1
|
Angira A, Baranwal VK, Ranjan A, Choudhary N. Optimization of DAC-ELISA and IC-RT-PCR using the developed polyclonal antibody and one-step RT-PCR assays for detection of Indian citrus ringspot virus in kinnow orange of Punjab, India. J Virol Methods 2024; 329:114972. [PMID: 38880340 DOI: 10.1016/j.jviromet.2024.114972] [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: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
Indian citrus ringspot virus (ICRSV), a member of the Mandarivirus genus, causes citrus ringspot disease, impacting kinnow orange quality and yield. Early and accurate detection methods are crucial before visible symptoms manifest in plants. In this study, a 507 bp partial coat protein gene (pCPG) segment was amplified from infected kinnow leaf tissues, cloned into a pET28a vector, and transformed into E. coli BL21(DE3) cells. Induced with IPTG, the cells overexpressed a recombinant partial coat protein (rpCP) of approximately 23 kDa, purified using Ni-NTA resin via affinity chromatography. Validated in western blot with an anti-His antibody, rpCP was used to generate an ICRSV-specific polyclonal antibody (PAb) in rabbits. PAb, optimized at 1:1000 dilution, successfully detected ICRSV in infected kinnow orange leaf extracts via DAC-ELISA and IC-RT-PCR assays. ICRSV was detectable in sample dilutions up to 1:640 and 1:10240 (w/v, g mL-1) by DAC-ELISA and IC-RT-PCR, respectively. One-step RT-PCR assays were also optimized, confirming the presence of ICRSV by amplifying a 507 bp pCPG fragment from total RNA extracted from kinnow orange leaves, with dilution up to 1:5120 (w/v, g mL-1). The result demonstrated that IC-RT-PCR has a 16-fold and 2-fold higher sensitivity than DAC-ELISA and one-step RT-PCR assays.
Collapse
Affiliation(s)
- Aniket Angira
- Amity Institute of Virology & Immunology, Amity University Uttar Pradesh, Noida 201313, India
| | - V K Baranwal
- Advanced Centre of Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Aashish Ranjan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nandlal Choudhary
- Amity Institute of Virology & Immunology, Amity University Uttar Pradesh, Noida 201313, India.
| |
Collapse
|
2
|
Mishra A, Pandey J, Ojha H, Sharma M, Kaur L, Pandey A, Sharma P, Murab S, Singhal R, Pathak M. A green and economic approach to synthesize magnetic Lagenaria siceraria biochar (γ-Fe 2O 3-LSB) for methylene blue removal from aqueous solution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:34038-34055. [PMID: 38696013 DOI: 10.1007/s11356-024-33477-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
In the printing and textile industries, methylene blue (a cationic azo dye) is commonly used. MB is a well-known carcinogen, and another major issue is its high content in industrial discharge. There are numerous removal methodologies that have been employed to remove it from industrial discharge; however, these current modalities have one or more limitations. In this research, a novel magnetized biochar (γ-Fe2O3-LSB) was synthesized using Lagenaria siceraria peels which were further magnetized via the co-precipitation method. The synthesized γ-Fe2O3-LSB was characterized using FTIR, X-ray diffraction, Raman, SEM-EDX, BET, and vibrating sample magnetometry (VSM) for the analysis of magnetic properties. γ-Fe2O3-LSB showed a reversible type IV isotherm, which is a primary characteristic of mesoporous materials. γ-Fe2O3-LSB had a specific surface area (SBET = 135.30 m2/g) which is greater than that of LSB (SBET = 11.54 m2/g). γ-Fe2O3-LSB exhibits a saturation magnetization value (Ms) of 3.72 emu/g which shows its superparamagnetic nature. The batch adsorption process was performed to analyze the adsorptive removal of MB dye using γ-Fe2O3-LSB. The adsorption efficiency of γ-Fe2O3-LSB for MB was analyzed by varying parameters like the initial concentration of adsorbate (MB), γ-Fe2O3-LSB dose, pH effect, contact time, and temperature. Adsorption isotherm, kinetic, and thermodynamics were also studied after optimizing the protocol. The non-linear Langmuir model fitted the best to explain the adsorption isotherm mechanism and resulting adsorption capacity ( q e =54.55 mg/g). The thermodynamics study showed the spontaneous and endothermic nature, and pseudo-second-order rate kinetics was followed during the adsorption process. Regeneration study showed that γ-Fe2O3-LSB can be used up to four cycles. In laboratory setup, the cost of γ-Fe2O3-LSB synthesis comes out to be 162.75 INR/kg which is low as compared to commercially available adsorbents. The results obtained suggest that magnetic Lagenaria siceraria biochar, which is economical and efficient, can be used as a potential biochar material for industrial applications in the treatment of wastewater.
Collapse
Affiliation(s)
- Ayushi Mishra
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, Uttar Pradesh, India
| | - Jyoti Pandey
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, Uttar Pradesh, India
| | - Himanshu Ojha
- Division of Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Brig S K Mazumdar Road, Timarpur, Delhi, 110054, India
| | - Malti Sharma
- Department of Chemistry, Miranda House, University of Delhi, Delhi, 110007, India
| | - Lajpreet Kaur
- Division of Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Brig S K Mazumdar Road, Timarpur, Delhi, 110054, India
| | - Akhilesh Pandey
- Solid State Physics Laboratory, DRDO, Lucknow Road, Timarpur, Delhi, 110054, India
| | - Pankaj Sharma
- BioX Center, School of Biosciences & Bioengineering, IIT Mandi, Kamand, Himachal Pradesh, 175075, India
| | - Sumit Murab
- BioX Center, School of Biosciences & Bioengineering, IIT Mandi, Kamand, Himachal Pradesh, 175075, India
| | - Rahul Singhal
- Department of Chemistry, Shivaji College, University of Delhi, Delhi, 110027, India
| | - Mallika Pathak
- Department of Chemistry, Miranda House, University of Delhi, Delhi, 110007, India.
| |
Collapse
|
3
|
Gupta N, Kumar R, Kishan G, Sharma SK, Srivastava N, Kumar A, Baranwal VK. Development of Simplified Recombinase Polymerase Amplification Assay for Rapid and Robust Detection of Citrus Yellow Vein Clearing Virus. Curr Microbiol 2024; 81:103. [PMID: 38386082 DOI: 10.1007/s00284-024-03614-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/06/2024] [Indexed: 02/23/2024]
Abstract
Citrus is an economically important fruit crop, belongs to family Rutaceae, cultivated commercially in over 130 countries, which holds a leading profitable position in the international market. The most important citrus varieties are mandarins, oranges, lemons, sweet limes, grapefruits and pomelos. Citrus yellow vein clearing virus (CYVCV) is an important graft transmissible plant pathogen known to reduce productivity of citrus fruits due to its predominant association and widespread occurrence. Requirement of fast, reliable, efficient & economical CYVCV indexing assay is a prerequisite for production of healthy planting material. Currently, nucleic acid isolation and thermal cycler-based assay available for CYVCV indexing is a cumbersome lab intensive method. The present study was undertaken to develop and validate reverse transcription-recombinase polymerase amplification (RT-RPA) assay requiring no tedious RNA isolation, separate cDNA synthesis and costlier instrument like thermo-cycler. Optimized RT-RPA assay was able to amplify CYVCV up to 10-7 dilution (equivalent to 0.1 pg/μl) with the prepared templates of both RNA and crude saps and showed higher sensitivity in detection of CYVCV infection in field samples as compared to the conventional RT-PCR. Developed RT-RPA assay showed high specificity without any cross-reaction with other citrus pathogens (Indian citrus ringspot virus, citrus yellow mosaic virus, citrus tristeza virus, citrus exocortis viroid and huanglongbing). RT-RPA using crude leaf sap as template is quite simple, robust, highly sensitive, time and cost effective; therefore, it can be used in resource constrained laboratories as screening tool, for field surveys and on-site testing programs in farms, nurseries and biosecurity. Present study, first time reports the development, optimization and validation of crude sap-based RT-RPA assay for the detection of CYVCV infection in citrus plants namely; Kinnow mandarin, Mosambi and Grape fruit.
Collapse
Affiliation(s)
- Nitika Gupta
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Rakesh Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopi Kishan
- ICAR-Indian Institute of Seed Science, Uttar Pradesh, Kushmaur, Mau, India
| | - Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nishant Srivastava
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ashwini Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| |
Collapse
|
4
|
Roy A, Grinstead S, Leon Martínez G, Pinzón JCC, Nunziata SO, Padmanabhan C, Hammond J. Meta-Transcriptomic Analysis Uncovers the Presence of Four Novel Viruses and Multiple Known Virus Genera in a Single Hibiscus rosa-sinensis Plant in Colombia. Viruses 2024; 16:267. [PMID: 38400042 PMCID: PMC10891833 DOI: 10.3390/v16020267] [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: 01/14/2024] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Hibiscus is not native to Colombia but well suited to its arid soil and dry climates. A single hibiscus plant from Risaralda, showing black spots on upper and lower sides of its leaves, was collected for virome analysis using meta-transcriptomic high-throughput sequencing technology. Bioinformatic analysis identified 12.5% of the total reads in the Ribo-Zero cDNA library which mapped to viral genomes. BLAST searches revealed the presence of carlavirus, potexvirus, and of known members of the genera Betacarmovirus, Cilevirus, Nepovirus, and Tobamovirus in the sample; confirmed by RT-PCR with virus-specific primers followed by amplicon sequencing. Furthermore, in silico analysis suggested the possibility of a novel soymovirus, and a new hibiscus strain of citrus leprosis virus C2 in the mixed infection. Both RNA dependent RNA polymerase and coat protein gene sequences of the potex and carla viruses shared less than 72% nucleotide and 80% amino acid identities with any alphaflexi- and betaflexi-virus sequences available in GenBank, identifying three novel carlavirus and one potexvirus species in the Hibiscus rosa-sinensis plant. The detection of physalis vein necrosis nepovirus and passion fruit green spot cilevirus in hibiscus are also new reports from Colombia. Overall, the meta-transcriptome analysis identified the complex virome associated with the black spot symptoms on hibiscus leaves and demonstrated the diversity of virus genera tolerated in the mixed infection of a single H. rosa-sinensis plant.
