151
|
Bernabé-Orts JM, Torre C, Méndez-López E, Hernando Y, Aranda MA. New Resources for the Specific and Sensitive Detection of the Emerging Tomato Brown Rugose Fruit Virus. Viruses 2021; 13:v13091680. [PMID: 34578261 PMCID: PMC8473139 DOI: 10.3390/v13091680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/13/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023] Open
Abstract
Plant viruses can evolve towards new pathogenic entities that may eventually cause outbreaks and become epidemics or even pandemics. Seven years ago, tomato brown rugose fruit virus (ToBRFV) emerged, overcoming the genetic resistance that had been employed for more than sixty years against tobamoviruses in tomato. Since then, ToBRFV has spread worldwide, producing significant losses in tomato crops. While new resistances are deployed, the only means of control is the implementation of effective prevention and eradication strategies. For this purpose, in this work, we have designed, assessed, and compared an array of tests for the specific and sensitive detection of the ToBRFV in leaf samples. First, two monoclonal antibodies were generated against a singular peptide of the ToBRFV coat protein; antibodies were utilized to devise a double-antibody-sandwich enzyme-linked immunosorbent assay (DAS-ELISA) test that sensitively detects this virus and has no cross-reactivity with other related tobamoviruses. Second, a real-time quantitative PCR (RT-qPCR) test targeting the RNA-dependent replicase open reading frame (ORF) was designed, and its performance and specificity validated in comparison with the CaTa28 and CSP1325 tests recommended by plant protection authorities in Europe. Third, in line with the tendency to use field-deployable diagnostic techniques, we developed and tested two sets of loop-mediated isothermal amplification (LAMP) primers to double-check the detection of the movement protein ORF of ToBRFV, and one set that works as an internal control. Finally, we compared all of these methods by employing a collection of samples with different ToBRFV loads to evaluate the overall performance of each test.
Collapse
Affiliation(s)
- Joan Miquel Bernabé-Orts
- Abiopep S.L. Parque Científico de Murcia. Ctra. Madrid Km 388, Complejo Espinardo. Edificio R 2ª Planta, Espinardo, 30100 Murcia, Spain; (J.M.B.-O.); (C.T.); (Y.H.)
| | - Covadonga Torre
- Abiopep S.L. Parque Científico de Murcia. Ctra. Madrid Km 388, Complejo Espinardo. Edificio R 2ª Planta, Espinardo, 30100 Murcia, Spain; (J.M.B.-O.); (C.T.); (Y.H.)
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, Edificio 25, Espinardo, 30100 Murcia, Spain;
| | - Yolanda Hernando
- Abiopep S.L. Parque Científico de Murcia. Ctra. Madrid Km 388, Complejo Espinardo. Edificio R 2ª Planta, Espinardo, 30100 Murcia, Spain; (J.M.B.-O.); (C.T.); (Y.H.)
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, Edificio 25, Espinardo, 30100 Murcia, Spain;
- Correspondence:
| |
Collapse
|
152
|
Bernabé-Orts JM, Torre C, Méndez-López E, Hernando Y, Aranda MA. New Resources for the Specific and Sensitive Detection of the Emerging Tomato Brown Rugose Fruit Virus. Viruses 2021; 13:v13091680. [PMID: 34578261 DOI: 10.1094/phytofr-08-21-0053-ta] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/13/2021] [Accepted: 08/23/2021] [Indexed: 05/24/2023] Open
Abstract
Plant viruses can evolve towards new pathogenic entities that may eventually cause outbreaks and become epidemics or even pandemics. Seven years ago, tomato brown rugose fruit virus (ToBRFV) emerged, overcoming the genetic resistance that had been employed for more than sixty years against tobamoviruses in tomato. Since then, ToBRFV has spread worldwide, producing significant losses in tomato crops. While new resistances are deployed, the only means of control is the implementation of effective prevention and eradication strategies. For this purpose, in this work, we have designed, assessed, and compared an array of tests for the specific and sensitive detection of the ToBRFV in leaf samples. First, two monoclonal antibodies were generated against a singular peptide of the ToBRFV coat protein; antibodies were utilized to devise a double-antibody-sandwich enzyme-linked immunosorbent assay (DAS-ELISA) test that sensitively detects this virus and has no cross-reactivity with other related tobamoviruses. Second, a real-time quantitative PCR (RT-qPCR) test targeting the RNA-dependent replicase open reading frame (ORF) was designed, and its performance and specificity validated in comparison with the CaTa28 and CSP1325 tests recommended by plant protection authorities in Europe. Third, in line with the tendency to use field-deployable diagnostic techniques, we developed and tested two sets of loop-mediated isothermal amplification (LAMP) primers to double-check the detection of the movement protein ORF of ToBRFV, and one set that works as an internal control. Finally, we compared all of these methods by employing a collection of samples with different ToBRFV loads to evaluate the overall performance of each test.
Collapse
Affiliation(s)
- Joan Miquel Bernabé-Orts
- Abiopep S.L. Parque Científico de Murcia. Ctra. Madrid Km 388, Complejo Espinardo. Edificio R 2ª Planta, Espinardo, 30100 Murcia, Spain
| | - Covadonga Torre
- Abiopep S.L. Parque Científico de Murcia. Ctra. Madrid Km 388, Complejo Espinardo. Edificio R 2ª Planta, Espinardo, 30100 Murcia, Spain
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, Edificio 25, Espinardo, 30100 Murcia, Spain
| | - Yolanda Hernando
- Abiopep S.L. Parque Científico de Murcia. Ctra. Madrid Km 388, Complejo Espinardo. Edificio R 2ª Planta, Espinardo, 30100 Murcia, Spain
| | - Miguel A Aranda
- Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones Científicas (CSIC), Campus Universitario de Espinardo, Edificio 25, Espinardo, 30100 Murcia, Spain
| |
Collapse
|
153
|
Wang X, Jiang Z, Yue N, Jin X, Zhang X, Li Z, Zhang Y, Wang X, Han C, Yu J, Li D. Barley stripe mosaic virus γb protein disrupts chloroplast antioxidant defenses to optimize viral replication. EMBO J 2021; 40:e107660. [PMID: 34254679 PMCID: PMC8365260 DOI: 10.15252/embj.2021107660] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 01/21/2023] Open
Abstract
The plant antioxidant system plays important roles in response to diverse abiotic and biotic stresses. However, the effects of virus infection on host redox homeostasis and how antioxidant defense pathway is manipulated by viruses remain poorly understood. We previously demonstrated that the Barley stripe mosaic virus (BSMV) γb protein is recruited to the chloroplast by the viral αa replicase to enhance viral replication. Here, we show that BSMV infection induces chloroplast oxidative stress. The versatile γb protein interacts directly with NADPH-dependent thioredoxin reductase C (NTRC), a core component of chloroplast antioxidant systems. Overexpression of NbNTRC significantly impairs BSMV replication in Nicotiana benthamiana plants, whereas disruption of NbNTRC expression leads to increased viral accumulation and infection severity. To counter NTRC-mediated defenses, BSMV employs the γb protein to competitively interfere with NbNTRC binding to 2-Cys Prx. Altogether, this study indicates that beyond acting as a helicase enhancer, γb also subverts NTRC-mediated chloroplast antioxidant defenses to create an oxidative microenvironment conducive to viral replication.
Collapse
Affiliation(s)
- Xueting Wang
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhihao Jiang
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Ning Yue
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xuejiao Jin
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xuan Zhang
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Zhaolei Li
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yongliang Zhang
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Xian‐Bing Wang
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Chenggui Han
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jialin Yu
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Dawei Li
- State Key Laboratory of Agro‐Biotechnology and Ministry of Agriculture Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijingChina
| |
Collapse
|
154
|
Hill SR, Twarock R, Dykeman EC. The impact of local assembly rules on RNA packaging in a T = 1 satellite plant virus. PLoS Comput Biol 2021; 17:e1009306. [PMID: 34428224 PMCID: PMC8384211 DOI: 10.1371/journal.pcbi.1009306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/26/2021] [Indexed: 02/05/2023] Open
Abstract
The vast majority of viruses consist of a nucleic acid surrounded by a protective icosahedral protein shell called the capsid. During viral infection of a host cell, the timing and efficiency of the assembly process is important for ensuring the production of infectious new progeny virus particles. In the class of single-stranded RNA (ssRNA) viruses, the assembly of the capsid takes place in tandem with packaging of the ssRNA genome in a highly cooperative co-assembly process. In simple ssRNA viruses such as the bacteriophage MS2 and small RNA plant viruses such as STNV, this cooperative process results from multiple interactions between the protein shell and sites in the RNA genome which have been termed packaging signals. Using a stochastic assembly algorithm which includes cooperative interactions between the protein shell and packaging signals in the RNA genome, we demonstrate that highly efficient assembly of STNV capsids arises from a set of simple local rules. Altering the local assembly rules results in different nucleation scenarios with varying assembly efficiencies, which in some cases depend strongly on interactions with RNA packaging signals. Our results provide a potential simple explanation based on local assembly rules for the ability of some ssRNA viruses to spontaneously assemble around charged polymers and other non-viral RNAs in vitro.
