the life traits of their fungal hosts, including aggressiveness, and are one of the factors influencing fungal pathogenicity. In this study, the RNA mycovirome of fifteen Botryosphaeriaceae isolates was characterized through the high-throughput sequencing of double-stranded RNA preparations from the respective samples. Eight mycoviruses were detected, including three potential novel species in the Narnaviridae family, as well as in the proposed Mycobunyaviridae and Fusagraviridae families. A large collection of Botryosphaeriaceae isolates was screened using RT-PCR assays specific for 20 Botryosphaeriaceae-infecting mycoviruses. Among the mycoviruses detected, some appeared to be specialists within a single host species, while others infected isolates belonging to multiple Botryosphaeriaceae species. This screening allowed us to conclude that one-third of the Botryosphaeriaceae isolates were infected by at least one mycovirus, and a significant proportion of isolates (43.5%) were found to be coinfected by several viruses, with very complex RNA mycoviromes for some N. parvum isolates.
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Affiliation(s)
- Gwenaëlle Comont
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Chantal Faure
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Thierry Candresse
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Marie Laurens
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, GenoToul, 31320 Castanet-Tolosan, France; (S.V.); (J.L.)
| | - Jérôme Lluch
- INRAE, US 1426, GeT-PlaGe, GenoToul, 31320 Castanet-Tolosan, France; (S.V.); (J.L.)
| | - Marie Lefebvre
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
| | - Sébastien Gambier
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Jérôme Jolivet
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Marie-France Corio-Costet
- UMR Santé et Agroécologie du Vignoble (1065), ISVV, Labex Cote, Plant Health Department, INRAE, 33140 Villenave d’Ornon, France; (G.C.); (M.L.); (S.G.); (J.J.)
| | - Armelle Marais
- UMR BFP, INRAE, University of Bordeaux, 33140 Villenave d’Ornon, France; (C.F.); (T.C.); (M.L.)
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7
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Gholampour Z, Zakiaghl M, Asquini E, Moser M, Gualandri V, Mehrvar M, Si-Ammour A. Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran. Viruses 2024; 16:204. [PMID: 38399980 PMCID: PMC10891595 DOI: 10.3390/v16020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
A comprehensive study on the whole spectrum of viruses and viroids in five Iranian grapevine cultivars was carried out using sRNA libraries prepared from phloem tissue. A comparison of two approaches to virus detection from sRNAome data indicated a significant difference in the results and performance of the aligners in viral genome reconstruction. The results showed a complex virome in terms of viral composition, abundance, and richness. Thirteen viruses and viroids were identified in five Iranian grapevine cultivars, among which the grapevine red blotch virus and grapevine satellite virus were detected for the first time in Iranian vineyards. Grapevine leafroll-associated virus 1 (GLRaV1) and grapevine fanleaf virus (GFLV) were highly dominant in the virome. However, their frequency and abundance were somewhat different among grapevine cultivars. The results revealed a mixed infection of GLRaV1/grapevine yellow speckle viroid 1 (GYSVd1) and GFLV/GYSVd1 in grapevines that exhibited yellows and vein banding. We also propose a threshold of 14% of complete reconstruction as an appropriate threshold for detection of grapevine viruses that can be used as indicators for reliable grapevine virome profiling or in quarantine stations and certification programs.
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Affiliation(s)
- Zahra Gholampour
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Mohammad Zakiaghl
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Elisa Asquini
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Mirko Moser
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Valeria Gualandri
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Mohsen Mehrvar
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Azeddine Si-Ammour
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
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8
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Luan Y, Fan W, Korxeelor X, Wu X. Isolation of dsRNA from Plants by Cellulose Chromatography. Methods Mol Biol 2024; 2771:13-17. [PMID: 38285385 DOI: 10.1007/978-1-0716-3702-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
As the constitutive molecules of double-stranded RNA (dsRNA) virus genomes and replicative intermediates of single-stranded RNA (ssRNA) viruses, the high-molecular-weight dsRNAs are commonly found in RNA virus-infected plants. Therefore, the dsRNA is recognized as a hallmark of RNA virus infection and the profile of dsRNA has been applied as an efficient tool for diagnoses or characterization of unreported RNA viruses. Cellulose chromatography is one of the most useful procedures for the isolation of viral dsRNAs from total nucleic acids. Here, we describe rapid cellulose-based methods for purification of dsRNAs from plant tissue.
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Affiliation(s)
- Yameng Luan
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wenqian Fan
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xayvangye Korxeelor
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaoyun Wu
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China.
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9
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Wang Y, Wang Z, Wu X. Rapid Purification of dsRNA Using Micro-Spin Cellulose Column. Methods Mol Biol 2024; 2771:19-25. [PMID: 38285386 DOI: 10.1007/978-1-0716-3702-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Double-stranded RNA (dsRNA) is the replication intermediates of all RNA viruses. Purification and analysis of the profile and sequence of dsRNA is vital in virus diagnoses and/or characterization. Cellulose is one of the common materials used for isolation of dsRNA. Cellulose specifically binds dsRNA fraction under 15% ethanol concentration, which allows to isolate dsRNA from total nucleic acid solution or cell lysate. Here, we describe a rapid and reliable method for purifying dsRNA using a home-made micro-spin cellulose column from the cell lysate of virus-infected plant tissue. This labor-saving and rapid method enables routinely high-throughput isolation and analysis of dsRNA in plant or fungi samples.
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Affiliation(s)
- Yuting Wang
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Ziyi Wang
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Xiaoyun Wu
- College of Plant Protection, Northeast Agricultural University, Harbin, Heilongjiang, China.
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10
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Zhao R, Su X, Yu F, Liu Z, Huang X. Identification and characterization of two closely related virga-like viruses latently infecting rubber trees ( Hevea brasiliensis). Front Microbiol 2023; 14:1286369. [PMID: 38156006 PMCID: PMC10752949 DOI: 10.3389/fmicb.2023.1286369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023] Open
Abstract
A novel virga-like virus, provisionally named Rubber tree latent virus 2 (RTLV2), was identified from rubber tree (Hevea brasiliensis). It is a close relative of the previously reported Rubber tree latent virus 1 (RTLV1). The complete genomes of RTLV1 and RTLV2 were sequenced and comparatively analyzed in terms of genome organization, putative gene products and phylogenetic relationship. Both RTLV1 and RTLV2 have positive-sense single-stranded RNA genomes that encode seven open reading frames (ORFs), forming a similar genomic layout. In phylogenetic analyses based on replicase and coat protein amino acid sequences, RTLV1 and RTLV2 were clustered with unclassified virga-like viruses. They are distinct from currently recognized plant virus families. RTLV1 and RTLV2 can be distinguished from members of Virgaviridae by the presence of a putative coat protein duplex and a poly(A) tail at the 3'-terminus. The authenticity of RTLV1 and RTLV2 as infectious viruses was confirmed through field investigations and transmissibility assays. In conclusion, RTLV1 and RTLV2 represent a novel plant virus group that does not readily fit into current virus families.
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Affiliation(s)
- Ruibai Zhao
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- School of Life Sciences, Hainan University, Haikou, China
| | - Xiaoqi Su
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Fengjuan Yu
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
| | - Zhu Liu
- School of Life Sciences, Hainan University, Haikou, China
| | - Xi Huang
- College of Tropical Crops, Sanya Nanfan Research Institute of Hainan University, Sanya, China
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11
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Yan C, Yin H, Zhang Y, Ren Z, Wang J, Li Y. Mixed infections with new emerging viruses associated with jujube mosaic disease. Int Microbiol 2023; 26:1103-1112. [PMID: 37118189 DOI: 10.1007/s10123-023-00365-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 04/30/2023]
Abstract
BACKGROUND Jujube is an economically important fruit tree and native to China. Viral disease is a new threat to jujube production, and several new viruses have been identified infecting jujube plants. During our field survey, jujube mosaic disease was widely distributed in Beijing, but the associated causal agents are still unknown. METHODS Small RNA deep sequencing was conducted to identify the candidate viruses associated with jujube mosaic. Further complete genome sequences of the viruses were cloned, and the genomic characterization of each virus was analyzed. The field distribution of these viruses was further explored with PCR/RT-PCR detection of field samples. RESULTS Mixed infection of four viruses was identified in a plant sample with the symptom of mosaic and leaf twisting, including the previously reported jujube yellow mottle-associated virus (JYMaV), persimmon ampelovirus (PAmpV), a new badnavirus tentatively named jujube-associated badnavirus (JaBV), and a new secovirus tentatively named jujube-associated secovirus (JaSV). PAmpV-jujube was 14,093 nt in length with seven putative open reading frames (ORFs) and shared highest (79.4%) nucleotide (nt) sequence identity with PAmpV PBs3. Recombination analysis showed that PAmpV-jujube was a recombinant originating from plum bark necrosis stem pitting-associated virus isolates nanjing (KC590347) and bark (EF546442). JaBV was 6449 bp in length with conserved genomic organization typical of badnaviruses. The conserved RT and RNAse H region shared highest 67.6% nt sequence identity with jujube mosaic-associated virus, which was below the 80% nt sequence identity value used as the species demarcation threshold in Badnavirus. The genome of JaSV composed of two RNA molecules of 5878 and 3337 nts in length, excluding the polyA tails. Each genome segment contained one large ORF that shared homology and phylogenetic identity with members of the family Secoviridae. Field survey showed JYMaV and JaBV were widely distributed in jujube trees in Beijing. CONCLUSION Two new viruses were identified from jujube plants, and mixed infections of JYMaV and JaBV were common in jujube in Beijing.