Collapse
Affiliation(s)
- Avijit Roy
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD 20705, USA
| | - Sam Grinstead
- Molecular Plant Pathology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture (USDA), Beltsville, MD 20705, USA
| | - Guillermo Leon Martínez
- AGROSAVIA, Centro de Investigación La Libertad, Km.17 vía Pto. Lopez, Villavicencio, Meta, Colombia
| | | | - Schyler O Nunziata
- Plant Pathogen Confirmatory Diagnostics Laboratory, Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, USDA, Laurel, MD 20708, USA
| | - Chellappan Padmanabhan
- Plant Pathogen Confirmatory Diagnostics Laboratory, Science and Technology, Plant Protection and Quarantine, Animal and Plant Health Inspection Service, USDA, Laurel, MD 20708, USA
| | - John Hammond
- Floral and Nursery Plants Research Unit, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| |
Collapse
|
5
|
Weng HT, Li YY, Chen JP, Zhang CX, Li JM, Xu ZT. Complete genome sequence of a novel robigovirus infecting Mentha arvensis. Arch Virol 2024; 169:19. [PMID: 38180588 DOI: 10.1007/s00705-023-05944-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
The complete genomic sequence of a novel robigovirus, provisionally named "Mentha arvensis robigovirus 1" (MARV1), was determined by combining next-generation sequencing (NGS), reverse transcription polymerase chain reaction (RT-PCR), and rapid amplification of cDNA ends (RACE) PCR. The complete genomic sequence of this new virus is 7617 nucleotides in length, excluding the 3' poly(A) tail. The MARV1 genome encodes a putative replicase, "triple gene block" proteins, and a coat protein. Phylogenetic analysis demonstrated that MARV1 is a member of the genus Robigovirus, with closest relationships to African oil palm ringspot virus (AOPRV). Furthermore, MARV1-derived small interfering RNAs (siRNAs) showed typical patterns of plant-virus-derived siRNAs produced by the host antiviral RNA interference pathway. This is the first report of a plant virus of the genus Robigovirus in M. arvensis.
Collapse
Affiliation(s)
- Hai-Tao Weng
- 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
| | - Yi-Yuan Li
- 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
| | - Jian-Ping Chen
- 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
| | - Chuan-Xi Zhang
- 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
| | - Jun-Min Li
- 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
| | - Zhong-Tian 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, 315211, China.
| |
Collapse
|
6
|
Cisneros AE, Martín-García T, Primc A, Kuziuta W, Sánchez-Vicente J, Aragonés V, Daròs JA, Carbonell A. Transgene-free, virus-based gene silencing in plants by artificial microRNAs derived from minimal precursors. Nucleic Acids Res 2023; 51:10719-10736. [PMID: 37713607 PMCID: PMC10602918 DOI: 10.1093/nar/gkad747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
Artificial microRNAs (amiRNAs) are highly specific, 21-nucleotide (nt) small RNAs designed to silence target transcripts. In plants, their application as biotechnological tools for functional genomics or crop improvement is limited by the need of transgenically expressing long primary miRNA (pri-miRNA) precursors to produce the amiRNAs in vivo. Here, we analyzed the minimal structural and sequence requirements for producing effective amiRNAs from the widely used, 521-nt long AtMIR390a pri-miRNA from Arabidopsis thaliana. We functionally screened in Nicotiana benthamiana a large collection of constructs transiently expressing amiRNAs against endogenous genes and from artificially shortened MIR390-based precursors and concluded that highly effective and accurately processed amiRNAs can be produced from a chimeric precursor of only 89 nt. This minimal precursor was further validated in A. thaliana transgenic plants expressing amiRNAs against endogenous genes. Remarkably, minimal but not full-length precursors produce authentic amiRNAs and induce widespread gene silencing in N. benthamiana when expressed from an RNA virus, which can be applied into leaves by spraying infectious crude extracts. Our results reveal that the length of amiRNA precursors can be shortened without affecting silencing efficacy, and that viral vectors including minimal amiRNA precursors can be applied in a transgene-free manner to induce whole-plant gene silencing.
Collapse
Affiliation(s)
- Adriana E Cisneros
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Tamara Martín-García
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Anamarija Primc
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Wojtek Kuziuta
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Javier Sánchez-Vicente
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| | - Alberto Carbonell
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Av. de los Naranjos s/n, 46022 Valencia, Spain
| |
Collapse
|
7
|
Read DA, Thompson GD, Swanevelder DZH, Pietersen G. Metaviromic Characterization of Betaflexivirus Populations Associated with a Vitis cultivar Collection in South Africa. Viruses 2023; 15:1474. [PMID: 37515161 PMCID: PMC10385141 DOI: 10.3390/v15071474] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
South Africa is associated with a centuries-old viticultural industry, accompanied by a diverse range of wine and table grape cultivars and an extensive history of pervasive introductions of vine material and associated viruses. The Vitis D2 collection in Stellenbosch represents the most comprehensive collection of Vitis species, hybrids, and cultivars in South Africa. We collected leaf petiole material from 229 accessions from this collection. Our metaviromic analyses revealed a total of 406 complete/near complete genomes of various betaflexiviruses. Among these, we identified the presence of grapevine rupestris stem pitting-associated virus and grapevine viruses A, B, E, F, H (GVH), I (GVI), and M (GVM). Notably, this study marks the first report of GVH, GVI, and GVM in South Africa, which were confirmed via RT-PCR. This research significantly contributes to our understanding of viral diversity and introductions in South African viticulture and emphasizes the need for vigilant monitoring and management of viral infections. Our findings lay the groundwork for strategies that mitigate the impact of viruses on South Africa's wine industry, which generates an annual revenue of approximately 500 million USD.
Collapse
Affiliation(s)
- David A Read
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Genevieve D Thompson
- Gene Vantage, 53 Kyalami Boulevard, Kyalami Business Park, Johannesburg 1684, South Africa
| | - Dirk Z H Swanevelder
- Agricultural Research Council (ARC)-Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria 0110, South Africa
| | | |
Collapse
|
8
|
Peng Z, Chen Y, Luo Z, Peng J, Zheng H, Wu G, Rao S, Wu J, Xu Z, Chen J, Lu Y, Guo F, Yan F. Complete genome sequence of a new virus from Allium sativum L in China. Arch Virol 2023; 168:167. [PMID: 37227509 DOI: 10.1007/s00705-023-05794-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023]
Abstract
The complete genome of a new virus belonging to the family Betaflexiviridae was identified in garlic and sequenced by next-generation sequencing and reverse transcription PCR. The complete RNA genome (GenBank accession number OP021693) is 8191 nucleotides in length, excluding the 3' poly(A) tail, and contains five open reading frames (ORFs). These open reading frames encode the viral replicase, triple gene block, and coat protein, and the genome organization is typical of members of the subfamily Quinvirinae. The virus has been tentatively named "garlic yellow curl virus" (GYCV). Phylogenetic analysis suggested that it represents an independent evolutionary lineage in the subfamily, clustering with the currently unclassified garlic yellow mosaic associated virus (GYMaV) and peony betaflexivirus 1 (PeV1). Differences between the phylogenies inferred for the replicase and coat protein indicate that the new virus does not belong to any established genus of the family Betaflexiviridae. This is the first report of GYCV in China.
Collapse
Affiliation(s)
- Zhengyu Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yi Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhaopeng Luo
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Hongying Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Guanwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Shaofei Rao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jian Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Zhongtian Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| | - Fengling Guo
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
9
|
Parreño R, Rodríguez-Alcocer E, Martínez-Guardiola C, Carrasco L, Castillo P, Arbona V, Jover-Gil S, Candela H. Turning Garlic into a Modern Crop: State of the Art and Perspectives. PLANTS (BASEL, SWITZERLAND) 2023; 12:1212. [PMID: 36986902 PMCID: PMC10057115 DOI: 10.3390/plants12061212] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Garlic is cultivated worldwide for the value of its bulbs, but its cultivation is challenged by the infertility of commercial cultivars and the accumulation of pathogens over time, which occurs as a consequence of vegetative (clonal) propagation. In this review, we summarize the state of the art of garlic genetics and genomics, highlighting recent developments that will lead to its development as a modern crop, including the restoration of sexual reproduction in some garlic strains. The set of tools available to the breeder currently includes a chromosome-scale assembly of the garlic genome and multiple transcriptome assemblies that are furthering our understanding of the molecular processes underlying important traits like the infertility, the induction of flowering and bulbing, the organoleptic properties and resistance to various pathogens.
Collapse
Affiliation(s)
- Ricardo Parreño
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Eva Rodríguez-Alcocer
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | | | - Lucía Carrasco
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Purificación Castillo
- Departamento I+D, Coopaman S.C.L., Carretera Peñas De San Pedro, km 1.6, 02006 Albacete, Spain
| | - Vicent Arbona
- Departament de Ciències Agràries i del Medi Natural, Universitat Jaume I, 12071 Castelló de la Plana, Spain
| | - Sara Jover-Gil
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| |
Collapse
|
10
|
Hadidi A, Barba M, Rubino L. The Fine Legacy of Giovanni P. Martelli (1935-2020), a Preeminent Plant Virologist and the Founder of Modern Grapevine Virology. Viruses 2023; 15:210. [PMID: 36680250 PMCID: PMC9866108 DOI: 10.3390/v15010210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Giovanni Paolo Martelli passed away on 8 January 2020 [...].