Collapse
Affiliation(s)
- Sam R. Hill
- Department of Mathematics, University of York, York, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, York, United Kingdom
- Department of Biology, University of York, York, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
| | - Eric C. Dykeman
- Department of Mathematics, University of York, York, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, United Kingdom
- * E-mail:
| |
Collapse
|
155
|
Zhu J, Eid FE, Tong L, Zhao W, Wang W, Heath LS, Kang L, Cui F. Characterization of protein-protein interactions between rice viruses and vector insects. Insect Sci 2021; 28:976-986. [PMID: 32537916 DOI: 10.1111/1744-7917.12840] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Planthoppers are the most notorious rice pests, because they transmit various rice viruses in a persistent-propagative manner. Protein-protein interactions (PPIs) between virus and vector are crucial for virus transmission by vector insects. However, the number of known PPIs for pairs of rice viruses and planthoppers is restricted by low throughput research methods. In this study, we applied DeNovo, a virus-host sequence-based PPI predictor, to predict potential PPIs at a genome-wide scale between three planthoppers and five rice viruses. PPIs were identified at two different confidence thresholds, referred to as low and high modes. The number of PPIs for the five planthopper-virus pairs ranged from 506 to 1985 in the low mode and from 1254 to 4286 in the high mode. After eliminating the "one-too-many" redundant interacting information, the PPIs with unique planthopper proteins were reduced to 343-724 in the low mode and 758-1671 in the high mode. Homologous analysis showed that 11 sets and 31 sets of homologous planthopper proteins were shared by all planthopper-virus interactions in the two modes, indicating that they are potential conserved vector factors essential for transmission of rice viruses. Ten PPIs between small brown planthopper and rice stripe virus (RSV) were verified using glutathione-S-transferase (GST)/His-pull down or co-immunoprecipitation assay. Five of the ten PPIs were proven positive, and three of the five SBPH proteins were confirmed to interact with RSV. The predicted PPIs provide new clues for further studies of the complicated relationship between rice viruses and their vector insects.
Collapse
Affiliation(s)
- Junjie Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | | | - Lu Tong
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wan Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Feng Cui
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
156
|
Liefting LW, Waite DW, Thompson JR. Application of Oxford Nanopore Technology to Plant Virus Detection. Viruses 2021; 13:v13081424. [PMID: 34452290 PMCID: PMC8402922 DOI: 10.3390/v13081424] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.
Collapse
|
157
|
Adkar-Purushothama CR, Iyer PS, Sano T, Perreault JP. sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling. Cells 2021; 10:cells10071771. [PMID: 34359940 PMCID: PMC8303536 DOI: 10.3390/cells10071771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/16/2022] Open
Abstract
Viroids are circular, highly structured, single-stranded, non-coding RNA pathogens known to infect and cause disease in several plant species. They are known to trigger the host plant’s RNA silencing machinery. The detection of viroid-derived small RNAs (vd-sRNA) in viroid-infected host plants opened a new avenue of study in host–viroid pathogenicity. Since then, several viroid research groups have studied the vd-sRNA retrieved from different host–viroid combinations. Such studies require the segregation of 21- to 24-nucleotide long small RNAs (sRNA) from a deep-sequencing databank, followed by separating the vd-sRNA from any sRNA within this group that showed sequence similarity with either the genomic or the antigenomic strands of the viroid. Such mapped vd-sRNAs are then profiled on both the viroid’s genomic and antigenomic strands for visualization. Although several commercial interfaces are currently available for this purpose, they are all programmed for linear RNA molecules. Hence, viroid researchers must develop a computer program that accommodates the sRNAs derived from the circular viroid genome. This is a laborious process, and consequently, it often creates a bottleneck for biologists. In order to overcome this constraint, and to help the research community in general, in this study, a python-based pattern matching interface was developed so as to be able to both profile and map sRNAs on a circular genome. A “matching tolerance” feature has been included in the program, thus permitting the mapping of the sRNAs derived from the quasi-species. Additionally, the “topology” feature allows the researcher to profile sRNA derived from both linear and circular RNA molecules. The efficiency of the program was tested using previously reported deep-sequencing data obtained from two independent studies. Clearly, this novel software should be a key tool with which to both evaluate the production of sRNA and to profile them on their target RNA species, irrespective of the topology of the target RNA molecule.
Collapse
Affiliation(s)
- Charith Raj Adkar-Purushothama
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 Rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
- Correspondence: (C.R.A.-P.); (J.-P.P.)
| | - Pavithran Sridharan Iyer
- Département de Physique, Université de Sherbrooke, 2500 Boul. Université, Sherbrooke, QC J1K 2R1, Canada;
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan;
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, 3201 Rue Jean-Mignault, Sherbrooke, QC J1E 4K8, Canada
- Correspondence: (C.R.A.-P.); (J.-P.P.)
| |
Collapse
|
158
|
Wang L, Wu Y, Du W, Yan Z, Qi Z, Tang W, Han Y, Liu C, Fan S, Hao J. Virus-induced gene silencing (VIGS) analysis shows involvement of the LsSTPK gene in lettuce ( Lactuca sativaL.) in high temperature-induced bolting. Plant Signal Behav 2021; 16:1913845. [PMID: 33955335 PMCID: PMC8205037 DOI: 10.1080/15592324.2021.1913845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/03/2021] [Accepted: 04/03/2021] [Indexed: 06/12/2023]
Abstract
To determine the effect of the serine/threonine protein kinase (STPK) gene on leaf lettuce bolting, we utilized virus-induced gene silencing (VIGS) using the TRV vector to silence the target gene. The 'GB30' leaf lettuce cultivar was the test material, and the methods included gene cloning, bioinformatics analysis, quantitative real-time PCR (qRT-PCR) and VIGS. LsSTPK, was cloned from the 'GB30' leaf lettuce cultivar via reverse transcription-polymerase chain reaction (RT-PCR). qRT-PCR analysis showed that the expression of LsSTPK in the stem of leaf lettuce was significantly greater than that in the roots and leaves, and after high-temperature treatment, the gene expression in the stems in the experimental group was markedly lower than that in the control groups. Following LsSTPK silencing via the VIGS method, the stem length in the treatment group was significantly greater than that in the blank and negative control groups, and the contents of auxin (IAA), GA3 and abscisic acid (ABA) in the treatment group were greater than those in the other two groups. Flower bud differentiation occurred in the treatment group but not in the control group. The above findings suggested that LsSTPK inhibits the bolting of leaf lettuce under high-temperature conditions.
Collapse
Affiliation(s)
- Lu Wang
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yang Wu
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Wei Du
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ziqi Yan
- University of Arizona, Tucson, Arizona, USA
| | - Zhengyang Qi
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Wenkun Tang
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yingyan Han
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Chaojie Liu
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Shuangxi Fan
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Jinghong Hao
- Beijing Key Laboratory for Agricultural Application and New Technology, National Demonstration Center for Experimental Plant Production Education, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| |
Collapse
|
159
|
Espindola AS, Sempertegui-Bayas D, Bravo-Padilla DF, Freire-Zapata V, Ochoa-Corona F, Cardwell KF. TASPERT: Target-Specific Reverse Transcript Pools to Improve HTS Plant Virus Diagnostics. Viruses 2021; 13:v13071223. [PMID: 34202758 PMCID: PMC8310100 DOI: 10.3390/v13071223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 12/03/2022] Open
Abstract
High-throughput sequencing (HTS) is becoming the new norm of diagnostics in plant quarantine settings. HTS can be used to detect, in theory, all pathogens present in any given sample. The technique’s success depends on various factors, including methods for sample management/preparation and suitable bioinformatic analysis. The Limit of Detection (LoD) of HTS for plant diagnostic tests can be higher than that of PCR, increasing the risk of false negatives in the case of low titer of the target pathogen. Several solutions have been suggested, particularly for RNA viruses, including rRNA depletion of the host, dsRNA, and siRNA extractions, which increase the relative pathogen titer in a metagenomic sample. However, these solutions are costly and time-consuming. Here we present a faster and cost-effective alternative method with lower HTS-LoD similar to or lower than PCR. The technique is called TArget-SPecific Reverse Transcript (TASPERT) pool. It relies on pathogen-specific reverse primers, targeting all RNA viruses of interest, pooled and used in double-stranded cDNA synthesis. These reverse primers enrich the sample for only pathogens of interest. Evidence on how TASPERT is significantly superior to oligodT, random 6-mer, and 20-mer in generating metagenomic libraries containing the pathogen of interest is presented in this proof of concept.