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Affiliation(s)
- Chenge Yan
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Hang Yin
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Zhengguang Ren
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Jinzhong Wang
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China
| | - Yongqiang Li
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing, 102206, China.
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing, 102206, China.
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12
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Ma J, Dissanayaka Mudiyanselage SD, Hao J, Wang Y. Cellular roadmaps of viroid infection. Trends Microbiol 2023; 31:1179-1191. [PMID: 37349206 PMCID: PMC10592528 DOI: 10.1016/j.tim.2023.05.014] [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: 03/16/2023] [Revised: 05/28/2023] [Accepted: 05/31/2023] [Indexed: 06/24/2023]
Abstract
Viroids are single-stranded circular noncoding RNAs that infect plants. According to the International Committee on Taxonomy of Viruses, there are 44 viroids known to date. Notably, more than 20 000 distinct viroid-like RNA sequences have recently been identified in existing sequencing datasets, suggesting an unprecedented complexity in biological roles of viroids and viroid-like RNAs. Interestingly, a human pathogen, hepatitis delta virus (HDV), also replicates via a rolling circle mechanism like viroids. Therefore, knowledge of viroid infection is informative for research on HDV and other viroid-like RNAs reported from various organisms. Here, we summarize recent advancements in understanding viroid shuttling among subcellular compartments for completing replication cycles, emphasizing regulatory roles of RNA motifs and structural dynamics in diverse biological processes. We also compare the knowledge of viroid intracellular trafficking with known pathways governing cellular RNA movement in cells. Future investigations on regulatory RNA structures and cognate factors in regulating viroid subcellular trafficking and replication will likely provide new insights into RNA structure-function relationships and facilitate the development of strategies controlling RNA localization and function in cells.
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Affiliation(s)
- Junfei Ma
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | | | - Jie Hao
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Current address: Plant Pathology Department, University of Florida, Gainesville, FL 32611, USA.
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13
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Svanella-Dumas L, Tsarmpopoulos I, Marais A, Faure C, Theil S, Glasa M, Predajna L, Gaudin J, Tian S, Porcher L, Gentit P, De Oliveira ML, Krause-Sakate R, Candresse T. Molecular and Biological Characterization of Novel and Known Family Secoviridae Members Infecting Lettuce. PHYTOPATHOLOGY 2023; 113:1595-1604. [PMID: 37081712 DOI: 10.1094/phyto-03-23-0095-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High-throughput sequencing of two lettuces showing virus-like symptoms in France provided evidence of infection by members of the family Secoviridae. One plant (JG1) had a complex mixed infection that involved, among others, a novel waikavirus (lettuce waikavirus 1) and two isolates of a sequivirus related to lettuce mottle virus (LeMoV). The second lettuce plant (JG2) was singly infected by LeMoV. Complete genomic sequences were obtained for all four isolates and, in addition, near complete genome sequences were obtained for other LeMoV or LeMoV-related isolates (from French cultivated and wild lettuces and from a Brazilian cultivated lettuce) and for two isolates of another family Asteraceae-infecting sequivirus, dandelion yellow mosaic virus (DaYMV). Analysis of these genomic sequences allows the proposal of tentative genome organization for the various viruses and clarification of their phylogenetic relationships. Sequence and host range comparisons point to significant differences between the two sequivirus isolates identified in the JG1 plant and LeMoV isolates from France and Brazil, suggesting they belong to a novel species for which the name lettuce star mosaic virus is proposed.
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Affiliation(s)
- Laurence Svanella-Dumas
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Iason Tsarmpopoulos
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Chantal Faure
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
| | - Lukas Predajna
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic
| | - Jonathan Gaudin
- INRAE, Bordeaux Sciences Agro, UMR Santé et Agroécologie du Vignoble, CS20032, 33882 Villenave d'Ornon Cedex, France
| | - Sixing Tian
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Laëtitia Porcher
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Pascal Gentit
- ANSES, Plant Health Laboratory, Unité de Bactériologie, Virologie et détection des OGM, 7 rue Jean Dixméras, 49044 Angers Cedex 01, France
| | - Milena Leite De Oliveira
- Laboratorio Central Multisuarios (LACEM), Faculdade de Ciências Agronômicas, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Renate Krause-Sakate
- Department of Plant Protection, Faculdade de Ciências Agronômicas, School of Agriculture, Sao Paulo State University (UNESP), Botucatu, Brazil
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR Biologie du fruit et Pathologie, CS20032, 33882 Villenave d'Ornon Cedex, France
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14
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Liu S, Han Y, Li WX, Ding SW. Infection Defects of RNA and DNA Viruses Induced by Antiviral RNA Interference. Microbiol Mol Biol Rev 2023; 87:e0003522. [PMID: 37052496 PMCID: PMC10304667 DOI: 10.1128/mmbr.00035-22] [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] [Indexed: 04/14/2023] Open
Abstract
Immune recognition of viral genome-derived double-stranded RNA (dsRNA) molecules and their subsequent processing into small interfering RNAs (siRNAs) in plants, invertebrates, and mammals trigger specific antiviral immunity known as antiviral RNA interference (RNAi). Immune sensing of viral dsRNA is sequence-independent, and most regions of viral RNAs are targeted by virus-derived siRNAs which extensively overlap in sequence. Thus, the high mutation rates of viruses do not drive immune escape from antiviral RNAi, in contrast to other mechanisms involving specific virus recognition by host immune proteins such as antibodies and resistance (R) proteins in mammals and plants, respectively. Instead, viruses actively suppress antiviral RNAi at various key steps with a group of proteins known as viral suppressors of RNAi (VSRs). Some VSRs are so effective in virus counter-defense that potent inhibition of virus infection by antiviral RNAi is undetectable unless the cognate VSR is rendered nonexpressing or nonfunctional. Since viral proteins are often multifunctional, resistance phenotypes of antiviral RNAi are accurately defined by those infection defects of VSR-deletion mutant viruses that are efficiently rescued by host deficiency in antiviral RNAi. Here, we review and discuss in vivo infection defects of VSR-deficient RNA and DNA viruses resulting from the actions of host antiviral RNAi in model systems.
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Affiliation(s)
- Si Liu
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Yanhong Han
- Vector-borne Virus Research Center, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wan-Xiang Li
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Shou-Wei Ding
- Department of Microbiology & Plant Pathology, University of California, Riverside, California, USA
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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15
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Miao Y, Bian J, Dong G, Dai T. DETIRE: a hybrid deep learning model for identifying viral sequences from metagenomes. Front Microbiol 2023; 14:1169791. [PMID: 37396369 PMCID: PMC10313334 DOI: 10.3389/fmicb.2023.1169791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/18/2023] [Indexed: 07/04/2023] Open
Abstract
A metagenome contains all DNA sequences from an environmental sample, including viruses, bacteria, archaea, and eukaryotes. Since viruses are of huge abundance and have caused vast mortality and morbidity to human society in history as a type of major pathogens, detecting viruses from metagenomes plays a crucial role in analyzing the viral component of samples and is the very first step for clinical diagnosis. However, detecting viral fragments directly from the metagenomes is still a tough issue because of the existence of a huge number of short sequences. In this study a hybrid Deep lEarning model for idenTifying vIral sequences fRom mEtagenomes (DETIRE) is proposed to solve the problem. First, the graph-based nucleotide sequence embedding strategy is utilized to enrich the expression of DNA sequences by training an embedding matrix. Then, the spatial and sequential features are extracted by trained CNN and BiLSTM networks, respectively, to enrich the features of short sequences. Finally, the two sets of features are weighted combined for the final decision. Trained by 220,000 sequences of 500 bp subsampled from the Virus and Host RefSeq genomes, DETIRE identifies more short viral sequences (<1,000 bp) than the three latest methods, such as DeepVirFinder, PPR-Meta, and CHEER. DETIRE is freely available at Github (https://github.com/crazyinter/DETIRE).