Collapse
Affiliation(s)
- Ahmed Hadidi
- U. S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Marina Barba
- CREA-Research Center for Plant Protection and Certification, 00156 Rome, Italy
| | - Luisa Rubino
- National Research Council, Institute for Sustainable Plant Protection, 70126 Bari, Italy
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
ÇELİK A. Incidence and coat protein characterization of apple stem pitting virus isolates from Isparta province of Turkey. ULUSLARARASI TARIM VE YABAN HAYATI BILIMLERI DERGISI 2022. [DOI: 10.24180/ijaws.1180101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Turkey is one of the major countries in the world in terms of fruit growing due to its climate diversity and geographical features. Apple, which is one of these fruits, is grown intensively in Turkey, and especially the Mediterranean Region is important for apple agriculture. Today, viral diseases are considered as an important yield loss factor in apple farming. This study investigated the incidence and molecular characterization of apple stem pitting virus (ASPV) in Isparta province, a significant apple-producing region in Turkey. By using the DAS-ELISA and RT-PCR methods, ASPV infection was found in 7 out of 70 collected apple leaf samples. The partial nucleotid sequences of ASPV were obtained and registered in GenBank for accession numbers. The generated similarity matrix by using the representative isolates revealed that the new ASPV isolates shared 79–93% of their nucleotide sequences with GenBank reference acessions. The isolates collected in this research were clustered in group 1 of the phylogenetic tree that was created by selecting a specific number of isolates from GenBank and thought to be reliable in the phylogenetic differentiation of ASPV. This is the first study to examine the prevalence of ASPV in the Isparta region and its phylogeny. It is possible that the results of the research will contribute to a better understanding of the situation of ASPV in Turkey.
Collapse
Affiliation(s)
- Ali ÇELİK
- Bolu Abant İzzet Baysal Üniversitesi
| |
Collapse
|
13
|
Lappe RR, Elmore MG, Lozier ZR, Jander G, Miller WA, Whitham SA. Metagenomic identification of novel viruses of maize and teosinte in North America. BMC Genomics 2022; 23:767. [DOI: 10.1186/s12864-022-09001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America.
Results
Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize.
Conclusions
Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.
Collapse
|
14
|
An Unwanted Association: The Threat to Papaya Crops by a Novel Potexvirus in Northwest Argentina. Viruses 2022; 14:v14102297. [DOI: 10.3390/v14102297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/10/2022] [Accepted: 10/15/2022] [Indexed: 11/17/2022] Open
Abstract
An emerging virus isolated from papaya (Carica papaya) crops in northwestern (NW) Argentina was sequenced and characterized using next-generation sequencing. The resulting genome is 6667-nt long and encodes five open reading frames in an arrangement typical of other potexviruses. This virus appears to be a novel member within the genus Potexvirus. Blast analysis of RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes showed the highest amino acid sequence identity (67% and 71%, respectively) with pitaya virus X. Based on nucleotide sequence similarity and phylogenetic analysis, the name papaya virus X is proposed for this newly characterized potexvirus that was mechanically transmitted to papaya plants causing chlorotic patches and severe mosaic symptoms. Papaya virus X (PapVX) was found only in the NW region of Argentina. This prevalence could be associated with a recent emergence or adaptation of this virus to papaya in NW Argentina.
Collapse
|
15
|
Suman R, Rani A, Rishi N, Dhir S, Hallan V, Chandel V. First report of apple stem grooving virus infection in loquat from India. Virusdisease 2022; 33:334-337. [PMID: 36277413 PMCID: PMC9481801 DOI: 10.1007/s13337-022-00783-x] [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: 06/03/2022] [Accepted: 07/16/2022] [Indexed: 11/30/2022] Open
Abstract
Loquat, commonly known as Eriobotrya japonica, is a major subtropical fruit from the Rosaceae family that is native to China but also found in most of Europe and Asia, including India. Apple stem grooving virus (ASGV) infecting loquat was detected using leaf samples collected from Himachal Pradesh (India) through DAC-ELISA followed by RT-PCR assays targeting coat protein (CP), movement protein (MP) and replicase (Rep) regions of ASGV genome. Sequencing of RT-PCR amplicons and sequence analyses revealed that CP, MP and Rep sequences of ASGV loquat Indian isolate of the current study shared a maximum of 98-100% nucleotide sequence identities with the corresponding sequences of available ASGV Indian isolates [LN559078, HE978837, MZ127820, MN912568]. Phylogenetic tree based on each sequenced gene confirmed the genetic diversity of ASGV. To the best of our knowledge, and based on review of the literature, this is the first report of ASGV infection in loquat from India.
Collapse
Affiliation(s)
- Rashmi Suman
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313 India
| | - Asha Rani
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313 India
| | - Narayan Rishi
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313 India
| | - Sunny Dhir
- Present Address: Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala, Haryana 133207 India
| | - Vipin Hallan
- Institute of Himalayan Bioresourse Technology, CSIR, Palampur, India
| | - Vanita Chandel
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, 201313 India
| |
Collapse
|
16
|
Massé D, Filloux D, Candresse T, Massart S, Marais A, Verdin E, Cassam N, Fernandez E, Roumagnac P, Teycheney PY, Lefeuvre P, Lett JM. Identification of a novel vitivirus from pineapple in Reunion Island. Arch Virol 2022; 167:2355-2357. [PMID: 35857149 DOI: 10.1007/s00705-022-05512-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/11/2022] [Indexed: 11/29/2022]
Abstract
We report the complete genome sequence of a novel member of the genus Vitivirus (family Betaflexiviridae, subfamily Trivirinae) infecting pineapple. The complete genome sequence of this virus was obtained from total RNA extracted from pineapple leaf samples collected in Reunion Island, using a combination of high-throughput sequencing technologies. The viral genome is 6,757 nt long, excluding the poly(A) tail, and shares all the hallmarks of vitiviruses. Phylogenetic analysis performed on the replication-associated protein and capsid protein gene sequences unambiguously place this new virus, for which we propose the name "pineapple virus A", in the genus Vitivirus.
Collapse
Affiliation(s)
- Delphine Massé
- ANSES, LSV RAPT, 97410, Saint Pierre, La Réunion, France.,Université de La Réunion, UMR PVBMT, 97410, Saint Pierre, La Réunion, France
| | - Denis Filloux
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgique
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon Cedex, France
| | - Eric Verdin
- INRAE, UR407 Unité de Pathologie Végétale, CS 60094, 84140, Montfavet, France
| | | | - Emmanuel Fernandez
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Philippe Roumagnac
- UMR PHIM, CIRAD, Campus International de Baillarguet, 34398, Montpellier Cedex-5, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | | | | | | |
Collapse
|
17
|
Igori D, Shin AY, Kim SE, Kwon S, Moon JS. Identification and molecular characterization of a novel kudzu-infecting virus of the family Betaflexiviridae. Arch Virol 2022; 167:1707-1711. [DOI: 10.1007/s00705-022-05468-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/28/2022] [Indexed: 11/02/2022]
|
18
|
Wang X, Larrea-Sarmiento A, Olmedo-Velarde A, Borth W, Suzuki JY, Wall MM, Melzer M, Hu J. Complete genome organization and characterization of Hippeastrum latent virus. Virus Genes 2022; 58:367-371. [PMID: 35426563 DOI: 10.1007/s11262-022-01901-z] [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: 01/07/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
The complete genome sequences of two carlaviruses were determined by high-throughput sequencing of RNA extracted from ringspot and mosaic, disease symptoms on leaves of spider lily plants (Crinum asiaticum, family Amaryllidaceae) growing as landscape plants in Hawaii. One, named Nerine latent virus (NeLV)-Hawaii with a genome of 8281 nucleotide exhibited the highest nucleotide identity and amino acid similarity of 95.5% and 96.0%, respectively, to the genome sequence of an isolate of NeLV from Narcissus sp. in Australia (JQ395044). The second, named Hippeastrum latent virus (HiLV)-Hawaii with a genome of 8497 nucleotides exhibited the highest nucleotide identity and amino acid similarity, 84.3% and 88.7%, respectively, to the sequence of a previously uncharacterized HiLV isolate from a potted flowering plant, Amaryllis (Hippeastrum hybridum Hort) in Taiwan (DQ098905). The amino acid sequence similarities of replicase (Rep) and coat protein (CP) between HiLV-Hawaii and NeLV-Hawaii were 44.8% and 38.4%, respectively. Results of viral protein Rep and CP amino acid sequence comparisons from various carlaviruses provide evidence that HiLV and NeLV, previously classified as synonymous viruses are in fact unique viruses. This is the first report for the complete sequence, organization, and phylogenetic characterization of HiLV and the first detection of HiLV both in C. asiaticum and in the USA.
Collapse
Affiliation(s)
- Xupeng Wang
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Adriana Larrea-Sarmiento
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Alejandro Olmedo-Velarde
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Wayne Borth
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Jon Y Suzuki
- United States Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Marisa M Wall
- United States Department of Agriculture, Agricultural Research Service, U.S. Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
| | - Michael Melzer
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - John Hu
- Department of Plant and Environmental Protection Sciences, University of Hawaii, Honolulu, HI, 96822, USA.
| |
Collapse
|
19
|
Veselova SV, Sorokan AV, Burkhanova GF, Rumyantsev SD, Cherepanova EA, Alekseev VY, Sarvarova ER, Kasimova AR, Maksimov IV. By Modulating the Hormonal Balance and Ribonuclease Activity of Tomato Plants Bacillus subtilis Induces Defense Response against Potato Virus X and Potato Virus Y. Biomolecules 2022; 12:biom12020288. [PMID: 35204789 PMCID: PMC8961569 DOI: 10.3390/biom12020288] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
Endophytic plant-growth-promoting microorganisms can protect plants against pathogens, but they have rarely been investigated as potential biocontrol agents and triggers of induced systemic resistance (ISR), regulated by phytohormones, against viruses. We studied the role of endophytic strains Bacillus subtilis 26D and B. subtilis Ttl2, which secrete ribonucleases and phytohormones, in the induction of tomato plant resistance against potato virus X and potato virus Y in a greenhouse condition. The endophytes reduced the accumulation of viruses in plants, increased the activity of plant ribonucleases and recovered the fruit yield of infected tomato plants. Both the 26D and Ttl2 strains induced ISR by activating the transcription of genes related to salicylate- and jasmonate-dependent responses. The 26D and Ttl2 strains increased the content of cytokinins and decreased the level of indolacetic acid in plants infected with PVX or PVY. PVY led to an increase of the abscisic acid (ABA) content in tomato plants, and PVX had the opposite effect. Both strains reduced the ABA content in plants infected with PVY and induced ABA accumulation in plants infected with PVX, which led to an increase in the resistance of plants. This is the first report of the protection of tomato plants against viral diseases by foliar application of endophytes.