Collapse
Affiliation(s)
- Andres S. Espindola
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
- Correspondence:
| | - Daniela Sempertegui-Bayas
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Danny F. Bravo-Padilla
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Viviana Freire-Zapata
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Francisco Ochoa-Corona
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Kitty F. Cardwell
- Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA; (D.S.-B.); (D.F.B.-P.); (V.F.-Z.); (F.O.-C.); (K.F.C.)
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
| |
Collapse
|
160
|
Saad N, Olmstead JW, Varsani A, Polston JE, Jones JB, Folimonova SY, Harmon PF. Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches. Viruses 2021; 13:1165. [PMID: 34207047 PMCID: PMC8234961 DOI: 10.3390/v13061165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 11/18/2022] Open
Abstract
Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RNA viromes from V. corymbosum plants collected from six locations (two cultivated and four wild) in North Central Florida were generated by high throughput sequencing (HTS) and analyzed using a bioinformatic analysis pipeline. De novo assembled contigs obtained from viromes of both commercial and wild sites produced sequences with similarities to plant virus species from a diverse range of families (Amalgaviridae, Caulimoviridae, Endornaviridae, Ophioviridae, Phenuiviridae, and Virgaviridae). In addition, this study has enabled the identification of blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) for the first time in Florida, as well as a tentative novel tepovirus (blueberry virus T) (BlVT) in blueberry. To the best of our knowledge, this is the first study that compares viral diversity in wild and cultivated blueberry using a metagenomic approach.
Collapse
Affiliation(s)
- Norsazilawati Saad
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - James W. Olmstead
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA;
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Jane E. Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
| | - Svetlana Y. Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
| | - Philip F. Harmon
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
| |
Collapse
|
161
|
Chiquito-Almanza E, Caballero-Pérez J, Acosta-Gallegos JA, Montero-Tavera V, Mariscal-Amaro LA, Anaya-López JL. Diversity and Distribution of Viruses Infecting Wild and Domesticated Phaseolus spp. in the Mesoamerican Center of Domestication. Viruses 2021; 13:v13061153. [PMID: 34208696 PMCID: PMC8235658 DOI: 10.3390/v13061153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/26/2021] [Accepted: 06/11/2021] [Indexed: 11/16/2022] Open
Abstract
Viruses are an important disease source for beans. In order to evaluate the impact of virus disease on Phaseolus biodiversity, we determined the identity and distribution of viruses infecting wild and domesticated Phaseolus spp. in the Mesoamerican Center of Domestication (MCD) and the western state of Nayarit, Mexico. We used small RNA sequencing and assembly to identify complete or near-complete sequences of forty-seven genomes belonging to nine viral species of five genera, as well as partial sequences of two putative new endornaviruses and five badnavirus- and pararetrovirus-like sequences. The prevalence of viruses in domesticated beans was significantly higher than in wild beans (97% vs. 19%; p < 0.001), and all samples from domesticated beans were positive for at least one virus species. In contrast, no viruses were detected in 80-83% of the samples from wild beans. The Bean common mosaic virus and Bean common mosaic necrosis virus were the most prevalent viruses in wild and domesticated beans. Nevertheless, Cowpea mild mottle virus, transmitted by the whitefly Bemisia tabaci, has the potential to emerge as an important pathogen because it is both seed-borne and a non-persistently transmitted virus. Our results provide insights into the distribution of viruses in cultivated and wild Phaseolus spp. and will be useful for the identification of emerging viruses and the development of strategies for bean viral disease management in a center of diversity.
Collapse
Affiliation(s)
- Elizabeth Chiquito-Almanza
- Biotechnology Department, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico; (E.C.-A.); (V.M.-T.)
| | - Juan Caballero-Pérez
- Faculty of Chemistry, Autonomous University of Querétaro, Santiago de Querétaro 76017, Mexico;
| | - Jorge A. Acosta-Gallegos
- Bean Breeding Program, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico;
| | - Victor Montero-Tavera
- Biotechnology Department, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico; (E.C.-A.); (V.M.-T.)
| | - Luis Antonio Mariscal-Amaro
- Forestry and Plant Protection Program, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico;
| | - José Luis Anaya-López
- Biotechnology Department, National Institute for Forestry Agriculture and Livestock Research (INIFAP), Celaya, Guanajuato 38110, Mexico; (E.C.-A.); (V.M.-T.)
- Correspondence:
| |
Collapse
|
162
|
Trzmiel K. Duplex-RT-PCR assay for the simultaneous detection and discrimination of Brome mosaic virus and Cocksfoot mottle virus in cereal plants. Mol Biol Rep 2021; 48:4981-4985. [PMID: 34132946 PMCID: PMC8260540 DOI: 10.1007/s11033-021-06485-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/08/2021] [Indexed: 11/25/2022]
Abstract
Brome mosaic virus (BMV) and cocksfoot mottle virus (CfMV) are pathogens of grass species including all economically important cereals. Both viruses have been identified in Poland therefore they create a potential risk to cereal crops. In this study, a duplex—reverse transcription—polymerase chain reaction (duplex-RT-PCR) was developed and optimized for simultaneous detection and differentiation of BMV and CfMV as well as for confirmation of their co-infection. Selected primers CfMVdiag-F/CfMVdiag-R and BMV2-F/BMV2-R amplified 390 bp and 798 bp RT-PCR products within coat protein (CP) region of CfMV and replicase gene of BMV, respectively. Duplex-RT-PCR was successfully applied for the detection of CfMV-P1 and different Polish BMV isolates. Moreover, one sample was found to be co-infected with BMV-ML1 and CfMV-ML1 isolates. The specificity of generated RT-PCR products was verified by sequencing. Duplex-RT-PCR, like conventional RT-PCR, was able to detect two viruses occurring in plant tissues in very low concentration (as low as 4.5 pg/µL of total RNA). In contrast to existing methods, newly developed technique offers a significant time and cost-saving advantage. In conclusion, duplex-RT-PCR is a useful tool which can be implemented by phytosanitary services to rapid detection and differentiation of BMV and CfMV.
Collapse
Affiliation(s)
- Katarzyna Trzmiel
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute (IPP-NRI), ul. Wł. Węgorka 20, 60-318, Poznań, Poland.
| |
Collapse
|
163
|
Khan A, Imtiaz Y, Tahir M, Briddon RW. Complete genome sequence of hollyhock vein yellowing virus, a novel monopartite begomovirus infecting hollyhock in Pakistan. Arch Virol 2021; 166:2607-2610. [PMID: 34115211 DOI: 10.1007/s00705-021-05134-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/23/2021] [Indexed: 11/26/2022]
Abstract
Hollyhock (Alcea rosea, family Malvaceae) is an ornamental plant grown widely in gardens across South Asia. In a bed of ornamental plants near the village of Chakri (Punjab Province, Pakistan) in 2014, hollyhock plants showing two distinct symptom types were identified: yellow vein mosaic and leaf crumple. PCR amplification with universal primers amplified a begomovirus from separate nucleic acid extracts of single plants of each type but amplified a betasatellite only from the plant with the yellow vein mosaic symptoms. No potential begomovirus DNA B component or alphasatellite could be identified in either sample. After cloning, the genome sequences of two viruses, one from a plant of each symptom type, were determined and shown to share 99.9% nucleotide sequence identity with each other but less than 91% nucleotide sequence identity with all previously characterized begomoviruses, with the highest identity (90%) to an isolate of pedilanthus leaf curl virus (PeLCV). This indicates that the two hollyhock plants were infected with a newly identified begomovirus for which the name "hollyhock vein yellowing virus" (HoVYV) is proposed. HoVYV likely has a recombinant origin. The betasatellite showed the highest nucleotide sequence identity to an isolate of cotton leaf curl Multan betasatellite (CLCuMuB), a betasatellite associated with cotton leaf curl disease across Pakistan and northwestern India. These findings add to the diversity of known begomoviruses in South Asia and again highlight the role of hollyhock as a reservoir of the cotton leaf curl begomovirus betasatellite complex. The results also suggest that the yellow vein mosaic symptoms in hollyhock are due to the betasatellite rather than the virus.