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16
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Togoobat B, Wu N, Wang X, Cao M, Xu Z. Viromic approach reveals differences in the composition, diversity and relative abundance of pumpkin viruses across main growing regions of China. Virology 2023; 585:61-71. [PMID: 37295338 DOI: 10.1016/j.virol.2023.05.005] [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: 04/16/2023] [Revised: 05/11/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023]
Abstract
China is the leading country for pumpkin production in the world. As other cucurbits, diseases caused by viruses are among the serious threats to pumpkin production, but our knowledge on the virus species infecting pumpkin plants is fragmentary. To understand the occurrence of viral diseases on pumpkin, we determined the geographical distribution characteristics, relative abundance and evolutionary relationship of pumpkin infected viruses by meta-transcriptome sequencing (RNA-seq) and viromic analysis of 159 samples exhibited typical viral symptoms collected across China in this study. Totally, 11 known and 3 new viruses were identified. Interestingly, 3 new viruses identified in this study should be positive-sense single-stranded RNA virus whose hosts are prokaryotes. The viruses identified in different sampling locations exhibit significant variations in term of virus species and relative abundance. Here, the results provide valuable information for understanding the virus species and their diversity in cultivated pumpkin across major growing regions of China.
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Affiliation(s)
- Batchimeg Togoobat
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China; Laboratory for Plant Pathology, Institute of Plant Protection, Ulaanbaatar, Mongolia
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Chongqing, China
| | - Zhongtian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo, China.
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17
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Li J, Wu X, Liu H, Wang X, Yi S, Zhong X, Wang Y, Wang Z. Identification and Molecular Characterization of a Novel Carlavirus Infecting Chrysanthemum morifolium in China. Viruses 2023; 15:v15041029. [PMID: 37113009 PMCID: PMC10141686 DOI: 10.3390/v15041029] [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: 03/28/2023] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium) is an important ornamental and medicinal plant suffering from many viruses and viroids worldwide. In this study, a new carlavirus, tentatively named Chinese isolate of Carya illinoinensis carlavirus 1 (CiCV1-CN), was identified from chrysanthemum plants in Zhejiang Province, China. The genome sequence of CiCV1-CN was 8795 nucleotides (nt) in length, with a 68-nt 5'-untranslated region (UTR) and a 76-nt 3'-UTR, which contained six predicted open reading frames (ORFs) that encode six corresponding proteins of various sizes. Phylogenetic analyses based on full-length genome and coat protein sequences revealed that CiCV1-CN is in an evolutionary branch with chrysanthemum virus R (CVR) in the Carlavirus genus. Pairwise sequence identity analysis showed that, except for CiCV1, CiCV1-CN has the highest whole-genome sequence identity of 71.3% to CVR-X6. At the amino acid level, the highest identities of predicted proteins encoded by the ORF1, ORF2, ORF3, ORF4, ORF5, and ORF6 of CiCV1-CN were 77.1% in the CVR-X21 ORF1, 80.3% in the CVR-X13 ORF2, 74.8% in the CVR-X21 ORF3, 60.9% in the CVR-BJ ORF4, 90.2% in the CVR-X6 and CVR-TX ORF5s, and 79.4% in the CVR-X21 ORF6. Furthermore, we also found a transient expression of the cysteine-rich protein (CRP) encoded by the ORF6 of CiCV1-CN in Nicotiana benthamiana plants using a potato virus X-based vector, which can result in a downward leaf curl and hypersensitive cell death over the time course. These results demonstrated that CiCV1-CN is a pathogenic virus and C. morifolium is a natural host of CiCV1.
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Affiliation(s)
- Jiapeng Li
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xiaoyin Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Hui Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaomei Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Shaokui Yi
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhanqi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou 313000, China
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18
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Ding SW. Transgene Silencing, RNA Interference, and the Antiviral Defense Mechanism Directed by Small Interfering RNAs. PHYTOPATHOLOGY 2023; 113:616-625. [PMID: 36441873 DOI: 10.1094/phyto-10-22-0358-ia] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
One important discovery in plant pathology over recent decades is the natural antiviral defense mechanism mediated by RNA interference (RNAi). In antiviral RNAi, virus infection triggers Dicer processing of virus-specific double-stranded RNA into small interfering RNAs (siRNAs). Frequently, further amplified by host enzyme and cofactors, these virus-derived siRNAs direct specific virus clearance in an Argonaute protein-containing effector complex. The siRNAs derived from viruses and viroids accumulate to very high levels during infection. Because they overlap extensively in nucleotide sequence, this allows for deep sequencing and bioinformatics assembly of total small RNAs for rapid discovery and identification of viruses and viroids. Antiviral RNAi acts as the primary defense mechanism against both RNA and DNA viruses in plants, yet viruses still successfully infect plants. They do so because all currently recognized plant viruses combat the RNAi response by encoding at least one protein as a viral suppressor of RNAi (VSR) required for infection, even though plant viruses have small genome sizes with a limited coding capacity. This review article will recapitulate the key findings that have revealed the genetic pathway for the biogenesis and antiviral activity of viral siRNAs and the specific role of VSRs in infection by antiviral RNAi suppression. Moreover, early pioneering studies on transgene silencing, RNAi, and virus-plant/virus-virus interactions paved the road to the discovery of antiviral RNAi.
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Affiliation(s)
- Shou-Wei Ding
- Department of Microbiology & Plant Pathology and Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, CA
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19
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Discovery of a Closterovirus Infecting Jujube Plants Grown at Aksu Area in Xinjiang of China. Viruses 2023; 15:v15020267. [PMID: 36851483 PMCID: PMC9958854 DOI: 10.3390/v15020267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/05/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023] Open
Abstract
Chinese jujube (Ziziphus jujuba Mill.) is a widely grown fruit crop at Aksu in Xinjiang Uygur Autonomous Region of China. Viral disease-like symptoms are common on jujube plants. Here, for the first time, we report a virus tentatively named persimmon ampelovirus jujube isolate (PAmpV-Ju) infecting jujube plants. The virus was identified using high-throughput sequencing from a jujube plant (ID: AKS15) and molecularly related to viruses in the family Closteroviridae. The genomic sequences of two PAmpV-Ju variants named AKS15-20 and AKS15-17 were determined by RT-PCR amplifications. The genome structure of PAmpV-Ju was identical to that of a recently reported persimmon ampelovirus (PAmpV) and consisted of seven open reading frames. The genomes of AKS15-20 and AKS15-17 shared 83.7% nt identity with each other, and the highest nt sequence identity of 79% with two variants of PAmpV. The incidence of PAmpV-Ju on Aksu jujube plants was evaluated by RT-PCR assays. The phylogenetic analysis of amplified partial sequences coding for polymerase, HSP70h, and CP revealed two phylogenetic clades represented by AKS15-20 and AKS15-17. Our study provides important evidence for understanding viruses infecting jujube plants and establishing efficient measures to prevent virus spread.
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20
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Villamor DEV, Mejia AS, Martin RR, Tzanetakis IE. Genomic Analysis and Development of Infectious Clone of a Novel Carlavirus Infecting Blueberry. PHYTOPATHOLOGY 2023; 113:98-103. [PMID: 35852469 DOI: 10.1094/phyto-05-22-0186-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new blueberry virus was discovered using high-throughput sequencing. Using sequence identity values, phylogenetics, and serological and biological properties, we propose the virus, putatively named blueberry virus S (BluVS), to be a distinct species within the genus Carlavirus (family Betaflexiviridae). The genome was analyzed in depth, and an infectious clone was developed to initiate studies on virus pathogenicity. Agroinfiltration of the binary vector construct produced severe systemic symptoms in Nicotiana occidentalis. Back-inoculation using sap from agroinfiltrated N. occidentalis produced identical symptoms to the recipient plants (N. occidentalis), and virus purification yielded flexuous carlavirus-like particles. However, unlike blueberry scorch virus (BlScV), BluVS caused symptomless infection in Chenopodium quinoa and reacted weakly to BlScV antibodies in an enzyme-linked immunosorbent assay. Collectively, the results provide evidence for the distinct speciation of BluVS. The availability of an infectious clone provides tools for future studies on the biology of the virus.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - A Sierra Mejia
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - R R Martin
- Oregon State University and U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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21
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Chen L, Guo C, Yan C, Sun R, Li Y. Genetic diversity and phylogenetic characteristics of viruses in lily plants in Beijing. Front Microbiol 2023; 14:1127235. [PMID: 37138632 PMCID: PMC10149822 DOI: 10.3389/fmicb.2023.1127235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/21/2023] [Indexed: 05/05/2023] Open
Abstract
Lily (Lilium) is an important bulbous perennial herb that is frequently infected by one or more viruses. To investigate the diversity of lily viruses, lilies with virus-like symptoms in Beijing were collected to perform small RNA deep sequencing. Then, the 12 complete and six nearly full-length viral genomes, including six known viruses and two novel viruses were determined. Based on sequence and phylogenetic analyses, two novel viruses were considered to be members of the genera Alphaendornavirus (Endornaviridae) and Polerovirus (Solemoviridae). These two novel viruses were provisionally named lily-associated alphaendornavirus 1 (LaEV-1) and lily-associated polerovirus 1 (LaPV-1). Based on sequence, phylogenetic and recombination analyses, strawberry latent ringspot virus (SLRSV) in the genus Stralarivirus (Secoviridae) was identified for the first time in China, and shown to exhibit the highest nucleotide (nt) diversity among the available full-length SLRSV genome sequences, with the highest identities of 79.5% for RNA1 and 80.9% for RNA2. Interestingly, the protease cofactor region in RNA1 was 752 aa in length, whereas those of the other 27 characterized isolates ranged from 700-719 aa in length. The genome sequences of lily virus A (Potyvirus), lily virus X (Potexvirus), and plantago asiatica mosaic virus (Potexvirus) exhibited varying degrees of sequence diversity at the nucleotide level compared with their corresponding characterized isolates. In addition, plantago asiatica mosaic virus (PlAMV) tended to cluster on a host species-basis. One identified lily mottle virus (Potyvirus) isolate was detected as a recombinant, and which clustered in a different group with four other isolates. Seven identified lily symptomless virus (Carlavirus) isolates, including one recombinant, were clustered into three clades. Our results revealed the genetic diversity of lily-infecting viruses, and sequence insertion, host species and recombination are factors that likely contribute to this diversity. Collectively, our results provide useful information regarding the control of viral disease in lily.