Collapse
|
20
|
Read DA, Thompson GD, Cordeur NL, Swanevelder D, Pietersen G. Genomic characterization of grapevine viruses N and O: novel vitiviruses from South Africa. Arch Virol 2022; 167:611-614. [PMID: 34988696 DOI: 10.1007/s00705-021-05333-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 10/28/2021] [Indexed: 11/02/2022]
Abstract
A survey was performed on a Vitis cultivar collection in Stellenbosch, South Africa. Metaviromes were generated for each cultivar, using an RNAtag-seq workflow. Analysis of assembled contigs indicated the presence of two putatively novel members of the genus Vitivirus, provisionally named "grapevine virus N" (GVN) and "grapevine virus O" (GVO). Comparisons of amino acid sequences showed that GVN and GVO are most closely related to grapevine virus G and grapevine virus E, respectively. The incidence of these novel viruses within the sampling site was low, with GVO and GVN associated with only five and two cultivars, respectively, of the 229 sampled.
Collapse
Affiliation(s)
- David A Read
- Agricultural Research Council (ARC)-Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa. .,Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Genevieve D Thompson
- Agricultural Research Council (ARC)-Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa.,Gene Vantage, 34 Monte Carlo Crescent, Kyalami Business Park, Johannesburg, 1684, South Africa
| | | | - Dirk Swanevelder
- Agricultural Research Council (ARC)-Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa
| | - Gerhard Pietersen
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| |
Collapse
|
21
|
Dickmeis C, Commandeur U. Advanced Fusion Strategies for the Production of Functionalized Potato Virus X Virions. Methods Mol Biol 2022; 2480:215-239. [PMID: 35616866 DOI: 10.1007/978-1-0716-2241-4_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant virions are ideal for nanotechnology applications because they are structurally diverse and can self-assemble naturally, allowing for large-scale production in plants by molecular farming. Potato virus X (PVX) is particularly amenable due to the unique properties of its filamentous and flexible capsid, but efficient strategies are required to adapt the surface properties of PVX, such as the attachment of proteins and peptides. This chapter describes the selection and utilization of 2A ribosomal skip sequences, allowing the presentation of heterologous proteins and peptides as N-terminal fusions to the PVX coat protein at different densities. Another strategy for the rapid modification of PVX capsids is the plug-and-display module of the SpyTag/SpyCatcher system. The SpyTag can be presented on the PVX surface, allowing for the attachment of any protein fused to the SpyCatcher sequence.
Collapse
Affiliation(s)
- Christina Dickmeis
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany.
| | - Ulrich Commandeur
- Institute for Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| |
Collapse
|
22
|
Venkataraman S, Apka P, Shoeb E, Badar U, Hefferon K. Plant Virus Nanoparticles for Anti-cancer Therapy. Front Bioeng Biotechnol 2021; 9:642794. [PMID: 34976959 PMCID: PMC8714775 DOI: 10.3389/fbioe.2021.642794] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
Plant virus nanoparticles (VNPs) are inexpensive to produce, safe, biodegradable and efficacious as treatments. The applications of r plant virus nanoparticles range from epitope carriers for vaccines to agents in cancer immunotherapy. Both VNPs and virus-like particles (VLPs) are highly immunogenic and are readily phagocytosed by antigen presenting cells (APCs), which in turn elicit antigen processing and display of pathogenic epitopes on their surfaces. Since the VLPs are composed of multiple copies of their respective capsid proteins, they present repetitive multivalent scaffolds which aid in antigen presentation. Therefore, the VLPs prove to be highly suitable platforms for delivery and presentation of antigenic epitopes, resulting in induction of more robust immune response compared to those of their soluble counterparts. Since the tumor microenvironment poses the challenge of self-antigen tolerance, VLPs are preferrable platforms for delivery and display of self-antigens as well as otherwise weakly immunogenic antigens. These properties, in addition to their diminutive size, enable the VLPs to deliver vaccines to the draining lymph nodes in addition to promoting APC interactions. Furthermore, many plant viral VLPs possess inherent adjuvant properties dispensing with the requirement of additional adjuvants to stimulate immune activity. Some of the highly immunogenic VLPs elicit innate immune activity, which in turn instigate adaptive immunity in tumor micro-environments. Plant viral VLPs are nontoxic, inherently stable, and capable of being mass-produced as well as being modified with antigens and drugs, therefore providing an attractive option for eliciting anti-tumor immunity. The following review explores the use of plant viruses as epitope carrying nanoparticles and as a novel tools in cancer immunotherapy.
Collapse
Affiliation(s)
| | - Paul Apka
- Theranostics and Drug Discovery Research Group, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Erum Shoeb
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Genetics, University of Karachi, Karachi, Pakistan
| | - Uzma Badar
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Department of Genetics, University of Karachi, Karachi, Pakistan
| | - Kathleen Hefferon
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
23
|
Identification and molecular characterization of a novel carlavirus infecting rose plants (Rosa chinensis Jacq.). Arch Virol 2021; 166:3499-3502. [PMID: 34636953 DOI: 10.1007/s00705-021-05260-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/23/2021] [Indexed: 10/20/2022]
Abstract
In the present study, the genome sequence of a potential novel virus, tentatively named "rose virus C" (RVC), was mined from publically available transcriptomic data from a Rosa chinensis plant. The complete genome sequence of RVC consists of 8,386 nt, excluding a 3' poly(A) tail, and contains five ORFs. Phylogenetic analysis showed that RVC clustered with members of the genus Carlavirus, family Betaflexiviridae. The replicase gene had 48.8-52.1% nt sequence identity to those of other carlaviruses, while the CP gene had 40.4-45.9% nt sequence identity, which is far below the species demarcation cutoff of 72%. The incidence of RVC in rose plants was low (5.4%). Overall, our data suggest that RVC is a novel atypical virus of the genus Carlavirus.
Collapse
|
24
|
Frontiers in Bioengineering and Biotechnology: Plant Nanoparticles for Anti-Cancer Therapy. Vaccines (Basel) 2021; 9:vaccines9080830. [PMID: 34451955 PMCID: PMC8402531 DOI: 10.3390/vaccines9080830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022] Open
Abstract
Naturally occurring viral nanomaterials have gained popularity owing to their biocompatible and biodegradable nature. Plant virus nanoparticles (VNPs) can be used as nanocarriers for a number of biomedical applications. Plant VNPs are inexpensive to produce, safe to administer and efficacious as treatments. The following review describes how plant virus architecture facilitates the use of VNPs for imaging and a variety of therapeutic applications, with particular emphasis on cancer. Examples of plant viruses which have been engineered to carry drugs and diagnostic agents for specific types of cancer are provided. The drug delivery system in response to the internal conditions is known as stimuli response, recently becoming more applicable using plant viruses based VNPs. The review concludes with a perspective of the future of plant VNPs and plant virus-like particles (VLPs) in cancer research and therapy.
Collapse
|
25
|
Read DA, Roberts R, Swanevelder D, Pietersen G, Thompson GD. Novel viruses associated with plants of the family Amaryllidaceae in South Africa. Arch Virol 2021; 166:2817-2823. [PMID: 34279720 DOI: 10.1007/s00705-021-05170-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/23/2021] [Indexed: 11/28/2022]
Abstract
Nineteen samples from members of the plant genera Agapanthus, Clivia, Hippeastrum, and Scadoxus were collected from gardens in the Gauteng and Western Cape provinces of South Africa. The plants displayed highly variable symptoms of viral disease, including chlorosis, necrosis, streaking, and ringspot. RNAtag-seq was used to characterize the associated viral populations. Plants of the genus Agapanthus were found to be associated with three novel viruses from the families Caulimoviridae, Closteroviridae, and Betaflexiviridae; plants of the genus Clivia were associated with novel members of the families Potyviridae and Betaflexiviridae; and plants of the genus Scadoxus were associated with a novel member of the family Tospoviridae. Nerine latent virus was associated with plants of the genera Agapanthus, Clivia, and Hippeastrum, while hippeastrum mosaic virus was associated exclusively with a Hippeastrum cultivar.
Collapse
Affiliation(s)
- David A Read
- Agricultural Research Council (ARC) - Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa. .,Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Hatfield, 0028, South Africa.
| | - Ronel Roberts
- ARC - Plant Health and Protection, Private Bag X134, Queenswood, Pretoria, 0121, South Africa
| | - Dirk Swanevelder
- Agricultural Research Council (ARC) - Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa
| | - Gerhard Pietersen
- Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Genevieve D Thompson
- Agricultural Research Council (ARC) - Biotechnology Platform, 100 Old Soutpan Road, Onderstepoort, Pretoria, 0110, South Africa.,Gene Vantage, 34 Monte Carlo Crescent, Kyalami Business Park, Johannesburg, 1684, South Africa
| |
Collapse
|
26
|
Kokane AD, Lawrence K, Kokane SB, Gubyad MG, Misra P, Reddy MK, Ghosh DK. Development of a SYBR Green-based RT-qPCR assay for the detection of Indian citrus ringspot virus. 3 Biotech 2021; 11:359. [PMID: 34295604 DOI: 10.1007/s13205-021-02903-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/19/2021] [Indexed: 10/21/2022] Open
Abstract
The Indian citrus ringspot virus (ICRSV) that causes ringspot disease, especially to 'Kinnow mandarin' hampers the sustainability of crop production. Presently, the disease is not amenable for control through host resistance or the introduction of chemicals, hence raising virus-free plants is one of the most effective approaches to manage the disease. Consequently, it is necessary to develop rapid, sensitive, specific, and early diagnostic methods for disease control. In the present study, newly designed primers targeting a 164 bp region of the ICRSV coat protein gene were used to develop and optimize a SYBR Green-based quantitative reverse transcription polymerase chain reaction (RT-qPCR) assay, for the detection of ICRSV. The RT-qPCR assay was evaluated and confirmed using viral RNA extracted from ICRSV infected plants maintained in screen house as well as field samples. The standard curves displayed a dynamic linear range across eight log units of ICRSV-cRNA copy number ranging from 9.48.1 fmol (5.709 × 109) to 0.000948 amol (5.709 × 102), with detection limit of 5.709 × 102 copies per reaction using serial tenfold diluted in vitro transcribed viral cRNA. The developed RT-qPCR is very specific to ICRSV does not react to other citrus pathogens, and approximately 100-fold more sensitive than conventional RT-PCR. Thus, this assay will be useful in laboratories, KVKs, and nurseries for the citrus budwood certification program as well as in plant quarantine stations. To our knowledge, this is the first study of the successful detection of ICRSV by RT-qPCR.