Collapse
Affiliation(s)
- Azkia Khan
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad, Pakistan
| | - Yaqoot Imtiaz
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad, Pakistan
| | - Muhammad Tahir
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Sector H-12, Islamabad, Pakistan.
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| |
Collapse
|
164
|
Kavalappara SR, Milner H, Konakalla NC, Morgan K, Sparks AN, McGregor C, Culbreath AK, Wintermantel WM, Bag S. High Throughput Sequencing-Aided Survey Reveals Widespread Mixed Infections of Whitefly-Transmitted Viruses in Cucurbits in Georgia, USA. Viruses 2021; 13:v13060988. [PMID: 34073397 PMCID: PMC8230054 DOI: 10.3390/v13060988] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 01/08/2023] Open
Abstract
Viruses transmitted by the sweet potato whitefly (Bemisia tabaci) have been detrimental to the sustainable production of cucurbits in the southeastern USA. Surveys were conducted in the fall of 2019 and 2020 in Georgia, a major cucurbit-producing state of the USA, to identify the viruses infecting cucurbits and their distribution. Symptomatic samples were collected and small RNA libraries were prepared and sequenced from three cantaloupes, four cucumbers, and two yellow squash samples. An analysis of the sequences revealed the presence of the criniviruses cucurbit chlorotic yellows virus (CCYV), cucurbit yellow stunting disorder virus (CYSDV), and the begomovirus cucurbit leaf crumple virus (CuLCrV). CuLCrV was detected in 76%, CCYV in 60%, and CYSDV in 43% of the total samples (n = 820) tested. The level of mixed infections was high in all the cucurbits, with most plants tested being infected with at least two of these viruses. Near-complete genome sequences of two criniviruses, CCYV and CYSDV, were assembled from the small RNA sequences. An analysis of the coding regions showed low genetic variability among isolates from different hosts. In phylogenetic analysis, the CCYV isolates from Georgia clustered with Asian isolates, while CYSDV isolates clustered with European and USA isolates. This work enhances our understanding of the distribution of viruses on cucurbits in South Georgia and will be useful to develop strategies for managing the complex of whitefly-transmitted viruses in the region.
Collapse
Affiliation(s)
- Saritha Raman Kavalappara
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Hayley Milner
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Naga Charan Konakalla
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Kaelyn Morgan
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - Alton N. Sparks
- Department of Entomology, University of Georgia, Tifton, GA 31793, USA;
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA;
| | - Albert K. Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
| | - William M. Wintermantel
- United States Department of Agriculture-Agricultural Research Service, Salinas, CA 93905, USA
- Correspondence: (W.M.W.); (S.B.)
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.R.K.); (H.M.); (N.C.K.); (K.M.); (A.K.C.)
- Correspondence: (W.M.W.); (S.B.)
| |
Collapse
|
165
|
Thuenemann EC, Byrne MJ, Peyret H, Saunders K, Castells-Graells R, Ferriol I, Santoni M, Steele JFC, Ranson NA, Avesani L, Lopez-Moya JJ, Lomonossoff GP. A Replicating Viral Vector Greatly Enhances Accumulation of Helical Virus-Like Particles in Plants. Viruses 2021; 13:885. [PMID: 34064959 PMCID: PMC8150850 DOI: 10.3390/v13050885] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient production. To examine this, we compared the accumulation of VLPs from two potexviruses, papaya mosaic virus and alternanthera mosaic virus (AltMV), when the coat proteins were expressed from a replicating potato virus X- based vector (pEff) and a non-replicating vector (pEAQ-HT). Significantly greater quantities of VLPs could be purified when pEff was used. The pEff system was also very efficient at producing VLPs of helical viruses from different virus families. Examination of the RNA content of AltMV and tobacco mosaic virus VLPs produced from pEff revealed the presence of vector-derived RNA sequences, suggesting that the replicating RNA acts as a scaffold for VLP assembly. Cryo-EM analysis of the AltMV VLPs showed they had a structure very similar to that of authentic potexvirus particles. Thus, we conclude that vectors generating replicating forms of RNA, such as pEff, are very efficient for producing helical VLPs.
Collapse
Affiliation(s)
- Eva C. Thuenemann
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
| | - Matthew J. Byrne
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (N.A.R.)
| | - Hadrien Peyret
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
| | - Keith Saunders
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
| | - Roger Castells-Graells
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Inmaculada Ferriol
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), 08193 Cerdanyola del Vallès, Spain; (I.F.); (J.J.L.-M.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
| | - Mattia Santoni
- Diamante srl. Strada Le Grazie, 15, 37134 Verona, Italy;
| | - John F. C. Steele
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
- Piramal Healthcare UK Ltd., Piramal Pharma Solutions, Earls Road, Grangemouth, Stirlingshire FK3 8XG, UK
| | - Neil A. Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (N.A.R.)
| | - Linda Avesani
- Department of Biotechnology, University of Verona, Strada Le Grazie, 15, 37134 Verona, Italy;
| | - Juan Jose Lopez-Moya
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), 08193 Cerdanyola del Vallès, Spain; (I.F.); (J.J.L.-M.)
- Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
| | - George P. Lomonossoff
- John Innes Centre, Department of Biochemistry and Metabolism, Norwich Research Park, Norwich NR4 7UH, UK; (H.P.); (K.S.); (R.C.-G.); (J.F.C.S.)
| |
Collapse
|
166
|
Kormelink R, Verchot J, Tao X, Desbiez C. The Bunyavirales: The Plant-Infecting Counterparts. Viruses 2021; 13:v13050842. [PMID: 34066457 PMCID: PMC8148189 DOI: 10.3390/v13050842] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 12/18/2022] Open
Abstract
Negative-strand (-) RNA viruses (NSVs) comprise a large and diverse group of viruses that are generally divided in those with non-segmented and those with segmented genomes. Whereas most NSVs infect animals and humans, the smaller group of the plant-infecting counterparts is expanding, with many causing devastating diseases worldwide, affecting a large number of major bulk and high-value food crops. In 2018, the taxonomy of segmented NSVs faced a major reorganization with the establishment of the order Bunyavirales. This article overviews the major plant viruses that are part of the order, i.e., orthospoviruses (Tospoviridae), tenuiviruses (Phenuiviridae), and emaraviruses (Fimoviridae), and provides updates on the more recent ongoing research. Features shared with the animal-infecting counterparts are mentioned, however, special attention is given to their adaptation to plant hosts and vector transmission, including intra/intercellular trafficking and viral counter defense to antiviral RNAi.
Collapse
Affiliation(s)
- Richard Kormelink
- Laboratory of Virology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaorong Tao
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | | |
Collapse
|
167
|
Petrzik K, Kmoch M, Brázdová S, Ševčík R. Complete genome sequences of novel Berlinvirus and novel Certrevirus lytic for Pectobacterium sp. causing soft rot and black leg disease of potato. Virus Genes 2021; 57:302-305. [PMID: 33914264 DOI: 10.1007/s11262-021-01838-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/23/2021] [Indexed: 11/25/2022]
Abstract
Two novel dsDNA bacteriophages named Pectobacterium virus CB251 (PcCB251) and Pectobacterium virus CB7V (PcCB7V) targeting plant pathogen Pectobacterium parmentieri have been isolated and sequenced. The PcCB251 genome consists of 40,557 bp with G+C content of 48.6% and contains 47 predicted genes on a single strand. The phage is classified in genus Berlinvirus, family Autographiviridae. The PcCB7V phage has a circular dsDNA genome of 146,054 bp with G+C content of 50.4% and contains 269 predicted protein genes on both strands and 13 tRNA genes. The PcCB7V phage can be classified in genus Certrevirus, subfamily Vequintavirinae. Both novel bacteriophages have narrow host ranges, but they extend the list of candidates for phage-based control of pectolytic bacteria causing soft rot disease of potato.