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Affiliation(s)
- Ling Chen
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Cheng Guo
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Chenge Yan
- College of Biological Science and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Rui Sun
- College of Biological Science and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Yongqiang Li
- College of Biological Science and Resources Environment, Beijing University of Agriculture, Beijing, China
- *Correspondence: Yongqiang Li,
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22
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Wang F, Zhu J, Zhu Y, Yan D, Dong Q, Jegede OJ, Wu Q. Complete genome sequence of a new badnavirus infecting a tea plant in China. Arch Virol 2022; 167:2811-2815. [PMID: 36269416 DOI: 10.1007/s00705-022-05592-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/25/2022] [Indexed: 12/14/2022]
Abstract
The complete genome of a novel virus, provisionally named "Camellia sinensis badnavirus 1" (CSBV1), was identified in tea plant (Camellia sinensis) leaves collected in Anhui Province, China. The genome of CSBV1 consists of 8,195 bp and possesses three open reading frames (ORFs), sharing 68.6 % nucleotide sequence identity with the genome of Camellia lemon glow virus (CLGV) from Camellia japonica. The genome organization of CSBV1 is highly similar to that of members of the genus Badnavirus (family Caulimoviridae). Phylogenetic analysis revealed that CSBV1, CLGV, and cacao swollen shoot virus form a separate clade within the genus Badnavirus, suggesting that CSBV1 is the first badnavirus infecting C. sinensis.
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Affiliation(s)
- Fang Wang
- Anhui Academy of Agricultural Sciences, 230031, Hefei, Anhui, P.R. China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, 230036, Hefei, Anhui, P.R. China
| | - Yu Zhu
- School of Life Sciences, University of Science and Technology of China, 230021, Hefei, Anhui, P.R. China
| | - Dankan Yan
- Anhui Academy of Agricultural Sciences, 230031, Hefei, Anhui, P.R. China
| | - Qing Dong
- Anhui Academy of Agricultural Sciences, 230031, Hefei, Anhui, P.R. China
| | - Oluwasegun J Jegede
- School of Life Sciences, University of Science and Technology of China, 230021, Hefei, Anhui, P.R. China
| | - Qingfa Wu
- School of Life Sciences, University of Science and Technology of China, 230021, Hefei, Anhui, P.R. China.
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23
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Yang S, Mao Q, Wang Y, He J, Yang J, Chen X, Xiao Y, He Y, Zhao M, Lu J, Yang Z, Dai Z, Liu Q, Yao Y, Lu X, Li H, Zhou R, Zeng J, Li W, Zhou C, Wang X, Shen Q, Xu H, Deng X, Delwart E, Shan T, Zhang W. Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal. ENVIRONMENTAL MICROBIOME 2022; 17:58. [PMID: 36437477 PMCID: PMC9703751 DOI: 10.1186/s40793-022-00453-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/17/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem. RESULTS We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common. CONCLUSIONS Our data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.
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Affiliation(s)
- Shixing Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qingqing Mao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yan Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jingxian He
- Suzhou Medical College of Soochow University, Suzhou, 215123, China
| | - Jie Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xu Chen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuqing Xiao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yumin He
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Min Zhao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Juan Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Zijun Yang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyuan Dai
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Qi Liu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yuxin Yao
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiang Lu
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hong Li
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Rui Zhou
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jian Zeng
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Wang Li
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Chenglin Zhou
- Department of Laboratory Medicine, Jiangsu Taizhou People's Hospital, Taizhou, 225300, Jiangsu, China
| | - Xiaochun Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Quan Shen
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Hui Xu
- The Affiliated Hospital of Jiangsu University, Zhenjiang, 212001, Jiangsu, China
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA, 94118, USA
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA, 94118, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, 94118, USA
| | - Tongling Shan
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, China.
| | - Wen Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
- International Genome Center, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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24
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Zhong X, Yang L, Li J, Tang Z, Wu C, Zhang L, Zhou X, Wang Y, Wang Z. Integrated next-generation sequencing and comparative transcriptomic analysis of leaves provides novel insights into the ethylene pathway of Chrysanthemum morifolium in response to a Chinese isolate of chrysanthemum virus B. Virol J 2022; 19:182. [DOI: 10.1186/s12985-022-01890-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Chrysanthemum virus B (CVB), a key member of the genus Carlavirus, family Betaflexiviridae, causes severe viral diseases in chrysanthemum (Chrysanthemum morifolium) plants worldwide. However, information on the mechanisms underlying the response of chrysanthemum plants to CVB is scant.
Methods
Here, an integrated next-generation sequencing and comparative transcriptomic analysis of chrysanthemum leaves was conducted to explore the molecular response mechanisms of plants to a Chinese isolate of CVB (CVB-CN) at the molecular level.
Results
In total, 4934 significant differentially expressed genes (SDEGs) were identified to respond to CVB-CN, of which 4097 were upregulated and 837 were downregulated. Gene ontology and functional classification showed that the majority of upregulated SDEGs were categorized into gene cohorts involved in plant hormone signal transduction, phenylpropanoid and flavonoid biosynthesis, and ribosome metabolism. Enrichment analysis demonstrated that ethylene pathway-related genes were significantly upregulated following CVB-CN infection, indicating a strong promotion of ethylene biosynthesis and signaling. Furthermore, disruption of the ethylene pathway in Nicotiana benthamiana, a model plant, using virus-induced gene silencing technology rendered them more susceptible to cysteine-rich protein of CVB-CN induced hypersensitive response, suggesting a crucial role of this pathway in response to CVB-CN infection.
Conclusion
This study provides evidence that ethylene pathway has an essential role of plant in response to CVB and offers valuable insights into the defense mechanisms of chrysanthemum against Carlavirus.
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25
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McLeish MJ, Zamfir AD, Babalola BM, Peláez A, Fraile A, García-Arenal F. Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities. Virus Evol 2022; 8:veac095. [PMID: 36405340 PMCID: PMC9667876 DOI: 10.1093/ve/veac095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/24/2022] [Accepted: 09/30/2022] [Indexed: 07/22/2023] Open
Abstract
The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.
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Affiliation(s)
| | | | | | - Adrián Peláez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
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26
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Liang X, Mei S, Yu H, Zhang S, Wu J, Cao M. Mixed infection of an emaravirus, a crinivirus, and a begomovirus in Pueraria lobata (Willd) Ohwi. Front Microbiol 2022; 13:926724. [PMID: 36246248 PMCID: PMC9557060 DOI: 10.3389/fmicb.2022.926724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pueraria lobata (Willd) (Pueraria montana var. lobata (Willd.) Maesen & S. M. Almeida ex Sanjappa & Predeep) is an important herbal medicine used in many countries. In P. lobata plants showing symptoms of mosaic, yellow spots, and mottling, mixed infection of new viruses provisionally named Pueraria lobata-associated emaravirus (PloAEV, genus Emaravirus), Pueraria lobata-associated crinivirus (PloACV, genus Crinivirus), and isolate CQ of the previously reported kudzu mosaic virus (KuMV-CQ, genus Begomovirus) was confirmed through high-throughput sequencing. PloAEV has five RNA segments, encoding a putative RNA-dependent RNA polymerase, glycoprotein precursor, nucleocapsid protein, movement protein, and P5, respectively. PloACV has two RNA segments, encoding 11 putative proteins. Only PloAEV could be mechanically transmitted from mixed infected symptomatic kudzu to Nicotiana benthamiana plants. All three viruses were detected in 35 symptomatic samples collected from five different growing areas, whereas no viruses were detected in 21 non-symptomatic plants, suggesting a high association between these three viruses. Thus, this study provides new knowledge on the diversity and molecular characteristics of viruses in P. lobata plants affected by the viral disease.