Collapse
|
27
|
Complete genome sequence of viola mottle virus, revealing its synonymous relationship to tulip virus X. Arch Virol 2021; 166:2343-2346. [PMID: 34097143 DOI: 10.1007/s00705-021-05129-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Viola mottle virus (VMoV) was discovered in Viola odorata showing symptoms of reduced growth, leaf mottling, and whitish stripes on flowers in northern Italy in 1977. This virus has been provisionally classified as a member of the genus Potexvirus based on its morphological, serological, and biological characteristics. However, since genetic information of VMoV has never been reported, the taxonomic status of this virus is unclear. Here, we report the first complete genome sequence of VMoV to clarify its taxonomic position. Its genomic RNA is 6,052 nucleotides long, excluding the 3'-terminal poly(A) tail, and has five open reading frames (ORFs) typical of potexviruses. Among potexviruses, VMoV showed the most similarity to tulip virus X (TVX) with 81.1-81.2% nucleotide and 90.4-90.7% amino acid sequence identity in ORF1 and 82.9-83.5% nucleotide and 93.2-95.2% amino acid sequence identity in ORF5. These values are much higher than the species demarcation threshold for the genus. Phylogenetic analysis also indicated that VMoV is nested within the clade of TVX isolates. These data demonstrate that VMoV and TVX are members of the same species.
Collapse
|
28
|
Dhir S, Mathioudakis MM, Hasiów-Jaroszewska B, Hallan V. Serological and molecular analysis indicates the presence of distinct viral genotypes of Apple stem pitting virus in India. 3 Biotech 2021; 11:278. [PMID: 34040927 DOI: 10.1007/s13205-021-02798-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/15/2021] [Indexed: 01/10/2023] Open
Abstract
Recombination leads to the generation of new viral progeny which remain undetected by routine testing procedures and may be a threat to the infected host. Here, we have characterised the complete genome sequences of two isolates of Apple stem pitting virus from apple cv. Red Chief (Palampur) and cv. Gold Spur (N) with distinct serological reactivities. The viral genomes consisted of 9267 nucleotides for isolate Palampur and 9254 nucleotides for isolate N, excluding the poly (A) tail and contained 5five open reading frames (ORFs). Isolate N shared 80.8% sequence identity with ASPV apple isolate GA2 from China, while isolate Palampur shared 81.4% sequence identity with ASPV apple isolate PB66 from the United Kingdom. The serological difference of isolates N and Palampur along with their low sequence identity indicated the existence of two distinct virus genotypes which was corroborated by evolutionary and genetic differentiation analyses. Recombination events were detected in the RdRp and CP sequences of Palampur isolate thereby suggesting the role of recombination in the evolution of distinct virus genotypes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02798-5.
Collapse
Affiliation(s)
- Sunny Dhir
- Plant Virus Lab, Council of Scientific & Industrial Research, Institute of Himalayan Bioresource Technology, Palampur, HP 176061 India
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, Uttar Pradesh 201313 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Matthaios M Mathioudakis
- Plant Pathology Laboratory, Institute of Olive Tree, Subtropical Crops and Viticulture, ELGO-DIMITRA, Karamanlis Ave. 167, 73134 Chania, Greece
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, ul. Wł. Węgorka 20, 60-318 Poznan, Poland
| | - Vipin Hallan
- Plant Virus Lab, Council of Scientific & Industrial Research, Institute of Himalayan Bioresource Technology, Palampur, HP 176061 India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| |
Collapse
|
29
|
Kim J, Lal A, Kil EJ, Kwak HR, Yoon HS, Choi HS, Kim M, Ali M, Lee S. Adaptation and Codon-Usage Preference of Apple and Pear-Infecting Apple Stem Grooving Viruses. Microorganisms 2021; 9:microorganisms9061111. [PMID: 34063757 PMCID: PMC8223792 DOI: 10.3390/microorganisms9061111] [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: 02/27/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 11/17/2022] Open
Abstract
Apple stem grooving virus (ASGV; genus Capillovirus) is an economically important virus. It has an approx. 6.5 kb, monopartite, linear, positive-sense, single-stranded RNA genome. The present study includes identification of 24 isolates—13 isolates from apple (Pyrus malus L.) and 11 isolates from pear (Pyrus communis L.)—from different agricultural fields in South Korea. The coat protein (CP) gene of the corresponding 23 isolates were amplified, sequenced, and analyzed. The CP sequences showed phylogenetic separation based on their host species, and not on the geography, indicating host adaptation. Further analysis showed that the ASGV isolated in this study followed host adaptation influenced and preferred by the host codon-usage.
Collapse
Affiliation(s)
- Jaedeok Kim
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
- Incheon International Airport Regional Office, Animal and Plant Quarantine Agency, Seoul 22382, Korea
| | - Aamir Lal
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
| | - Eui-Joon Kil
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
- Department of Plant Medicals, Andong National University, Andong 36729, Korea
| | - Hae-Ryun Kwak
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea; (H.-R.K.); (H.-S.C.)
| | - Hwan-Su Yoon
- Department of Biological Science, Sungkyunkwan University, Suwon 16419, Korea;
| | - Hong-Soo Choi
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea; (H.-R.K.); (H.-S.C.)
| | - Mikyeong Kim
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea; (H.-R.K.); (H.-S.C.)
- College of Agriculture, Life and Environment Sciences, Chungbuk National University, Cheongju 28644, Korea
- Correspondence: (M.K.); (M.A.); (S.L.); Tel.: +82-43-261-2509 (M.K.); +92-312-9959558 (M.A.); +82-31-290-7866 (S.L.); Fax: +82-43-271-4414 (M.K.); +82-31-290-7892 (S.L.)
| | - Muhammad Ali
- Department of Life Sciences, School of Science, University of Management and Technology (UMT), Johar Town, Lahore 54770, Pakistan
- Correspondence: (M.K.); (M.A.); (S.L.); Tel.: +82-43-261-2509 (M.K.); +92-312-9959558 (M.A.); +82-31-290-7866 (S.L.); Fax: +82-43-271-4414 (M.K.); +82-31-290-7892 (S.L.)
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon 16419, Korea; (J.K.); (A.L.); (E.-J.K.)
- Correspondence: (M.K.); (M.A.); (S.L.); Tel.: +82-43-261-2509 (M.K.); +92-312-9959558 (M.A.); +82-31-290-7866 (S.L.); Fax: +82-43-271-4414 (M.K.); +82-31-290-7892 (S.L.)
| |
Collapse
|
30
|
Park D, Hahn Y. Rapid protein sequence evolution via compensatory frameshift is widespread in RNA virus genomes. BMC Bioinformatics 2021; 22:251. [PMID: 34000995 PMCID: PMC8127213 DOI: 10.1186/s12859-021-04182-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/10/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND RNA viruses possess remarkable evolutionary versatility driven by the high mutability of their genomes. Frameshifting nucleotide insertions or deletions (indels), which cause the premature termination of proteins, are frequently observed in the coding sequences of various viral genomes. When a secondary indel occurs near the primary indel site, the open reading frame can be restored to produce functional proteins, a phenomenon known as the compensatory frameshift. RESULTS In this study, we systematically analyzed publicly available viral genome sequences and identified compensatory frameshift events in hundreds of viral protein-coding sequences. Compensatory frameshift events resulted in large-scale amino acid differences between the compensatory frameshift form and the wild type even though their nucleotide sequences were almost identical. Phylogenetic analyses revealed that the evolutionary distance between proteins with and without a compensatory frameshift were significantly overestimated because amino acid mismatches caused by compensatory frameshifts were counted as substitutions. Further, this could cause compensatory frameshift forms to branch in different locations in the protein and nucleotide trees, which may obscure the correct interpretation of phylogenetic relationships between variant viruses. CONCLUSIONS Our results imply that the compensatory frameshift is one of the mechanisms driving the rapid protein evolution of RNA viruses and potentially assisting their host-range expansion and adaptation.
Collapse
Affiliation(s)
- Dongbin Park
- Department of Life Science, Chung-Ang University, Seoul, 06794, South Korea
| | - Yoonsoo Hahn
- Department of Life Science, Chung-Ang University, Seoul, 06794, South Korea.
| |
Collapse
|
31
|
High-Throughput Sequencing Indicates Novel Varicosavirus, Emaravirus, and Deltapartitivirus Infections in Vitis coignetiae. Viruses 2021; 13:v13050827. [PMID: 34063722 PMCID: PMC8147796 DOI: 10.3390/v13050827] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/01/2021] [Accepted: 05/02/2021] [Indexed: 11/17/2022] Open
Abstract
Vitis coignetiae samples were collected from several locations in the northern area of Japan, and virome analysis using a high-throughput sequencing technique was performed. The data indicated that some of the collected samples were in mixed infections by various RNA viruses. Among these viruses, three were identified as newly recognized species with support of sequence identity and phylogenetic analysis. The viruses have been provisionally named the Vitis varicosavirus, Vitis emaravirus, and Vitis crypticvirus, and were assigned to the genus Varicosavirus, Emaravirus, and Deltapartitivirus, respectively.