Collapse
Affiliation(s)
- Karel Petrzik
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic.
| | - Martin Kmoch
- Potato Research Institute Havlíčkův Brod, Dobrovského 2366, Havlíčkův Brod, 580 01, Czech Republic
| | - Sára Brázdová
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, Czech Republic
| | - Rudolf Ševčík
- University of Chemistry and Technology Prague, Technická 1905/5, Prague 6-Dejvice, Prague, Czech Republic
| |
Collapse
|
168
|
Li J, Gu H, Liu Y, Wei S, Hu G, Wang X, McNeill MR, Ban L. RNA-seq reveals plant virus composition and diversity in alfalfa, thrips, and aphids in Beijing, China. Arch Virol 2021; 166:1711-1722. [PMID: 33866416 DOI: 10.1007/s00705-021-05067-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/22/2021] [Indexed: 11/27/2022]
Abstract
Viruses are widespread in alfalfa (Medicago sativa L.), representing a key limitation to the production of this important forage plant. Understanding the diversity of plant viruses in alfalfa and their potential vectors will play an important role in management to minimize the emergence, transmission, and impact of viruses. Next-generation sequencing (NGS) targeting the transcriptome was applied to monitor the virus communities in alfalfa and its two main pests, thrips (Odontothrips loti Haliday and Frankliniella intonsa Trybom) and aphids (Acyrthosiphon pisum Mordvilko and Therioaphis trifolii Monell). A comparison of transcriptome datasets with reference databases revealed the presence of eight candidate viruses. Five out of the eight viruses, alfalfa mosaic virus (AMV), Medicago sativa alphapartitivirus 1 (MsAPV1), Medicago sativa deltapartitivirus 1 (MsDPV1), Medicago sativa amalgavirus 1 (MsAV1), and bean yellow mosaic virus (BYMV), were confirmed by RT-PCR. We identified and determined the presence of four RNA viruses from alfalfa samples, two viruses (AMV and MsAPV1) from thrips samples, and one virus (BYMV) from T. trifolii. All sequences isolated from the insect samples were more than 95% identical to the sequences from the alfalfa samples or to sequences from the National Center for Biotechnology Information (NCBI) reference database. The RNA-seq results of this study suggest that AMV and MsAPV1 are the predominant RNA plant viruses infecting alfalfa and that they are carried by the major pests. This lays the foundation for future research on the vectors and transmission of these viruses. In addition, the sequence data have enabled the assembly of the first complete genome sequence of MsDPV1 from alfalfa.
Collapse
Affiliation(s)
- Jin Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Hongchang Gu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yanqi Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, China
| | - Shuhua Wei
- Ningxia Academy of Agriculture and Forestry Sciences, Institute of Plant Protection, Yinchuan, Ningxia, China
| | - Guixin Hu
- Pratacultural College, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xuemin Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mark Richard McNeill
- AgResearch, Resilient Agriculture Innovative Centre of Excellence, Lincoln, New Zealand
| | - Liping Ban
- College of Grassland Science and Technology, China Agricultural University, Beijing, China.
| |
Collapse
|
169
|
Liu J, Carino E, Bera S, Gao F, May JP, Simon AE. Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs. Viruses 2021; 13:646. [PMID: 33918656 PMCID: PMC8068935 DOI: 10.3390/v13040646] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/13/2022] Open
Abstract
We report the biological and structural characterization of umbravirus-like associated RNAs (ulaRNAs), a new category of coat-protein dependent subviral RNA replicons that infect plants. These RNAs encode an RNA-dependent RNA polymerase (RdRp) following a -1 ribosomal frameshift event, are 2.7-4.6 kb in length, and are related to umbraviruses, unlike similar RNA replicons that are related to tombusviruses. Three classes of ulaRNAs are proposed, with citrus yellow vein associated virus (CYVaV) placed in Class 2. With the exception of CYVaV, Class 2 and Class 3 ulaRNAs encode an additional open reading frame (ORF) with movement protein-like motifs made possible by additional sequences just past the RdRp termination codon. The full-length secondary structure of CYVaV was determined using Selective 2' Hydroxyl Acylation analyzed by Primer Extension (SHAPE) structure probing and phylogenic comparisons, which was used as a template for determining the putative structures of the other Class 2 ulaRNAs, revealing a number of distinctive structural features. The ribosome recoding sites of nearly all ulaRNAs, which differ significantly from those of umbraviruses, may exist in two conformations and are highly efficient. The 3' regions of Class 2 and Class 3 ulaRNAs have structural elements similar to those of nearly all umbraviruses, and all Class 2 ulaRNAs have a unique, conserved 3' cap-independent translation enhancer. CYVaV replicates independently in protoplasts, demonstrating that the reported sequence is full-length. Additionally, CYVaV contains a sequence in its 3' UTR that confers protection to nonsense mediated decay (NMD), thus likely obviating the need for umbravirus ORF3, a known suppressor of NMD. This initial characterization lays down a road map for future investigations into these novel virus-like RNAs.
Collapse
Affiliation(s)
- Jingyuan Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA; (J.L.); (E.C.); (S.B.)
| | - Elizabeth Carino
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA; (J.L.); (E.C.); (S.B.)
| | - Sayanta Bera
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA; (J.L.); (E.C.); (S.B.)
| | - Feng Gao
- Silvec Biologics, Rockville, MD 20850, USA;
| | - Jared P. May
- Department of Cell and Molecular Biology and Biochemistry, University of Missouri-Kansas City, Kansas City, MO 64110, USA;
| | - Anne E. Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA; (J.L.); (E.C.); (S.B.)
| |
Collapse
|
170
|
Nie X, Singh M, Chen D, Gilchrist C, Soqrat Y, Shukla M, Creelman A, Dickison V, Nie B, Lavoie J, Bisht V. Development of High-Resolution DNA Melting Analysis for Simultaneous Detection of Potato Mop-Top Virus and Its Vector, Spongospora subterranea, in Soil. Plant Dis 2021; 105:948-957. [PMID: 32915119 DOI: 10.1094/pdis-06-20-1321-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, a set of duplex reverse transcription PCR (RT-PCR)-mediated high-resolution DNA melting (HRM) analyses for simultaneous detection of potato mop-virus (PMTV) and its protist vector, Spongospora subterranea f. sp. subterranea (Sss), was developed. The infestation of soil by PMTV was detected with a tobacco-based baiting system. Total RNA extracted from the soil led to successful RT-PCR gel electrophoresis detection of both PMTV and Sss. To facilitate more efficient detection, newly designed primer pairs for PMTV RNA species (i.e., RNA-Rep, RNA-CP, and RNA-TGB) were analyzed together with the existing Sss primers via real-time RT-PCR. The resulting amplicons exhibited melting profiles that could be readily differentiated. Under duplex RT-PCR format, all PMTV and Sss primer combinations led to successful detection of respective PMTV RNA species and Sss in the samples by HRM analyses. When the duplex HRM assay was applied to soil samples collected from six fields at four different sites in New Brunswick, Canada, positive detection of PMTV or Sss was found in 63 to 100% samples collected from fields in which PMTV-infected tubers had been observed. In contrast, the samples from fields where neither PMTV- nor Sss-infected tubers had been observed resulted in negative detection by the assay. Bait tobacco bioassay for PMTV and Sss produced similar results. Of the soil samples collected from PMTV-infested fields, 63 to 83% and 100% led to PMTV and Sss infections in the bait tobacco plants, respectively, whereas no PMTV- or Sss-infected plants were obtained from soil samples collected from PMTV- and Sss-free fields.
Collapse
Affiliation(s)
- Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Mathuresh Singh
- Agricultural Certification Services, Fredericton, NB E3B 8B7, Canada
| | - Dahu Chen
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Cassandra Gilchrist
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Yasmine Soqrat
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Biology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Manisha Shukla
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Alexa Creelman
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Virginia Dickison
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Bihua Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Jacques Lavoie
- New Brunswick Department of Agriculture, Aquaculture and Fisheries, Potato Development Centre, Wicklow, NB E7L 3S4, Canada
| | - Vikram Bisht
- Manitoba Agriculture, Carman, MB R0G 0J0, Canada
| |
Collapse
|
171
|
Abstract
Plant viruses have been engineered to express heterologous proteins and RNAs in plants for several decades. This viral system can now be applied to editing plant genomes. Virus vectors can deliver Cas proteins and guide RNAs, two key components of the CRISPR gene-editing system, into a plant cell without a complicated experimental procedure. In some cases, plant viruses move to meristematic cells and express gene-editing components in the cell, which results in the production of mutant seeds. Here, we focus on three main issues of the virus-induced genome editing (VIGE) technology in plants: (1) how to express the relatively large size of Cas proteins, (2) how to express guide RNA, and (3) how to increase the efficiency with which viruses are delivered into meristematic cells. We highlight recent advances in how plant virus vectors can be used efficiently in plant-genome editing.