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27
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The full-length genome sequence of a novel amalgavirus in Lilium spp. in China. Arch Virol 2022; 167:2103-2107. [PMID: 35834002 DOI: 10.1007/s00705-022-05523-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/22/2022] [Indexed: 11/02/2022]
Abstract
We report for the first time the complete genome sequence of a novel amalgavirus, tentatively designated as 'lily amalgavirus 1' (LAV-1), isolated from Lilium spp. in China. LAV-1 is a 3448-nt double-stranded RNA virus that encodes two putative proteins. Open reading frame 1 (ORF1) encodes a 394-aa protein with unknown function. ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp) of 895 aa. The two ORFs putatively encode a '1 + 2' fusion protein generated by a '+1' programmed ribosomal frameshift (PRF). BLASTp analysis revealed that the complete genome sequence of LAV-1 shares 48.23-59.80% sequence identity (query sequence coverage > 77%) with those of members of the genus Amalgavirus, with the highest nucleotide sequence identity of 59.80% with that of Allium cepa amalgavirus 1 (query sequence coverage, 87%). The genome structure, phylogenetic relationships, and sequence similarities to other plant amalgaviruses suggest that LAV-1 is a new member of the genus Amalgavirus.
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28
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Guevara-Rivera EA, Rodríguez-Negrete EA, Aréchiga-Carvajal ET, Leyva-López NE, Méndez-Lozano J. From Metagenomics to Discovery of New Viral Species: Galium Leaf Distortion Virus, a Monopartite Begomovirus Endemic in Mexico. Front Microbiol 2022; 13:843035. [PMID: 35547137 PMCID: PMC9083202 DOI: 10.3389/fmicb.2022.843035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Begomoviruses (Family Geminiviridae) are a major group of emerging plant viruses worldwide. The knowledge of begomoviruses is mostly restricted to crop plant systems. Nevertheless, it has been described that non-cultivated plants are important reservoirs and vessels of viral evolution that leads to the emergence of new diseases. High-throughput sequencing (HTS) has provided a powerful tool for speeding up the understanding of molecular ecology and epidemiology of plant virome and for discovery of new viral species. In this study, by performing earlier metagenomics library data mining, followed by geminivirus-related signature single plant searching and RCA-based full-length viral genome cloning, and based on phylogenetic analysis, genomes of two isolates of a novel monopartite begomovirus species tentatively named Galium leaf distortion virus (GLDV), which infects non-cultivated endemic plant Galium mexicanum, were identified in Colima, Mexico. Analysis of the genetic structure of both isolates (GLDV-1 and GLDV-2) revealed that the GLDV genome displays a DNA-A-like structure shared with the new world (NW) bipartite begomoviruses. Nonetheless, phylogenetic analysis using representative members of the main begomovirus American clades for tree construction grouped both GLDV isolates in a clade of the monopartite NW begomovirus, Tomato leaf deformation virus (ToLDeV). A comparative analysis of viral replication regulatory elements showed that the GLDV-1 isolate possesses an array and sequence conservation of iterons typical of NW begomovirus infecting the Solanaceae and Fabaceae families. Interestingly, GLDV-2 showed iteron sequences described only in monopartite begomovirus from OW belonging to a sweepovirus clade that infects plants of the Convolvulaceae family. In addition, the rep iteron related-domain (IRD) of both isolates display FRVQ or FRIS amino acid sequences corresponding to NW and sweepobegomovirus clades for GMV-1 and GMV-2, respectively. Finally, the lack of the GLDV DNA-B segment (tested by molecular detection and biological assays using GLDV-1/2 infectious clones) confirmed the monopartite nature of GLDV. This is the first time that a monopartite begomovirus is described in Mexican ecosystems, and “in silico” geometagenomics analysis indicates that it is restricted to a specific region. These data revealed additional complexity in monopartite begomovirus genetics and geographic distribution and highlighted the importance of metagenomic approaches in understanding global virome ecology and evolution.
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Affiliation(s)
- Enrique A Guevara-Rivera
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Edgar A Rodríguez-Negrete
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Elva T Aréchiga-Carvajal
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología-Unidad de Manipulación Genética, San Nicolás de los Garza, Mexico
| | - Norma E Leyva-López
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
| | - Jesús Méndez-Lozano
- Instituto Politécnico Nacional, CIIDIR-Unidad Sinaloa, Departamento de Biotecnología Agrícola, Guasave, Mexico
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29
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Tarquini G, Martini M, Maestri S, Firrao G, Ermacora P. The Virome of ‘Lamon Bean’: Application of MinION Sequencing to Investigate the Virus Population Associated with Symptomatic Beans in the Lamon Area, Italy. PLANTS 2022; 11:plants11060779. [PMID: 35336661 PMCID: PMC8951528 DOI: 10.3390/plants11060779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022]
Abstract
‘Lamon bean’ is a protected geographical indication (PGI) for a product of four varieties of bean (Phaseolus vulgaris L.) grown in a specific area of production, which is located in the Belluno district, Veneto region (N.E. of Italy). In the last decade, the ‘Lamon bean’ has been threatened by severe virus epidemics that have compromised its profitability. In this work, the full virome of seven bean samples showing different foliar symptoms was obtained by MinION sequencing. Evidence that emerged from sequencing was validated through RT-PCR and ELISA in a large number of plants, including different ecotypes of Lamon bean and wild herbaceous hosts that may represent a virus reservoir in the field. Results revealed the presence of bean common mosaic virus (BCMV), cucumber mosaic virus (CMV), peanut stunt virus (PSV), and bean yellow mosaic virus (BYMV), which often occurred as mixed infections. Moreover, both CMV and PSV were reported in association with strain-specific satellite RNAs (satRNAs). In conclusion, this work sheds light on the cause of the severe diseases affecting the ‘Lamon bean’ by exploitation of MinION sequencing.
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Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Marta Martini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Simone Maestri
- Department of Biotechnology, University of Verona, I-37134 Verona, Italy;
| | - Giuseppe Firrao
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
- Correspondence:
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30
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Villamor DEV, Keller KE, Martin RR, Tzanetakis IE. Comparison of High Throughput Sequencing to Standard Protocols for Virus Detection in Berry Crops. PLANT DISEASE 2022; 106:518-525. [PMID: 34282931 DOI: 10.1094/pdis-05-21-0949-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We completed a comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium, and eight Rubus) with known virus profiles. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, reverse transcription (RT) PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared with RT-PCR on a wide spectrum of variants and discovery of novel viruses. More importantly, in most cases in which the two protocols showed parallel virus detection, 11 viruses in 16 selections were not consistently detected by both methods at all sampling points. Based on these data, we propose a testing requirement of four sampling times over two growing seasons for berry and potentially other crops, to ensure that no virus remains undetected independent of titer, distribution, or other virus-virus or virus-host interactions.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - K E Keller
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - R R Martin
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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31
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Rodríguez-Verástegui LL, Ramírez-Zavaleta CY, Capilla-Hernández MF, Gregorio-Jorge J. Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective. PLANTS (BASEL, SWITZERLAND) 2022; 11:203. [PMID: 35050091 PMCID: PMC8778216 DOI: 10.3390/plants11020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 05/12/2023]
Abstract
Trees and herbs that produce fruits represent the most valuable agricultural food commodities in the world. However, the yield of these crops is not fully achieved due to biotic factors such as bacteria, fungi, and viruses. Viruses are capable of causing alterations in plant growth and development, thereby impacting the yield of their hosts significantly. In this work, we first compiled the world's most comprehensive list of known edible fruits that fits our definition. Then, plant viruses infecting those trees and herbs that produce fruits with commercial importance in the global market were identified. The identified plant viruses belong to 30 families, most of them containing single-stranded RNA genomes. Importantly, we show the overall picture of the host range for some virus families following an evolutionary approach. Further, the current knowledge about plant-virus interactions, focusing on the main disorders they cause, as well as yield losses, is summarized. Additionally, since accurate diagnosis methods are of pivotal importance for viral diseases control, the current and emerging technologies for the detection of these plant pathogens are described. Finally, the most promising strategies employed to control viral diseases in the field are presented, focusing on solutions that are long-lasting.
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Affiliation(s)
| | - Candy Yuriria Ramírez-Zavaleta
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - María Fernanda Capilla-Hernández
- Cuerpo Académico Procesos Biotecnológicos, Universidad Politécnica de Tlaxcala, Av. Universidad Politécnica 1, San Pedro Xalcaltzinco 90180, Mexico; (C.Y.R.-Z.); (M.F.C.-H.)
| | - Josefat Gregorio-Jorge
- Consejo Nacional de Ciencia y Tecnología, Universidad Politécnica de Tlaxcala, Av. Insurgentes Sur 1582, Col. Crédito Constructor, Ciudad de Mexico 03940, Mexico
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Latent potential of current plant diagnostics for detection of sugarcane diseases. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Raza A, Wu Q. Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses. Methods Mol Biol 2022; 2400:225-243. [PMID: 34905206 DOI: 10.1007/978-1-0716-1835-6_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample. This protocol describes the details of RNA extraction and purification from wild rice plant and their yield, RNA purity, and integrity assessment. As a final step, bioinformatics data analysis including demultiplexing, quality control, de novo transcriptome assembly, taxonomic allocation and read mapping following Illumina HiSeq small and total RNA sequencing are described. Furthermore, the total RNAs extraction protocol and an additional ribosomal rRNAs depletion step which are significantly important for viral genomes construction are provided.