Collapse
|
32
|
Molecular Characterization of the Coat Protein Gene of Greek Apple Stem Pitting Virus Isolates: Evolution through Deletions, Insertions, and Recombination Events. PLANTS 2021; 10:plants10050917. [PMID: 34063623 PMCID: PMC8147640 DOI: 10.3390/plants10050917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/12/2023]
Abstract
A RT–PCR assay developed to amplify the full coat protein (CP) gene of apple stem pitting virus (ASPV) was evaluated using 180 Greek apple and pear samples and showed a broad detection range. This method was used to investigate the presence of ASPV in quince in Greece and showed a high incidence of 52%. The sequences of 14 isolates from various hosts with a distinct RFLP profile were determined. ASPV population genetics and the factors driving ASPV evolution were analyzed using the Greek ASPV sequences, novel sequences from Brazilian apple trees and Chinese botanical Pyrus species, and homologous sequences retrieved from GenBank. Fourteen variant types of Greek, Brazilian and botanical isolates, which differ in CP gene length and presence of indels, were identified. In addition, these analyses showed high intra- and inter-group variation among isolates from different countries and hosts, indicating the significant variability present in ASPV. Recombination events were detected in four isolates originating from Greek pear and quince and two from Brazilian apples. In a phylogenetic analysis, there was a tendency for isolates to cluster together based on CP gene length, the isolation host, and the detection method applied. Although there was no strict clustering based on geographical origin, most isolates from a given country tended to regroup in specific clusters. Interestingly, it was found that the phylogeny was correlated to the type, position, and pattern of indels, which represent hallmarks of specific lineages and indicate their possible role in virus diversification, rather than the CP size itself. Evidence of recombination between isolates from botanical and cultivated species and the clustering of isolates from botanical species and isolates from cultivated species suggest the existence of a possible undetermined transmission mechanism allowing the exchange of ASPV isolates between the cultivated and wild/ornamental hosts.
Collapse
|
33
|
Kokane AD, Kokane SB, Warghane AJ, Gubyad MG, Sharma AK, Reddy MK, Ghosh DK. A Rapid and Sensitive Reverse Transcription-Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for the Detection of Indian Citrus Ringspot Virus. PLANT DISEASE 2021; 105:1346-1355. [PMID: 32990524 DOI: 10.1094/pdis-06-20-1349-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Indian citrus ringspot virus (ICRSV) is a devastating pathogen that has a particularly deleterious effect on the 'Kinnow mandarin', a commercial citrus crop cultivated in the northwest of India. ICRSV belongs to the Mandarivirus genus within the family of Alphaflexiviridae and has a positive sense single-stranded RNA (ssRNA) genome consisting of six open reading frames (ORFs). Severe cases of ICRSV result in a significant reduction in both the yield and quality of crops. Consequently, there is an urgent need to develop methods to detect ICRSV in an accurate and timely manner. Current methods involve a two-step reverse transcription polymerase chain reaction (RT-PCR) that is time consuming. Here, we describe a novel, one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) method for the sensitive and rapid detection of ICRSV. To standardize the RT-LAMP assay, four different primers were designed and tested to target the coat protein gene of ICRSV. Amplification results were visualized by a color change after addition of SYBR Green I. The standardized RT-LAMP assay was highly specific and successfully detected all 35 ICRSV isolates tested from the Punjab and Haryana states of India. Furthermore, there was no cross-reaction with 17 isolates of five other citrus pathogens that are common in India. The ICRSV RT-LAMP assay developed in the present study is a simple, rapid, sensitive, specific technique. Moreover, the assay consists of only a single step and is more cost effective than existing methods. This is the first application of RT-LAMP for the detection of ICRSV. Our RT-LAMP assay is a powerful tool for the detection of ICRSV and will be particularly useful for large-scale indexing of field samples in diagnostic laboratories, in nurseries, and for quarantine applications.
Collapse
Affiliation(s)
- Amol D Kokane
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Sunil B Kokane
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Ashish J Warghane
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Mrugendra G Gubyad
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology, Roorkee-247 667, Uttarakhand, India
| | - M Krishna Reddy
- ICAR-Indian Institute of Horticultural Research, Bangalore-560 089, Karnataka, India
| | - Dilip Kumar Ghosh
- Plant Virology Lab, ICAR-Central Citrus Research Institute, Nagpur-440 033, Maharashtra, India
| |
Collapse
|
34
|
Uranga M, Aragonés V, Selma S, Vázquez‐Vilar M, Orzáez D, Daròs J. Efficient Cas9 multiplex editing using unspaced sgRNA arrays engineering in a Potato virus X vector. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:555-565. [PMID: 33484202 PMCID: PMC8251967 DOI: 10.1111/tpj.15164] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 05/18/2023]
Abstract
Systems based on the clustered, regularly interspaced, short palindromic repeat (CRISPR) and CRISPR-associated proteins (Cas) have revolutionized genome editing in many organisms, including plants. Most CRISPR-Cas strategies in plants rely on genetic transformation using Agrobacterium tumefaciens to supply the gene editing reagents, such as Cas nucleases or the synthetic guide RNA (sgRNA). While Cas nucleases are constant elements in editing approaches, sgRNAs are target-specific and a screening process is usually required to identify those most effective. Plant virus-derived vectors are an alternative for the fast and efficient delivery of sgRNAs into adult plants, due to the virus capacity for genome amplification and systemic movement, a strategy known as virus-induced genome editing. We engineered Potato virus X (PVX) to build a vector that easily expresses multiple sgRNAs in adult solanaceous plants. Using the PVX-based vector, Nicotiana benthamiana genes were efficiently targeted, producing nearly 80% indels in a transformed line that constitutively expresses Streptococcus pyogenes Cas9. Interestingly, results showed that the PVX vector allows expression of arrays of unspaced sgRNAs, achieving highly efficient multiplex editing in a few days in adult plant tissues. Moreover, virus-free edited progeny can be obtained from plants regenerated from infected tissues or infected plant seeds, which exhibit a high rate of heritable biallelic mutations. In conclusion, this new PVX vector allows easy, fast and efficient expression of sgRNA arrays for multiplex CRISPR-Cas genome editing and will be a useful tool for functional gene analysis and precision breeding across diverse plant species, particularly in Solanaceae crops.
Collapse
Affiliation(s)
- Mireia Uranga
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)Avenida de los Naranjos s/nValencia46022Spain
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)Avenida de los Naranjos s/nValencia46022Spain
| | - Sara Selma
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)Avenida de los Naranjos s/nValencia46022Spain
| | - Marta Vázquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)Avenida de los Naranjos s/nValencia46022Spain
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)Avenida de los Naranjos s/nValencia46022Spain
| | - José‐Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas‐Universitat Politècnica de València)Avenida de los Naranjos s/nValencia46022Spain
| |
Collapse
|
35
|
Balsak SC, Buzkan N. Prevalence and genetic variability of grapevine virus A in Turkish autochthonous grapevine varieties. Arch Virol 2021; 166:943-947. [PMID: 33495897 DOI: 10.1007/s00705-021-04953-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/24/2020] [Indexed: 11/26/2022]
Abstract
This work describes the first molecular characterization of grapevine virus A (GVA) in Turkish grapevine varieties based on the coat protein gene. RT-PCR detection revealed a high infection rate of GVA in two major viticultural areas, Eastern Mediterranean (EM) and Southeast Anatolia (SEA). The number of infected varieties was higher in SEA, where very ancient and traditional cultivars are in use and no foreign grapevine material has been introduced. High nucleotide and amino acid sequence similarity were seen between the Turkish GVA isolates and the reference isolates in group I and II. The viral isolates from the same location and cultivars were not phylogenetically related.
Collapse
Affiliation(s)
- Selin Ceren Balsak
- Sütçü Imam University, Agriculture Faculty, Plant protection Department, Kahramanmaraş, Turkey
| | - Nihal Buzkan
- Sütçü Imam University, Agriculture Faculty, Plant protection Department, Kahramanmaraş, Turkey.
| |
Collapse
|
36
|
Luo Q, Hu S, Lin Q, Xu F, Peng J, Zheng H, Wu G, Rao S, Chen J, Lu Y, Guo F, Yan F. Complete genome sequence of a novel foveavirus isolated from Allium sativum L. in China. Arch Virol 2021; 166:983-986. [PMID: 33439325 DOI: 10.1007/s00705-021-04957-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/27/2020] [Indexed: 02/02/2023]
Abstract
The complete genome sequence of a novel foveavirus identified in garlic (Allium sativum L.) in China was determined using RNA-seq, reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The entire genomic RNA (GenBank accession MT981417) is 8748 nucleotides long excluding the 3'-terminal poly(A) tail and contains five open reading frames (ORFs). These ORFs encode the viral replicase, a triple gene block, and a coat protein. The virus was tentatively named "garlic yellow stripe associated virus" (GarYSaV). Pairwise comparisons of protein sequences show that GarYSaV encodes proteins that share less than 47% identity with those of other foveaviruses, suggesting that it represents a new species in the genus. Phylogenetic analysis of amino acid sequences of the replicase and CP confirm that GarYSaV is a member of the genus Foveavirus. To our knowledge, this is the first report of a foveavirus in a monocot plant.
Collapse
Affiliation(s)
- Qi Luo
- 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
| | - Shuzhen Hu
- 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
| | - Qi Lin
- 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
| | - Fei Xu
- Public Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jiejun Peng
- 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
| | - Hongying Zheng
- 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
| | - Guanwei Wu
- 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
| | - Shaofei Rao
- 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
| | - Jianping Chen
- 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
| | - Yuwen Lu
- 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.
| | - Fengling Guo
- Institute of Economic Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, 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.
| |
Collapse
|
37
|
Nemchinov LG, Grinstead S. Identification of a Novel Isolate of Alfalfa virus S from China Suggests a Possible Role of Seed Contamination in the Distribution of the Virus. PLANT DISEASE 2020; 104:3115-3117. [PMID: 33058717 DOI: 10.1094/pdis-04-20-0906-sc] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Recently, alfalfa virus S (AVS), a new species in the family Alphaflexiviridae, was identified in alfalfa samples originating from Sudan, northern Africa. Here, we report on the identification and complete genomic sequence of an AVS isolate found in 7-day-old seedlings grown from alfalfa seeds acquired from China. The Chinese isolate of AVS differed in its nucleotide sequence from the Sudanese isolate by 8.6%. The detection of AVS in alfalfa seedlings developed from the germinated seeds may indicate a potential role of seed transmission in the distribution of this virus. The results obtained suggest that AVS may be far more widespread than previously thought.