Collapse
Affiliation(s)
- Youngbin Oh
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon 34141, Republic of Korea
| | - Hyeonjin Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon 34141, Republic of Korea
| | - Sang-Gyu Kim
- Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon 34141, Republic of Korea.
| |
Collapse
|
172
|
Maina S, Zheng L, Rodoni BC. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses. Viruses 2021; 13:583. [PMID: 33808381 PMCID: PMC8066983 DOI: 10.3390/v13040583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10-8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
Collapse
Affiliation(s)
- Solomon Maina
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
| | - Linda Zheng
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
| | - Brendan C. Rodoni
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Victoria 3083, Australia
| |
Collapse
|
173
|
de Souza DD, de Queiroz AP, Pereira FS, de Campos Dianese É, Fajardo TVM, Nhani Júnior A, Lau D, da Silva LA, Ribeiro BM, Coelho ASG, Aguiar RWDS, de Mello RN, da Silva FN. Molecular characterization and sequence analysis of four Brazilian rice stripe necrosis virus isolates. Arch Virol 2021; 166:1763-1767. [PMID: 33755801 DOI: 10.1007/s00705-021-05037-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/28/2021] [Indexed: 11/25/2022]
Abstract
Rice (Oryza sativa L.) is an important food crop for humanity, being cultivated in tropical and temperate regions of the world. This study reports the nearly complete genome sequences of four Brazilian rice stripe necrosis virus (RSNV) isolates. The nucleotide sequences of the RNA1 and RNA2 genome segments of these Brazilian isolates were 96.5 to 99.9% identical, indicating their close phylogenetic relationship to each other. Phylogeny and recombination analysis indicated that the genome of one of the isolates consisted of RNA segments of different origins, suggesting that a reassortment event had occurred.
Collapse
|
174
|
Bester R, Cook G, Breytenbach JHJ, Steyn C, De Bruyn R, Maree HJ. Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids. Virol J 2021; 18:61. [PMID: 33752714 PMCID: PMC7986492 DOI: 10.1186/s12985-021-01523-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. METHODS Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. RESULTS The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. CONCLUSIONS This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.
Collapse
Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
| | | | - Chanel Steyn
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Rochelle De Bruyn
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
| | - Hans 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.
| |
Collapse
|
175
|
Jiang Z, Zhao Q, Bai R, Yu R, Diao P, Yan T, Duan H, Ma X, Zhou Z, Fan Y, Wuriyanghan H. Host sunflower-induced silencing of parasitism-related genes confers resistance to invading Orobanche cumana. Plant Physiol 2021; 185:424-440. [PMID: 33721890 PMCID: PMC8133596 DOI: 10.1093/plphys/kiaa018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/08/2020] [Indexed: 05/04/2023]
Abstract
Orobanche cumana is a holoparasitic plant that attaches to host-plant roots and seriously reduces the yield of sunflower (Helianthus annuus L.). Effective control methods are lacking with only a few known sources of genetic resistance. In this study, a seed-soak agroinoculation (SSA) method was established, and recombinant tobacco rattle virus vectors were constructed to express RNA interference (RNAi) inducers to cause virus-induced gene silencing (VIGS) in sunflower. A host target gene HaTubulin was systemically silenced in both leaf and root tissues by the SSA-VIGS approach. Trans-species silencing of O. cumana genes were confirmed for 10 out of 11 target genes with silencing efficiency of 23.43%-92.67%. Knockdown of target OcQR1, OcCKX5, and OcWRI1 genes reduced the haustoria number, and silencing of OcEXPA6 caused further phenotypic abnormalities such as shorter tubercles and necrosis. Overexpression of OcEXPA6 caused retarded root growth in alfalfa (Medicago sativa). The results demonstrate that these genes play an important role in the processes of O. cumana parasitism. High-throughput small RNA (sRNA) sequencing and bioinformatics analyses unveiled the distinct features of target gene-derived siRNAs in O. cumana such as siRNA transitivity, strand polarity, hotspot region, and 21/22-nt siRNA predominance, the latter of which was confirmed by Northern blot experiments. The possible RNAi mechanism is also discussed by analyzing RNAi machinery genes in O. cumana. Taken together, we established an efficient host-induced gene silencing technology for both functional genetics studies and potential control of O. cumana. The ease and effectiveness of this strategy could potentially be useful for other species provided they are amenable to SSA.
Collapse
Affiliation(s)
- Zhengqiang Jiang
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Qiqi Zhao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Runyao Bai
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Ruonan Yu
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Pengfei Diao
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Ting Yan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Huimin Duan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Xuesong Ma
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Zikai Zhou
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Yanyan Fan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
| | - Hada Wuriyanghan
- Key Laboratory of Forage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, P. R. China
- Author for communication:
| |
Collapse
|
176
|
Werner Ribeiro C, Dugé de Bernonville T, Glévarec G, Lanoue A, Oudin A, Pichon O, St-Pierre B, Courdavault V, Besseau S. ALSV-Based Virus-Induced Gene Silencing in Apple Tree (Malus × domestica L.). Methods Mol Biol 2021; 2172:183-197. [PMID: 32557370 DOI: 10.1007/978-1-0716-0751-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Virus-induced gene silencing (VIGS) is a fast and efficient tool to investigate gene function in plant as an alternative to knock down/out transgenic lines, especially in plant species difficult to transform and challenging to regenerate such as perennial woody plants. In apple tree, a VIGS vector has been previously developed based on the Apple latent spherical virus (ALSV) and an efficient inoculation method has been optimized using biolistics. This report described detailed step-by-step procedure to design and silence a gene of interest (GOI) in apple tree tissues using the ALSV-based vector.
Collapse
Affiliation(s)
| | | | - Gaëlle Glévarec
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Arnaud Lanoue
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Audrey Oudin
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Olivier Pichon
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Benoit St-Pierre
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Vincent Courdavault
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
| | - Sébastien Besseau
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France.
| |
Collapse
|
177
|
Fei Y, Nyikó T, Molnar A. Non-perfectly matching small RNAs can induce stable and heritable epigenetic modifications and can be used as molecular markers to trace the origin and fate of silencing RNAs. Nucleic Acids Res 2021; 49:1900-1913. [PMID: 33524108 PMCID: PMC7913690 DOI: 10.1093/nar/gkab023] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/04/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Short non-coding RNA molecules (sRNAs) play a fundamental role in gene regulation and development in higher organisms. They act as molecular postcodes and guide AGO proteins to target nucleic acids. In plants, sRNA-targeted mRNAs are degraded, reducing gene expression. In contrast, sRNA-targeted DNA sequences undergo cytosine methylation referred to as RNA-directed DNA methylation (RdDM). Cytosine methylation can suppress transcription, thus sRNAs are potent regulators of gene expression. sRNA-mediated RdDM is involved in genome stability through transposon silencing, mobile signalling for epigenetic gene control and hybrid vigour. Since cytosine methylation can be passed on to subsequent generations, RdDM contributes to transgenerational inheritance of the epigenome. Using a novel approach, which can differentiate between primary (inducer) and secondary (amplified) sRNAs, we show that initiation of heritable RdDM does not require complete sequence complementarity between the sRNAs and their nuclear target sequences. sRNAs with up to four regularly interspaced mismatches are potent inducers of RdDM, however, the number and disruptive nature of nucleotide polymorphisms negatively correlate with their efficacy. Our findings contribute to understanding how sRNA can directly shape the epigenome and may be used in designing the next generation of RNA silencing constructs.
Collapse
Affiliation(s)
- Yue Fei
- University of Edinburgh, Institute of Molecular Plant Sciences, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Tünde Nyikó
- Agricultural Biotechnology Institute, Szent-Györgyi A. 4., Gödöllő 2100, Hungary
| | - Attila Molnar
- University of Edinburgh, Institute of Molecular Plant Sciences, Max Born Crescent, Edinburgh EH9 3BF, UK
| |
Collapse
|
178
|
Sánchez Pina MA, Gómez-Aix C, Méndez-López E, Gosalvez Bernal B, Aranda MA. Imaging Techniques to Study Plant Virus Replication and Vertical Transmission. Viruses 2021; 13:358. [PMID: 33668729 PMCID: PMC7996213 DOI: 10.3390/v13030358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
Plant viruses are obligate parasites that need to usurp plant cell metabolism in order to infect their hosts. Imaging techniques have been used for quite a long time to study plant virus-host interactions, making it possible to have major advances in the knowledge of plant virus infection cycles. The imaging techniques used to study plant-virus interactions have included light microscopy, confocal laser scanning microscopy, and scanning and transmission electron microscopies. Here, we review the use of these techniques in plant virology, illustrating recent advances in the area with examples from plant virus replication and virus plant-to-plant vertical transmission processes.