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Affiliation(s)
- Ali Raza
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.
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Kochetov AV, Pronozin AY, Shatskaya NV, Afonnikov DA, Afanasenko OS. Potato spindle tuber viroid. Vavilovskii Zhurnal Genet Selektsii 2021; 25:269-275. [PMID: 34901723 PMCID: PMC8628614 DOI: 10.18699/vj21.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 11/24/2022] Open
Abstract
Viroids belong to a very interesting class of molecules attracting researchers in phytopathology and
molecular evolution. Here we review recent literature data concerning the genetics of Potato spindle tuber viroid
(PSTVd) and the mechanisms related to its pathological effect on the host plants. PSTVd can be transmitted vertically through microspores and macrospores, but not with pollen from another infected plant. The 359 nucleotidelong genomic RNA of PSTVd is highly structured and its 3D-conformation is responsible for interaction with host
cellular factors to mediate replication, transport between tissues during systemic infection and the severity of
pathological symptoms. RNA replication is prone to errors and infected plants contain a population of mutated
forms of the PSTVd genome. Interestingly, at 7 DAI, only 25 % of the newly synthesized RNAs were identical to
the master copy, but this proportion increased to up to 70 % at 14 DAI and remained the same afterwards. PSTVd
infection induces the immune response in host plants. There are PSTVd strains with a severe, a moderate or a mild
pathological effect. Interestingly, viroid replication itself does not necessarily induce strong morphological or
physiological symptoms. In the case of PSTVd, disease symptoms may occur due to RNA-interference, which decreases the expression levels of some important cellular regulatory factors, such as, for example, potato StTCP23
from the gibberellic acid pathway with a role in tuber morphogenesis or tomato FRIGIDA-like protein 3 with an
early flowering phenotype. This association between the small segments of viroid genomic RNAs complementary
to the untranslated regions of cellular mRNAs and disease symptoms provides a way for new resistant cultivars to
be developed by genetic editing. To conclude, viroids provide a unique model to reveal the fundamental features
of living systems, which appeared early in evolution and still remain undiscovered.
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Affiliation(s)
- A V Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - A Y Pronozin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - N V Shatskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - D A Afonnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - O S Afanasenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia All-Russian Institute of Plant Protection, Pushkin, St. Petersburg, Russia
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Jia A, Yan C, Yin H, Sun R, Xia F, Gao L, Zhang Y, Li Y. Small RNA and Transcriptome Sequencing of a Symptomatic Peony Plant Reveals Mixed Infections with Novel Viruses. PLANT DISEASE 2021; 105:3816-3828. [PMID: 34156278 DOI: 10.1094/pdis-01-21-0007-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To identify the viruses in tree peony plants associated with the symptoms of yellowing, leaf rolling, stunted growth, and decline, high-throughput sequencing of small RNA and mRNA was conducted from a single symptomatic plant. Bioinformatic analyses and reconstruction of viral genomes indicated mixed viral infections involving cycas necrotic stunt virus, apple stem grooving virus, lychnis mottle virus, grapevine line pattern virus, and three new viruses designated as peony yellowing-associated citrivirus (PYaCV, Citrivirus in Betaflexiviridae), peony betaflexivirus 1 (PeV1, unclassified in Betaflexiviridae), and peony leafroll-associated virus (PLRaV, Ampelovirus in Closteroviridae). PYaCV was 8,666 nucleotides (nt) in length, comprising three open reading frames (ORFs), and shared 63.8 to 75.9% nt sequence identity with citrus leaf blotch virus (CLBV) isolates. However, the ORF encoding the replication-associated protein (REP) shared 57 and 52% sequence identities at the nt and amino acid (aa) level, respectively, with other reported CLBV isolates, which were below the criterion for species classification within the family Betaflexiviridae. Recombination analysis identified putative recombination sites in PYaCV, which originated from CLBV. PeV1, only identified from the transcriptome data, was 8,124 nt in length, with five ORFs encoding the REP (ORF1), triple gene block (ORF2 to 4) and coat protein (CP, ORF5). Phylogenetic analysis and sequence comparison showed that PeV1 clustered with an unassigned member, the garlic yellow mosaic-associated virus within the Betaflexiviridae family, into a separate clade. Partial genome sequence analysis of PLRaV (12,545 nt) showed it contained seven ORFs encoding the partial polyprotein 1a, the RNA-dependent RNA polymerase (RdRp), two small hydrophobic proteins p11 and p6, HSP70h, p55, and a CP duplicate, which shared low aa sequence identity with Closteroviridae family members. Phylogenetic analysis based on the aa sequences of RdRp or HSP70h indicated that PLRaV clustered with grapevine leafroll-associated virus 1 (GLRaV-1) and GLRaV-13 in the Ampelovirus genus. Field investigation confirmed the wide distribution of these viruses, causing mixed infections of peony plants in Beijing.
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Affiliation(s)
- Anning Jia
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China
| | - Chenge Yan
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China
| | - Hang Yin
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China
| | - Rui Sun
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China
| | - Fei Xia
- Beijing Institute of Landscape Architecture, Beijing 100102, China
| | - Lan Gao
- Beijing JingShan Park, Beijing 100009, China
| | - Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Yongqiang Li
- College of Bioscience and Resource Environment, Beijing University of Agriculture, Beijing 102206, China
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture, Beijing 102206, China
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Moradi Z, Mehrvar M. Whole-Genome Characterization of Alfalfa Mosaic Virus Obtained from Metagenomic Analysis of Vinca minor and Wisteria sinensis in Iran: with Implications for the Genetic Structure of the Virus. THE PLANT PATHOLOGY JOURNAL 2021; 37:619-631. [PMID: 34897253 PMCID: PMC8666234 DOI: 10.5423/ppj.oa.10.2021.0151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/30/2021] [Accepted: 11/02/2021] [Indexed: 06/14/2023]
Abstract
Alfalfa mosaic virus (AMV), an economically important pathogen, is present worldwide with a very wide host range. This work reports for the first time the infection of Vinca minor and Wisteria sinensis with AMV using RNA sequencing and reverse transcription polymerase chain reaction confirmation. De novo assembly and annotating of contigs revealed that RNA1, RNA2, and RNA3 genomic fragments consist of 3,690, 2,636, and 2,057 nucleotides (nt) for IR-VM and 3,690, 2,594, and 2,057 nt for IR-WS. RNA1 and RNA3 segments of IR-VM and IR-WS closely resembled those of the Chinese isolate HZ, with 99.23-99.26% and 98.04-98.09% nt identity, respectively. Their RNA2 resembled that of Canadian isolate CaM and American isolate OH-2-2017, with 97.96-98.07% nt identity. The P2 gene revealed more nucleotide diversity compared with other genes. Genes in the AMV genome were under dominant negative selection during evolution, and the P1 and coat protein (CP) proteins were subject to the strongest and weakest purifying selection, respectively. In the population genetic analysis based on the CP gene sequences, all 107 AMV isolates fell into two main clades (A, B) and isolates of clade A were further divided into three groups with significant subpopulation differentiation. The results indicated moderate genetic variation within and no clear geographic or genetic structure between the studied populations, implying moderate gene flow can play an important role in differentiation and distribution of genetic diversity among populations. Several factors have shaped the genetic structure and diversity of AMV: selection, recombination/reassortment, gene flow, and random processes such as founder effects.