Collapse
Affiliation(s)
- Lev G Nemchinov
- USDA/ARS, Beltsville Agricultural Research Center, Molecular Plant Pathology Laboratory, Beltsville, MD 20705
| | - Samuel Grinstead
- USDA/ARS, Beltsville Agricultural Research Center, National Germplasm Resources Laboratory, Beltsville, MD 20705
| |
Collapse
|
38
|
Wu J, Zhang S, Atta S, Yang C, Zhou Y, Di Serio F, Zhou C, Cao M. Discovery and Survey of a New Mandarivirus Associated with Leaf Yellow Mottle Disease of Citrus in Pakistan. PLANT DISEASE 2020; 104:1593-1600. [PMID: 32357118 DOI: 10.1094/pdis-08-19-1744-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During biological indexing for viruses in citrus trees, in a collection of Symons sweet orange (SSO) (Citrus sinensis L. Osbeck) graft inoculated with bark tissues of citrus trees from the Punjab Province in Pakistan, several SSO trees exhibited leaf symptoms of vein yellowing and mottle. High-throughput sequencing by Illumina of RNA preparation depleted of ribosomal RNAs from one symptomatic tree, followed by BLAST analyses, allowed identification of a novel virus, tentatively named citrus yellow mottle-associated virus (CiYMaV). Genome features of CiYMaV are typical of members of the genus Mandarivirus (family Alphaflexiviridae). Virus particles with elongated flexuous shape and size resembling those of mandariviruses were observed by transmission electron microscopy. The proteins encoded by CiYMaV share high sequence identity, conserved motifs, and phylogenetic relationships with the corresponding proteins encoded by Indian citrus ringspot virus (ICRSV) and citrus yellow vein clearing virus (CYVCV), the two current members of the genus Mandarivirus. Although CYVCV is the virus most closely related to CiYMaV, the two viruses can be serologically and biologically discriminated from each other. A reverse-transcription PCR method designed to specifically detect CiYMaV revealed high prevalence (62%) of this virus in 120 citrus trees from the Punjab Province, Pakistan, where the novel virus was found mainly in mixed infection with CYVCV and citrus tristeza virus. However, a preliminary survey on samples from 200 citrus trees from the Yunnan Province, China failed to detect CiYMaV in this region, suggesting that the molecular, serological, and biological data provided here are timely and can help to prevent the spread of this virus in citrus-producing countries.
Collapse
Affiliation(s)
- Jiaxing Wu
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Sagheer Atta
- Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan 32200, Pakistan
| | - Caixia Yang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering Shenyang University, Shenyang 110044, China
| | - Yan Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| |
Collapse
|
39
|
Yang X, Lu Y, Wang F, Chen Y, Tian Y, Jiang L, Peng J, Zheng H, Lin L, Yan C, Taliansky M, MacFarlane S, Wu Y, Chen J, Yan F. Involvement of the chloroplast gene ferredoxin 1 in multiple responses of Nicotiana benthamiana to Potato virus X infection. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2142-2156. [PMID: 31872217 PMCID: PMC7094082 DOI: 10.1093/jxb/erz565] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/20/2019] [Indexed: 05/14/2023]
Abstract
The chloroplast protein ferredoxin 1 (FD1), with roles in the chloroplast electron transport chain, is known to interact with the coat proteins (CPs) of Tomato mosaic virus and Cucumber mosaic virus. However, our understanding of the roles of FD1 in virus infection remains limited. Here, we report that the Potato virus X (PVX) p25 protein interacts with FD1, whose mRNA and protein levels are reduced by PVX infection or by transient expression of p25. Silencing of FD1 by Tobacco rattle virus-based virus-induced gene silencing (VIGS) promoted the local and systemic infection of plants by PVX. Use of a drop-and-see (DANS) assay and callose staining revealed that the permeability of plasmodesmata (PDs) was increased in FD1-silenced plants together with a consistently reduced level of PD callose deposition. After FD1 silencing, quantitative reverse transcription-real-time PCR (qRT-PCR) analysis and LC-MS revealed these plants to have a low accumulation of the phytohormones abscisic acid (ABA) and salicylic acid (SA), which contributed to the decreased callose deposition at PDs. Overexpression of FD1 in transgenic plants manifested resistance to PVX infection, but the contents of ABA and SA, and the PD callose deposition were not increased in transgenic plants. Overexpression of FD1 interfered with the RNA silencing suppressor function of p25. These results demonstrate that interfering with FD1 function causes abnormal plant hormone-mediated antiviral processes and thus enhances PVX infection.
Collapse
Affiliation(s)
- Xue Yang
- 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
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, China
| | - Yuwen Lu
- 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
| | - Fang Wang
- Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Ying Chen
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, China
| | - Yanzhen Tian
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liangliang Jiang
- 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
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiejun Peng
- 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
| | - Hongying Zheng
- 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
| | - Lin Lin
- 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
| | - Chengqi Yan
- Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Michael Taliansky
- The James Hutton Institute, Cell and Molecular Sciences Group, Invergowrie, Dundee, UK
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the RAS, Moscow, Russia
| | - Stuart MacFarlane
- The James Hutton Institute, Cell and Molecular Sciences Group, Invergowrie, Dundee, UK
| | - Yuanhua Wu
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, China
| | - Jianping Chen
- 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
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Department of Plant Protection, Shenyang Agriculture University, Shenyang, 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, China
- Key Laboratory of Biotechnology in Plant Protection of MOA and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
40
|
Grinzato A, Kandiah E, Lico C, Betti C, Baschieri S, Zanotti G. Atomic structure of potato virus X, the prototype of the Alphaflexiviridae family. Nat Chem Biol 2020; 16:564-569. [DOI: 10.1038/s41589-020-0502-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 02/16/2020] [Indexed: 01/31/2023]
|
41
|
Maree HJ, Blouin AG, Diaz-Lara A, Mostert I, Al Rwahnih M, Candresse T. Status of the current vitivirus taxonomy. Arch Virol 2019; 165:451-458. [PMID: 31845154 DOI: 10.1007/s00705-019-04500-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 11/12/2019] [Indexed: 11/25/2022]
Abstract
Since the establishment of the genus Vitivirus, several additional viruses have been sequenced and proposed to represent new species of this genus. Currently, the International Committee on Taxonomy of Viruses recognizes 15 vitivirus species. The report of new vitiviruses that fail to completely adhere to the species demarcation criteria, the incorporation of non-vitivirus grapevine viruses in the unofficial "naming system", and the existence of non-grapevine vitiviruses lead to inconsistencies in classification. In this report, we give a brief overview of vitiviruses and use currently available information to clarify the present status of the vitivirus taxonomy.
Collapse
Affiliation(s)
- H J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
- Citrus Research International, P.O. Box 2201, Matieland, 7602, South Africa.
| | - A G Blouin
- Integrated and Urban Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - A Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - I Mostert
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - M Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - T Candresse
- INRAE, Univ. Bordeaux, UMR BFP, 33882, Villenave d'Ornon Cedex, France
| |
Collapse
|
42
|
Complete genome sequence of a novel capillovirus infecting Hevea brasiliensis in China. Arch Virol 2019; 165:249-252. [PMID: 31748875 DOI: 10.1007/s00705-019-04459-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/05/2019] [Indexed: 10/25/2022]
Abstract
Tapping panel dryness (TPD) is a complex disorder that causes partial or complete cessation of latex drainage upon tapping of rubber trees (Hevea brasiliensis). In this work, we determined the complete genome sequences of a novel virus identified in a rubber tree with TPD syndrome in China. The genome of the virus consists of 6811 nt and possesses two overlapping open reading frames (ORF1 and ORF2), encoding a polyprotein and a movement protein, respectively. The polyprotein shares 37% amino acid sequence identity with cherry virus A (CVA, ARQ83874.1) over 99% coverage. The genome architecture is similar to that of members of the genus Capillovirus (family Betaflexiviridae). Phylogenetic analysis of the replicase proteins showed that the virus clustered together with members of the genus Capillovirus. The new virus is tentatively called "rubber tree virus 1" (RTV1). RTV1 is the first virus reported to infect rubber trees. This work lays a foundation for research into finding the potential causal agent of TPD in Hevea brasiliensis.
Collapse
|
43
|
Diaz-Lara A, Mollov D, Golino D, Al Rwahnih M. Complete genome sequence of rose virus A, the first carlavirus identified in rose. Arch Virol 2019; 165:241-244. [PMID: 31701224 DOI: 10.1007/s00705-019-04460-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/05/2019] [Indexed: 11/29/2022]
Abstract
A novel virus was discovered in a Rosa wichuraiana Crep. by high-throughput sequencing and tentatively named "rose virus A" (RVA). Based on sequence identity and phylogenetic analysis, RVA represents a new member of the genus Carlavirus (family Betaflexiviridae). The genome of RVA is 8,849 nucleotides long excluding the poly(A) tail and contains six open reading frames (ORFs). The predicted ORFs code for a replicase, triple gene block (TGB), coat protein, and nucleic acid binding protein, as in a typical carlavirus. RVA is the first carlavirus identified in rose and has the highest nucleotide sequence similarity to poplar mosaic virus. Reverse transcription-PCR-based assays were developed to confirm the presence of RVA in the original source and to screen additional rose plants.