Collapse
Affiliation(s)
- María Amelia Sánchez Pina
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
| | - Cristina Gómez-Aix
- Abiopep S.L., R&D Department, Parque Científico de Murcia, Ctra. de Madrid, Km 388, Complejo de Espinardo, Edf. R, 2º, 30100 Murcia, Spain;
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
| | - Blanca Gosalvez Bernal
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), Departamento de Biología del Estrés y Patología Vegetal, Grupo de Patología Vegetal, 30100 Murcia, Spain; (E.M.-L.); (B.G.B.)
| |
Collapse
|
179
|
Marquez‐Molins J, Gomez G, Pallas V. Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid-host interactions. Mol Plant Pathol 2021; 22:153-162. [PMID: 33305492 PMCID: PMC7814962 DOI: 10.1111/mpp.13022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/03/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
TAXONOMY Hop stunt viroid (HSVd) is the type species of the genus Hostuviroid (family Pospiviroidae). The other species of this genus is Dahlia latent viroid, which presents an identical central conserved region (CCR) but lacks other structural hallmarks present in Hop stunt viroid. HSVd replication occurs in the nucleus through an asymmetric rolling-circle model as in the other members of the family Pospiviroidae, which also includes the genera Pospiviroid, Cocadviroid, Apscaviroid, and Coleoviroid. PHYSICAL PROPERTIES Hop stunt viroid consists of a single-stranded, circular RNA of 295-303 nucleotides depending on isolates and sequence variants. The most stable secondary structure is a rod-like or quasi-rod-like conformation with two characteristic domains: a CCR and a terminal conserved hairpin similar to that of cocadviroids. HSVd lacks a terminal conserved region. HOSTS AND SYMPTOMS HSVd infects a very broad range of natural hosts and has been reported to be the causal agent of five different diseases (citrus cachexia, cucumber pale fruit, peach and plum apple apricot distortion, and hop stunt). It is distributed worldwide. TRANSMISSION HSVd is transmitted mechanically and by seed.
Collapse
Affiliation(s)
- Joan Marquez‐Molins
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas, Universitat de ValènciaPaternaSpain
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas, Universitat Politècnica de ValènciaValenciaSpain
| | - Gustavo Gomez
- Institute for Integrative Systems Biology (I2SysBio)Consejo Superior de Investigaciones Científicas, Universitat de ValènciaPaternaSpain
| | - Vicente Pallas
- Instituto de Biología Molecular y Celular de PlantasConsejo Superior de Investigaciones Científicas, Universitat Politècnica de ValènciaValenciaSpain
| |
Collapse
|
180
|
Mahillon M, Decroës A, Peduzzi C, Romay G, Legrève A, Bragard C. RNA silencing machinery contributes to inability of BSBV to establish infection in Nicotiana benthamiana: evidence from characterization of agroinfectious clones of Beet soil-borne virus. J Gen Virol 2021; 102. [PMID: 33215984 DOI: 10.1099/jgv.0.001530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Beet soil-borne virus (BSBV) is a sugar beet pomovirus frequently associated with Beet necrotic yellow veins virus, the causal agent of the rhizomania disease. BSBV has been detected in most of the major beet-growing regions worldwide, yet its impact on this crop remains unclear. With the aim to understand the life cycle of this virus and clarify its putative pathogenicity, agroinfectious clones have been engineered for each segment of its tripartite genome. The biological properties of these clones were then studied on different plant species. Local infection was obtained on agroinfiltrated leaves of Beta macrocarpa. On leaves of Nicotiana benthamiana, similar results were obtained, but only when heterologous viral suppressors of RNA silencing were co-expressed or in a transgenic line down regulated for both dicer-like protein 2 and 4. On sugar beet, local infection following agroinoculation was obtained on cotyledons, but not on other tested plant parts. Nevertheless, leaf symptoms were observed on this host via sap inoculation. Likewise, roots were efficiently mechanically infected, highlighting low frequency of root necrosis and constriction, and enabling the demonstration of transmission by the vector Polymyxa betae. Altogether, the entire viral cycle was reproduced, validating the constructed agroclones as efficient inoculation tools, paving the way for further studies on BSBV and its related pathosystem.
Collapse
Affiliation(s)
- Mathieu Mahillon
- UCLouvain, Earth and Life Institute, Applied Microbiology-Phytopathology, Croix du Sud 2-L07.05.03, 1348 Louvain-la-Neuve, Belgium
| | - Alain Decroës
- UCLouvain, Earth and Life Institute, Applied Microbiology-Phytopathology, Croix du Sud 2-L07.05.03, 1348 Louvain-la-Neuve, Belgium
| | - Chloé Peduzzi
- UCLouvain, Earth and Life Institute, Applied Microbiology-Phytopathology, Croix du Sud 2-L07.05.03, 1348 Louvain-la-Neuve, Belgium
| | - Gustavo Romay
- UCLouvain, Earth and Life Institute, Applied Microbiology-Phytopathology, Croix du Sud 2-L07.05.03, 1348 Louvain-la-Neuve, Belgium
| | - Anne Legrève
- UCLouvain, Earth and Life Institute, Applied Microbiology-Phytopathology, Croix du Sud 2-L07.05.03, 1348 Louvain-la-Neuve, Belgium
| | - Claude Bragard
- UCLouvain, Earth and Life Institute, Applied Microbiology-Phytopathology, Croix du Sud 2-L07.05.03, 1348 Louvain-la-Neuve, Belgium
| |
Collapse
|
181
|
Leonetti P, Ghasemzadeh A, Consiglio A, Gursinsky T, Behrens S, Pantaleo V. Endogenous activated small interfering RNAs in virus-infected Brassicaceae crops show a common host gene-silencing pattern affecting photosynthesis and stress response. New Phytol 2021; 229:1650-1664. [PMID: 32945560 PMCID: PMC7821159 DOI: 10.1111/nph.16932] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/04/2020] [Indexed: 05/14/2023]
Abstract
Viral infections are accompanied by a massive production of small interfering RNAs (siRNAs) of plant origin, such as virus-activated (va)siRNAs, which drive the widespread silencing of host gene expression, and whose effects in plant pathogen interactions remain unknown. By combining phenotyping and molecular analyses, we characterized vasiRNAs that are associated with typical mosaic symptoms of cauliflower mosaic virus infection in two crops, turnip (Brassica rapa) and oilseed rape (Brassica napus), and the reference plant Arabidopsis thaliana. We identified 15 loci in the three infected plant species, whose transcripts originate vasiRNAs. These loci appear to be generally affected by virus infections in Brassicaceae and encode factors that are centrally involved in photosynthesis and stress response, such as Rubisco activase (RCA), senescence-associated protein, heat shock protein HSP70, light harvesting complex, and membrane-related protein CP5. During infection, the expression of these factors is significantly downregulated, suggesting that their silencing is a central component of the plant's response to virus infections. Further findings indicate an important role for 22 nt long vasiRNAs in the plant's endogenous RNA silencing response. Our study considerably enhances knowledge about the new class of vasiRNAs that are triggered in virus-infected plants and will help to advance strategies for the engineering of gene clusters involved in the development of crop diseases.
Collapse
Affiliation(s)
- Paola Leonetti
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
| | - Aysan Ghasemzadeh
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
- Department of Plant PathologyFaculty of AgricultureTarbiat Modares UniversityTehran14115‐111Iran
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Arianna Consiglio
- Department of Biomedical SciencesInstitute for Biomedical TechnologiesBari UnitCNRBari70126Italy
| | - Torsten Gursinsky
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Sven‐Erik Behrens
- Institute of Biochemistry and Biotechnology (NFI)Section Microbial BiotechnologyMartin Luther University Halle‐WittenbergHalle/SaaleD‐06120Germany
| | - Vitantonio Pantaleo
- Department of Biology, Agricultural and Food SciencesInstitute for Sustainable Plant ProtectionBari UnitCNRBari70126Italy
| |
Collapse
|
182
|
Cao Y, Zhou H, Zhou X, Li F. Conferring Resistance to Plant RNA Viruses with the CRISPR/CasRx System. Virol Sin 2021; 36:814-817. [PMID: 33459978 DOI: 10.1007/s12250-020-00338-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/21/2020] [Indexed: 12/20/2022] Open
Affiliation(s)
- Yongsen Cao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huanbin Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fangfang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
183
|
Agranovsky A. Enhancing Capsid Proteins Capacity in Plant Virus-Vector Interactions and Virus Transmission. Cells 2021; 10:cells10010090. [PMID: 33430410 PMCID: PMC7827187 DOI: 10.3390/cells10010090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 12/02/2022] Open
Abstract
Vector transmission of plant viruses is basically of two types that depend on the virus helper component proteins or the capsid proteins. A number of plant viruses belonging to disparate groups have developed unusual capsid proteins providing for interactions with the vector. Thus, cauliflower mosaic virus, a plant pararetrovirus, employs a virion associated p3 protein, the major capsid protein, and a helper component for the semi-persistent transmission by aphids. Benyviruses encode a capsid protein readthrough domain (CP-RTD) located at one end of the rod-like helical particle, which serves for the virus transmission by soil fungal zoospores. Likewise, the CP-RTD, being a minor component of the luteovirus icosahedral virions, provides for persistent, circulative aphid transmission. Closteroviruses encode several CPs and virion-associated proteins that form the filamentous helical particles and mediate transmission by aphid, whitefly, or mealybug vectors. The variable strategies of transmission and evolutionary ‘inventions’ of the unusual capsid proteins of plant RNA viruses are discussed.