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Affiliation(s)
- Zohreh Moradi
- Department of Plant Pathology, Faculty of Crop Sciences, Sari Agricultural Sciences and Natural Resources University, P.O. Box 578, Sari,
Iran
| | - Mohsen Mehrvar
- Department of Plant Pathology, Faculty of Agriculture, Ferdowsi University of Mashhad, P.O. Box 91779-1163, Mashhad,
Iran
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Yoffe L, Kuperman AA, Isakov O, Haguel D, Polsky AL, Farberov L, Pillar N, Gurevich V, Haviv I, Shomron N. Assessing the involvement of the placental microbiome and virome in preeclampsia using non coding RNA sequencing. J Perinat Med 2021; 49:1071-1083. [PMID: 34114389 DOI: 10.1515/jpm-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/29/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Preeclampsia is a dangerous pregnancy complication. The source of preeclampsia is unknown, though the placenta is believed to have a central role in its pathogenesis. An association between maternal infection and preeclampsia has been demonstrated, yet the involvement of the placental microbiome in the etiology of preeclampsia has not been determined. In this study, we examined whether preeclampsia is associated with an imbalanced microorganism composition in the placenta. METHODS To this end, we developed a novel method for the identification of bacteria/viruses based on sequencing of small non-coding RNA, which increases the microorganism-to-host ratio, this being a major challenge in microbiome methods. We validated the method on various infected tissues and demonstrated its efficiency in detecting microorganisms in samples with extremely low bacterial/viral biomass. We then applied the method to placenta specimens from preeclamptic and healthy pregnancies. Since the placenta is a remarkably large and heterogeneous organ, we explored the bacterial and viral RNA at each of 15 distinct locations. RESULTS Bacterial RNA was detected at all locations and was consistent with previous studies of the placental microbiome, though without significant differences between the preeclampsia and control groups. Nevertheless, the bacterial RNA composition differed significantly between various areas of the placenta. Viral RNA was detected in extremely low quantities, below the threshold of significance, thus viral abundance could not be determined. CONCLUSIONS Our results suggest that the bacterial and viral abundance in the placenta may have only limited involvement in the pathogenesis of preeclampsia. The evidence of a heterogenic bacterial RNA composition in the various placental locations warrants further investigation to capture the true nature of the placental microbiome.
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Affiliation(s)
- Liron Yoffe
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amir A Kuperman
- Blood Coagulation Service and Pediatric Hematology Clinic, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ofer Isakov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Internal Medicine "T", Tel Aviv Medical Center, Tel Aviv, Israel
| | | | | | - Luba Farberov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Pillar
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Izhak Haviv
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Characterization of the Mycovirome from the Plant-Pathogenic Fungus Cercospora beticola. Viruses 2021; 13:v13101915. [PMID: 34696345 PMCID: PMC8537984 DOI: 10.3390/v13101915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 12/25/2022] Open
Abstract
Cercospora leaf spot (CLS) caused by Cercospora beticola is a devastating foliar disease of sugar beet (Beta vulgaris), resulting in high yield losses worldwide. Mycoviruses are widespread fungi viruses and can be used as a potential biocontrol agent for fugal disease management. To determine the presence of mycoviruses in C. beticola, high-throughput sequencing analysis was used to determine the diversity of mycoviruses in 139 C. beticola isolates collected from major sugar beet production areas in China. The high-throughput sequencing reads were assembled and searched against the NCBI database using BLASTn and BLASTx. The results showed that the obtained 93 contigs were derived from eight novel mycoviruses, which were grouped into 3 distinct lineages, belonging to the families Hypoviridae, Narnaviridae and Botourmiaviridae, as well as some unclassified (−)ssRNA viruses in the order Bunyavirales and Mononegavirales. To the best of our knowledge, this is the first identification of highly diverse mycoviruses in C. beticola. The novel mycoviruses explored in this study will provide new viral materials to biocontrol Cercospora diseases. Future studies of these mycoviruses will aim to assess the roles of each mycovirus in biological function of C. beticola in the future.
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Molecular characterization of a novel wheat-infecting virus of the family Betaflexiviridae. Arch Virol 2021; 166:2875-2879. [PMID: 34297223 DOI: 10.1007/s00705-021-05175-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/27/2021] [Indexed: 10/20/2022]
Abstract
Wheat plants showing yellowing and mosaic in leaves and stunting were collected from wheat fields in Henan Province, China. Analysis of these plants by transmission electron microscopy showed that they contained two types of filamentous virus-like particles with a length of 200-500 nm and 1000-1300 nm, respectively. RNA-seq revealed a coinfection with wheat yellow mosaic virus (WYMV) and an unknown wheat-infecting virus. The genome of the unknown virus is 8,410 nucleotides long, excluding its 3' poly(A) tail. It has six open reading frames (ORFs). ORF1 encodes a putative viral replication-associated protein (Rep), and ORFs 2, 3, and 4 encode the triple gene block (TGB) proteins. ORFs 5 and 6 encode the capsid protein (CP) and a protein with unknown function, respectively. Phylogenetic analysis showed that this novel virus is evolutionarily related to members of the subfamily Quinvirinae, family Betaflexiviridae. It is, however, distinct from the viruses in the currently established genera. Based on the species and genus demarcation criteria set by the International Committee on Taxonomy of Viruses (ICTV), we tentatively name this novel virus "wheat yellow stunt-associated betaflexivirus" (WYSaBV), and we propose it to be a member of a new genus in the family Betaflexiviridae.
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Demian E, Holczbauer A, Galbacs ZN, Jaksa-Czotter N, Turcsan M, Olah R, Varallyay E. Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary. Viruses 2021; 13:1119. [PMID: 34200935 PMCID: PMC8230486 DOI: 10.3390/v13061119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/02/2022] Open
Abstract
Grapevine virus T (GVT) is a recently described foveavirus, which was identified from a transcriptome of a Teroldego grapevine cultivar in 2017. Recently, we surveyed vineyards and rootstock plantations in Hungary using small RNA (sRNA) high-throughput sequencing (HTS), at a time when GVT had not yet been described. A re-analysis of our sRNA HTS datasets and a survey of grapevines by RT-PCR revealed the presence of GVT in most of the vineyards tested, while at rootstock fields its presence was very rare. The presence and high variability of the virus in the country was confirmed by sequence analysis of strains originating from different vineyards. In this study, we demonstrate the presence of GVT in Hungary and show its high diversity, suggesting that GVT presence may not seriously affect grapevine health and that it could have been present in European vineyards for a long time as a latent infection.
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Affiliation(s)
- Emese Demian
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Aliz Holczbauer
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Zsuzsanna Nagyne Galbacs
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Nikoletta Jaksa-Czotter
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Mihaly Turcsan
- Institute for Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary; (M.T.); (R.O.)
| | - Robert Olah
- Institute for Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary; (M.T.); (R.O.)
| | - Eva Varallyay
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
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Kim NY, Lee HJ, Kim HS, Lee SH, Moon JS, Jeong RD. Identification of Plant Viruses Infecting Pear Using RNA Sequencing. THE PLANT PATHOLOGY JOURNAL 2021; 37:258-267. [PMID: 34111915 PMCID: PMC8200581 DOI: 10.5423/ppj.oa.01.2021.0009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/30/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Asian pear (Pyrus pyrifolia) is a widely cultivated and commercially important fruit crop, which is occasionally subject to severe economic losses due to latent viral infections. Thus, the aim of the present study was to examine and provide a comprehensive overview of virus populations infecting a major pear cultivar ('Singo') in Korea. From June 2017 to October 2019, leaf samples (n = 110) of pear trees from 35 orchards in five major pear-producing regions were collected and subjected to RNA sequencing. Most virus-associated contigs matched the sequences of known viruses, including apple stem grooving virus (ASGV) and apple stem pitting virus (ASPV). However, some contigs matched the sequences of apple green crinkle-associated virus and cucumber mosaic virus. In addition, three complete or nearly complete genomes were constructed based on transcriptome data and subjected to phylogenetic analyses. Based on the number of virus-associated reads, ASGV and ASPV were identified as the dominant viruses of 'Singo.' The present study describes the virome of a major pear cultivar in Korea, and looks into the diversity of viral communities in this cultivar. This study can provide valuable information on the complexity of genetic variability of viruses infecting pear trees.
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Affiliation(s)
- Nam-Yeon Kim
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
| | - Hong-Sup Kim
- Seed Testing & Research Center, Korea Seed & Variety Service, Gimcheon 39660, Korea
| | - Su-Heon Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 98411, Korea
| | - Jae-Sun Moon
- Plant Genome Research Center, Korea Research Institute of Biosciences & Biotechnology, Daejeon 34141, Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju 61185, Korea
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Kavalappara SR, Milner H, Konakalla NC, Morgan K, Sparks AN, McGregor C, Culbreath AK, Wintermantel WM, Bag S. High Throughput Sequencing-Aided Survey Reveals Widespread Mixed Infections of Whitefly-Transmitted Viruses in Cucurbits in Georgia, USA. Viruses 2021; 13:v13060988. [PMID: 34073397 PMCID: PMC8230054 DOI: 10.3390/v13060988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 01/08/2023] Open
Abstract
Viruses transmitted by the sweet potato whitefly (Bemisia tabaci) have been detrimental to the sustainable production of cucurbits in the southeastern USA. Surveys were conducted in the fall of 2019 and 2020 in Georgia, a major cucurbit-producing state of the USA, to identify the viruses infecting cucurbits and their distribution. Symptomatic samples were collected and small RNA libraries were prepared and sequenced from three cantaloupes, four cucumbers, and two yellow squash samples. An analysis of the sequences revealed the presence of the criniviruses cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and the begomovirus cucurbit leaf crumple virus (CuLCrV). CuLCrV was detected in 76%, CCYV in 60%, and CYSDV in 43% of the total samples (n = 820) tested. The level of mixed infections was high in all the cucurbits, with most plants tested being infected with at least two of these viruses. Near-complete genome sequences of two criniviruses, CCYV and CYSDV, were assembled from the small RNA sequences. An analysis of the coding regions showed low genetic variability among isolates from different hosts. In phylogenetic analysis, the CCYV isolates from Georgia clustered with Asian isolates, while CYSDV isolates clustered with European and USA isolates. This work enhances our understanding of the distribution of viruses on cucurbits in South Georgia and will be useful to develop strategies for managing the complex of whitefly-transmitted viruses in the region.