Collapse
Affiliation(s)
- Alfredo Diaz-Lara
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Dimitre Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD, 20705, USA
| | - Deborah Golino
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA, 95616, USA.
| |
Collapse
|
44
|
Souiri A, Zemzami M, Laatiris H, Amzazi S, Ennaji MM. Genetic Characterization of Pepino Mosaic Virus Isolates from Morocco. Open Virol J 2019. [DOI: 10.2174/1874357901913010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Introduction:
Throughout the past few years, Pepino Mosaic Virus (PepMV) has rapidly evolved from an emerging virus to endemic pathogen that causes significant losses in tomato crops worldwide. Reliable detection and molecular characterization are very important tools to support disease control. Cross-protection can also be an effective strategy, but the efficacy depends strongly on the genotype. The genetic composition of the PepMV population in Morocco has not yet been determined.
Aims:
The current study aims to genetically characterize twelve PepMV isolates (PepMV-MA), all from different Moroccan tomato production areas, by analyzing nucleotide sequences of a part of the RNA-dependent RNA polymerase (RdRp), Triple Gene Block (TGB) and Coat Protein (CP) genes.
Results:
The sequence analysis of the twelve PepMV-MA isolates shows minor nucleotide differences between them, which implies a homogenous population. The phylogenetic analysis, based on the comparison with the major genotypes, showed that Moroccan PepMV populations share a very high sequence identity, 98%, with the Chilean strain (CH2), while the shared identity with the European strains (EU) is only 85%. Interestingly, Moroccan isolates reveal specific single nucleotide polymorphisms, some of which lead to amino acids changes. These mutations have never been described before, suggesting distinct variants that may enhance aggressiveness and symptomatology.
Conclusion:
Our careful sequence analysis and genotype determination, which placing homogenous Moroccan PepMV strains into CH2 genotype, would be a prerequisite for deploying effective cross-protection strategies for controlling the pathogen in the field.
Collapse
|
45
|
Questions surrounding the taxonomic validity of the species Garlic mite-borne filamentous virus (genus Allexivirus). Arch Virol 2019; 164:2367-2370. [PMID: 31256263 DOI: 10.1007/s00705-019-04333-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/01/2019] [Indexed: 10/26/2022]
Abstract
Garlic mite-borne filamentous virus is one of the oldest recognized allexivirus species but, paradoxically, one with the least well studied member viruses. In this paper, we review the history of this taxon and highlight problems in designating a holotype (exemplar isolate). Analyses are presented that suggest that GarMbFV is conspecific with Garlic virus A, and therefore the former taxon should be abolished.
Collapse
|
46
|
Ali A, Melcher U. Modeling of Mutational Events in the Evolution of Viruses. Viruses 2019; 11:v11050418. [PMID: 31060293 PMCID: PMC6563203 DOI: 10.3390/v11050418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/27/2019] [Accepted: 05/02/2019] [Indexed: 11/24/2022] Open
Abstract
Diverse studies of viral evolution have led to the recognition that the evolutionary rates of viral taxa observed are dependent on the time scale being investigated—with short-term studies giving fast substitution rates, and orders of magnitude lower rates for deep calibrations. Although each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause should be considered. We sought to test computationally whether the basic phenomena of virus evolution (mutation, replication, and selection) can explain the relationships between the evolutionary and phylogenetic distances. We tested, by computational inference, the hypothesis that the phylogenetic distances between the pairs of sequences are functions of the evolutionary path lengths between them. A Basic simulation revealed that the relationship between simulated genetic and mutational distances is non-linear, and can be consistent with different rates of nucleotide substitution at different depths of branches in phylogenetic trees.
Collapse
Affiliation(s)
- Akhtar Ali
- Department of Biological Sciences, University of Tulsa, Tulsa, OK 74104, USA.
| | - Ulrich Melcher
- Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, OK 74078-3035, USA.
| |
Collapse
|
47
|
Honma H, Tsushima D, Kawakami H, Fujihara N, Tsusaka T, Kawashimo M, Nishimura T, Fuji S. Complete nucleotide sequence of a new potexvirus, 'Cnidium virus X', isolated from Cnidium officinale in Japan. Arch Virol 2019; 164:1931-1935. [PMID: 31011816 DOI: 10.1007/s00705-019-04261-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 03/27/2019] [Indexed: 10/27/2022]
Abstract
A flexuous virus was detected in a Cnidium officinale plant in Japan showing mosaic symptoms. The virus was assigned to the genus Potexvirus based on analysis of its complete nucleotide sequence. The genomic RNA of the virus was 5,964 nucleotides in length, excluding the 3'-terminal poly(A) tail. It contained five open reading frames (ORFs), consistent with other members of Potexvirus. The ORF sequences differ from those of previously reported potexviruses. Phylogenetic analysis indicated that the polymerase of the virus is closely related to that of strawberry mild yellow edge virus; and the CP, to those of both yam virus X and vanilla virus X. We propose that this virus be designated as "cnidium virus X" (CnVX).
Collapse
Affiliation(s)
- H Honma
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - D Tsushima
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan.
| | - H Kawakami
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - N Fujihara
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - T Tsusaka
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - M Kawashimo
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - T Nishimura
- Botanical Raw Materials Research Laboratories, Tsumura & Co., Ibaraki, Japan
| | - S Fuji
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| |
Collapse
|
48
|
Ur Rehman A, Li Z, Yang Z, Waqas M, Wang G, Xu W, Li F, Hong N. The Coat Protein of Citrus Yellow Vein Clearing Virus Interacts with Viral Movement Proteins and Serves as an RNA Silencing Suppressor. Viruses 2019; 11:E329. [PMID: 30959816 PMCID: PMC6520955 DOI: 10.3390/v11040329] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 01/29/2023] Open
Abstract
Citrus yellow vein clearing virus is a newly accepted member of the genus Mandarivirus in the family Alphaflexiviridae. The triple gene block proteins (TGBp1, TGBp2 and TGBp3) encoded by plant viruses in this family function on facilitating virus movement. However, the protein function of citrus yellow vein clearing virus (CYVCV) have never been explored. Here, we showed in both yeast two-hybrid (Y2H) and bimolecular fluorescence (BiFC) assays that the coat protein (CP), TGBp1 and TGBp2 of CYVCV are self-interacting. Its CP also interacts with all three TGB proteins, and TGBp1 and TGBp2 interact with each other but not with TGBp3. Furthermore, the viral CP colocalizes with TGBp1 and TGBp3 at the plasmodesmata (PD) of epidermal cells of Nicotiana benthamiana leaves, and TGBp1 can translocate TGBp2 from granular-like structures embedded within ER networks to the PD. The results suggest that these proteins could coexist at the PD of epidermal cells of N. benthamiana. Using Agrobacterium infiltration-mediated RNA silencing assays, we show that CYVCV CP is a strong RNA silencing suppressor (RSS) triggered by positive-sense green fluorescent protein (GFP) RNA. The presented results provide insights for further revealing the mechanism of the viral movement and suppression of RNA silencing.
Collapse
Affiliation(s)
- Atta Ur Rehman
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China.
- Plant Pathology Section, Central Cotton Research Institute, Sakrand, Sindh 67210, Pakistan.
| | - Zhuoran Li
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Zuokun Yang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China.
| | - Muhammad Waqas
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guoping Wang
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China.
| | - Wenxing Xu
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China.
| | - Feng Li
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ni Hong
- Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Horticultural Crop (Fruit Trees) Biology and Germplasm Creation of the Ministry of Agriculture, Wuhan 430070, China.
| |
Collapse
|
49
|
Svanella-Dumas L, Τsarmpopoulos Ι, Marais A, Theil S, Faure C, Gaudin J, Candresse T. Complete genome sequence of lettuce chordovirus 1 isolated from cultivated lettuce in France. Arch Virol 2018; 163:2543-2545. [PMID: 29730706 DOI: 10.1007/s00705-018-3858-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/27/2018] [Indexed: 10/17/2022]
Abstract
Double-stranded RNAs purified from cultivated (Lactuca sativa) or wild (L. serriola) lettuce from southwest France were analyzed by high-throughput sequencing. For both samples, BLAST annotation revealed contigs with homology to Betaflexiviridae family members. The full genome sequence of the isolate from cultivated lettuce (JG1) was completed (8,536 nucleotides [nt], excluding the poly(A) tail). The sequence of the 3' half of the genome (4,800 nt) of a wild lettuce isolate (P22) was determined and found to share 95.1% nt sequence identity with the JG1 isolate. The JG1 genome contains four open reading frames, encoding a replicase, a movement protein, a capsid protein, and a protein of unknown function, respectively. Based on genome organization and phylogenetic relationships, the lettuce virus is most closely related to the recently described carrot chordoviruses 1 and 2 in the family Betaflexiviridae. Considering the species demarcation criteria in this family, the two lettuce viruses represent isolates of a new chordovirus species for which the name "lettuce chordovirus 1" (LeCV1) is proposed.
Collapse
Affiliation(s)
- Laurence Svanella-Dumas
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Ιason Τsarmpopoulos
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Chantal Faure
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Jonathan Gaudin
- UMR 1065, Santé et Agroécologie du Vignoble, INRA, Bordeaux Sciences Agro, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- UMR 1332, Biologie du Fruit et Pathologie, INRA, Univ. Bordeaux, CS20032, 33882, Villenave d'Ornon Cedex, France.
| |
Collapse
|
50
|
Thekke-Veetil T, Ho T, Postman JD, Martin RR, Tzanetakis IE. A Virus in American Blackcurrant ( Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales. Viruses 2018; 10:v10080406. [PMID: 30081487 PMCID: PMC6115964 DOI: 10.3390/v10080406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 07/16/2018] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.
Collapse
Affiliation(s)
- Thanuja Thekke-Veetil
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Thien Ho
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Joseph D Postman
- National Clonal Germplasm Repository, United States Department of Agriculture, Corvallis, OR 97333, USA.
| | - Robert R Martin
- Horticultural Crops Research Unit, United States Department of Agriculture, Corvallis, OR 97331, USA.
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| |
Collapse
|