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Affiliation(s)
- Saritha Raman Kavalappara
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Hayley Milner
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Naga Charan Konakalla
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Kaelyn Morgan
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Alton N. Sparks
- Department of Entomology, University of Georgia, Tifton, GA 31793, USA;
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA;
| | - Albert K. Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - William M. Wintermantel
- United States Department of Agriculture-Agricultural Research Service, Salinas, CA 93905, USA
- Correspondence: (W.M.W.); (S.B.)
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
- Correspondence: (W.M.W.); (S.B.)
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Maina S, Zheng L, Rodoni BC. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses. Viruses 2021; 13:583. [PMID: 33808381 PMCID: PMC8066983 DOI: 10.3390/v13040583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10-8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
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Affiliation(s)
- Solomon Maina
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
| | - Linda Zheng
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
| | - Brendan C. Rodoni
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Victoria 3083, Australia
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Venkataraman S, Badar U, Shoeb E, Hashim G, AbouHaidar M, Hefferon K. An Inside Look into Biological Miniatures: Molecular Mechanisms of Viroids. Int J Mol Sci 2021; 22:2795. [PMID: 33801996 PMCID: PMC8001946 DOI: 10.3390/ijms22062795] [Citation(s) in RCA: 3] [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: 12/13/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022] Open
Abstract
Viroids are tiny single-stranded circular RNA pathogens that infect plants. Viroids do not encode any proteins, yet cause an assortment of symptoms. The following review describes viroid classification, molecular biology and spread. The review also discusses viroid pathogenesis, host interactions and detection. The review concludes with a description of future prospects in viroid research.
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Affiliation(s)
| | | | | | | | | | - Kathleen Hefferon
- Cell and System Biology, University of Toronto, Toronto, ON M5S 3B2, Canada; (S.V.); (U.B.); (E.S.); (G.H.); (M.A.)
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Shahid MS, Sattar MN, Iqbal Z, Raza A, Al-Sadi AM. Next-Generation Sequencing and the CRISPR-Cas Nexus: A Molecular Plant Virology Perspective. Front Microbiol 2021; 11:609376. [PMID: 33584572 PMCID: PMC7874184 DOI: 10.3389/fmicb.2020.609376] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, next-generation sequencing (NGS) and contemporary Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated (Cas) technologies have revolutionized the life sciences and the field of plant virology. Both these technologies offer an unparalleled platform for sequencing and deciphering viral metagenomes promptly. Over the past two decades, NGS technologies have improved enormously and have impacted plant virology. NGS has enabled the detection of plant viruses that were previously undetectable by conventional approaches, such as quarantine and archeological plant samples, and has helped to track the evolutionary footprints of viral pathogens. The CRISPR-Cas-based genome editing (GE) and detection techniques have enabled the development of effective approaches to virus resistance. Different versions of CRISPR-Cas have been employed to successfully confer resistance against diverse plant viruses by directly targeting the virus genome or indirectly editing certain host susceptibility factors. Applications of CRISPR-Cas systems include targeted insertion and/or deletion, site-directed mutagenesis, induction/expression/repression of the gene(s), epigenome re-modeling, and SNPs detection. The CRISPR-Cas toolbox has been equipped with precision GE tools to engineer the target genome with and without double-stranded (ds) breaks or donor templates. This technique has also enabled the generation of transgene-free genetically engineered plants, DNA repair, base substitution, prime editing, detection of small molecules, and biosensing in plant virology. This review discusses the utilities, advantages, applications, bottlenecks of NGS, and CRISPR-Cas in plant virology.
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Affiliation(s)
- Muhammad Shafiq Shahid
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | | | - Zafar Iqbal
- Central Laboratories, King Faisal University, Hofuf, Saudi Arabia
| | - Amir Raza
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Abdullah M. Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
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Zhang S, Huang A, Zhou X, Li Z, Dietzgen RG, Zhou C, Cao M. Natural Defect of a Plant Rhabdovirus Glycoprotein Gene: A Case Study of Virus-Plant Coevolution. PHYTOPATHOLOGY 2021; 111:227-236. [PMID: 32648524 DOI: 10.1094/phyto-05-20-0191-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Seven isolates of a putative cytorhabdovirus (family Rhabdoviridae, order Mononegavirales) designated as citrus-associated rhabdovirus (CiaRV) were identified in citrus, passion fruit, and paper bush from the same geographical area in China. CiaRV, bean-associated cytorhabdovirus (Brazil), and papaya virus E (Ecuador) should be taxonomically classified in the species Papaya cytorhabdovirus. Due to natural mutations, the glycoprotein (G) and P4 genes were impaired in citrus-infecting isolates of CiaRV, resulting in an atypical rhabdovirus genome organization of 3' leader-N-P-P3-M-L-5' trailer. The P3 protein of CiaRV shared a common origin with begomoviral movement proteins (family Geminiviridae). Secondary structure analysis and trans-complementation of movement-deficient tomato mosaic virus and potato virus X mutants by CiaRV P3 supported its function in viral cell-to-cell trafficking. The wide geographical dispersal of CiaRV and related viruses suggests an efficient transmission mechanism, as well as an underlying risk to global agriculture. Both the natural phenomenon and experimental analyses demonstrated presence of the "degraded" type of CiaRV in citrus, in parallel to "undegraded" types in other host plant species. This case study shows a plant virus losing the function of an important but nonessential gene, likely due to host shift and adaption, which deepened our understanding of course of natural viral diversification.
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Affiliation(s)
- Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Aijun Huang
- National Navel Orange Research Center, College of Life Science, Gannan Normal University, Ganzhou, China
| | - Xin Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, 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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48
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Soybean Viromes in the Republic of Korea Revealed by RT-PCR and Next-Generation Sequencing. Microorganisms 2020; 8:microorganisms8111777. [PMID: 33198273 PMCID: PMC7698195 DOI: 10.3390/microorganisms8111777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/25/2022] Open
Abstract
Soybean (Glycine max L.) is one of the most important crop plants in the Republic of Korea. Here, we conducted a soybean virome study. We harvested a total of 172 soybean leaf samples showing disease symptoms from major soybean-growing regions in the Republic of Korea. Individual samples were examined for virus infection by RT-PCR. Moreover, we generated eight libraries representing eight provinces by pooling samples and four libraries from single samples. RNA-seq followed by bioinformatics analyses revealed 10 different RNA viruses infecting soybean. The proportion of viral reads in each transcriptome ranged from 0.2 to 31.7%. Coinfection of different viruses in soybean plants was very common. There was a single dominant virus in each province, and this geographical difference might be related to the soybean seeds that transmit viruses. In this study, 32 viral genome sequences were assembled and successfully used to analyze the phylogenetic relationships and quasispecies nature of the identified RNA viruses. Moreover, RT-PCR with newly developed primers confirmed infection of the identified viruses in each library. Taken together, our soybean virome study provides a comprehensive overview of viruses infecting soybean in eight geographical regions in the Republic of Korea and four single soybean plants in detail.
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Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics. Int J Mol Sci 2020; 21:ijms21207565. [PMID: 33066322 PMCID: PMC7593927 DOI: 10.3390/ijms21207565] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/23/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022] Open
Abstract
Tomato (Lycopersicum esculentum L.) and pepper (Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carried out metatranscriptomics using RNA sequencing followed by bioinformatics analyses to identify viruses and viroids infecting tomato and pepper plants in Vietnam. We prepared a total of 16 libraries, including eight tomato and eight pepper libraries derived from different geographical regions in Vietnam. We identified a total of 602 virus-associated contigs, which were assigned to 18 different virus species belonging to nine different viral genera. We identified 13 different viruses and two viroids infecting tomato plants and 12 viruses and two viroids infecting pepper plants with viruses as dominantly observed pathogens. Our results showed that multiple infection of different viral pathogens was common in both plants. Moreover, geographical region and host plant were two major factors to determine viral populations. Taken together, our results provide the comprehensive overview of viral pathogens infecting two important plants in the family Solanaceae grown in Vietnam.
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50
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Bejerman N, Debat H, Dietzgen RG. The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes. Front Microbiol 2020; 11:588427. [PMID: 33042103 PMCID: PMC7524893 DOI: 10.3389/fmicb.2020.588427] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our ‘new eyes,’ are unraveling in real time the richness and magnitude of the plant RNA virosphere.
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Affiliation(s)
- Nicolás Bejerman
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Humberto Debat
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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