Collapse
|
184
|
Goodin M, Verchot J. Introduction to Special Issue of Plant Virus Emergence. Viruses 2021; 13:v13010055. [PMID: 33401517 PMCID: PMC7824620 DOI: 10.3390/v13010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
We are pleased to present in this Special Issue a series of reviews and research studies on the topic of "Plant Virus Emergence" [...].
Collapse
Affiliation(s)
- Michael Goodin
- Plant Pathology Department, University of Kentucky, Lexington, KY 40546, USA
- Correspondence: (M.G.); (J.V.); Tel.: +1-979-845-1788 (J.V.)
| | - Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77802, USA
- Correspondence: (M.G.); (J.V.); Tel.: +1-979-845-1788 (J.V.)
| |
Collapse
|
185
|
Abstract
The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data. In this review, we discuss the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multidisciplinary approach to tackling disease risk. The ability to make sense of the information now generated in this integrated setting is by far the most substantial obstacle to the ultimate goal of plant virology to minimize the threats to food security posed by disease. To achieve this goal, it is imperative to understand and forecast how populations respond to future changes in complex natural systems.
Collapse
Affiliation(s)
- Michael J McLeish
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM) and Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, UPM, 28223 Pozuelo de Alarcón, Madrid, Spain
| |
Collapse
|
186
|
Sherlock ME, Hartwick EW, MacFadden A, Kieft JS. Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses. RNA 2021; 27:27-39. [PMID: 33008837 PMCID: PMC7749636 DOI: 10.1261/rna.076968.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/26/2020] [Indexed: 05/26/2023]
Abstract
Viruses commonly use specifically folded RNA elements that interact with both host and viral proteins to perform functions important for diverse viral processes. Examples are found at the 3' termini of certain positive-sense ssRNA virus genomes where they partially mimic tRNAs, including being aminoacylated by host cell enzymes. Valine-accepting tRNA-like structures (TLSVal) are an example that share some clear homology with canonical tRNAs but have several important structural differences. Although many examples of TLSVal have been identified, we lacked a full understanding of their structural diversity and phylogenetic distribution. To address this, we undertook an in-depth bioinformatic and biochemical investigation of these RNAs, guided by recent high-resolution structures of a TLSVal We cataloged many new examples in plant-infecting viruses but also in unrelated insect-specific viruses. Using biochemical and structural approaches, we verified the secondary structure of representative TLSVal substrates and tested their ability to be valylated, confirming previous observations of structural heterogeneity within this class. In a few cases, large stem-loop structures are inserted within variable regions located in an area of the TLS distal to known host cell factor binding sites. In addition, we identified one virus whose TLS has switched its anticodon away from valine, causing a loss of valylation activity; the implications of this remain unclear. These results refine our understanding of the structural and functional mechanistic details of tRNA mimicry and how this may be used in viral infection.
Collapse
MESH Headings
- Anticodon/chemistry
- Anticodon/metabolism
- Base Sequence
- Binding Sites
- Computational Biology
- Genetic Variation
- Insect Viruses/classification
- Insect Viruses/genetics
- Insect Viruses/metabolism
- Models, Molecular
- Molecular Mimicry
- Phylogeny
- Plant Viruses/classification
- Plant Viruses/genetics
- Plant Viruses/metabolism
- RNA Folding
- RNA, Transfer, Val/chemistry
- RNA, Transfer, Val/genetics
- RNA, Transfer, Val/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Sequence Homology, Nucleic Acid
- Valine/metabolism
Collapse
Affiliation(s)
- Madeline E Sherlock
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Erik W Hartwick
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Andrea MacFadden
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
| |
Collapse
|
187
|
Zhang S, Huang A, Zhou X, Li Z, Dietzgen RG, Zhou C, Cao M. Natural Defect of a Plant Rhabdovirus Glycoprotein Gene: A Case Study of Virus-Plant Coevolution. Phytopathology 2021; 111:227-236. [PMID: 32648524 DOI: 10.1094/phyto-05-20-0191-fi] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Seven isolates of a putative cytorhabdovirus (family Rhabdoviridae, order Mononegavirales) designated as citrus-associated rhabdovirus (CiaRV) were identified in citrus, passion fruit, and paper bush from the same geographical area in China. CiaRV, bean-associated cytorhabdovirus (Brazil), and papaya virus E (Ecuador) should be taxonomically classified in the species Papaya cytorhabdovirus. Due to natural mutations, the glycoprotein (G) and P4 genes were impaired in citrus-infecting isolates of CiaRV, resulting in an atypical rhabdovirus genome organization of 3' leader-N-P-P3-M-L-5' trailer. The P3 protein of CiaRV shared a common origin with begomoviral movement proteins (family Geminiviridae). Secondary structure analysis and trans-complementation of movement-deficient tomato mosaic virus and potato virus X mutants by CiaRV P3 supported its function in viral cell-to-cell trafficking. The wide geographical dispersal of CiaRV and related viruses suggests an efficient transmission mechanism, as well as an underlying risk to global agriculture. Both the natural phenomenon and experimental analyses demonstrated presence of the "degraded" type of CiaRV in citrus, in parallel to "undegraded" types in other host plant species. This case study shows a plant virus losing the function of an important but nonessential gene, likely due to host shift and adaption, which deepened our understanding of course of natural viral diversification.
Collapse
Affiliation(s)
- Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Aijun Huang
- National Navel Orange Research Center, College of Life Science, Gannan Normal University, Ganzhou, China
| | - Xin Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Changyong Zhou
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
| |
Collapse
|
188
|
Wu J, Bisaro DM. Biased Pol II fidelity contributes to conservation of functional domains in the Potato spindle tuber viroid genome. PLoS Pathog 2020; 16:e1009144. [PMID: 33351860 PMCID: PMC7787683 DOI: 10.1371/journal.ppat.1009144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 01/06/2021] [Accepted: 11/10/2020] [Indexed: 01/25/2023] Open
Abstract
Accurate calculation of mutation rates for viruses and viroids is necessary for evolutionary studies and to evaluate adaptation potential. However, estimation of in vivo mutation rates is complicated by selection, which leads to loss or proliferation of certain mutations. To minimize this concern, lethal mutations, including nonsense and non-synonymous mutations, have been used to determine mutation rates for several viruses and viroids, including Potato spindle tuber viroid (PSTVd). However, this approach has limitations, including focus on a relatively small number of genome sites and the possibility that mutations may not actually be lethal or may be maintained by wild type individuals. To avoid selection bias altogether, we sequenced minus-strand PSTVd dimers from concatemeric replication intermediates. The underlying rationale is that mutations found in only one of the monomers were likely generated de novo during RNA polymerase II (Pol II) transcription of the circular plus-strand RNA genome. This approach yielded an apparent Pol II error rate of ~1/1837 nucleotides per transcription cycle, and an estimated mutation rate of ~1/919 nucleotides for a single replication cycle. Remarkably, de novo mutations were nearly absent from the most conserved, replication-critical regions of the PSTVd genome, suggesting that sequence conservation is a consequence of both essential function and template optimization for greater Pol II fidelity. Such biased fidelity may constitute a novel strategy to ensure population success while allowing abundant sampling of sequence space in other genome regions. Comparison with variants in progeny populations derived from a cloned, wild type PSTVd master sequence revealed that most de novo mutations were lost through selection. Polymerase errors are the major source of variation in virus and viroid genomes, and as a consequence polymerase error rates are major determinants of adaptation potential. Accurate calculation of in vivo mutation rates is complicated by selection. To circumvent this issue, dimeric PSTVd minus-strand replication intermediates generated in vivo by host RNA polymerase II (Pol II) were sequenced to identify de novo mutations. This analysis revealed a very high error rate for Pol II transcribing genomic PSTVd RNA, leading to an extremely high mutation rate. Remarkably, however, de novo mutations were rare in the most highly conserved, replication-critical genome regions, suggesting these sequences are selected for both function and enhanced transcription fidelity. This biased fidelity may reveal a novel strategy to ensure population survival while maximizing adaptation potential. Further, comparison of mutations identified by minus-strand dimer sequencing with mutations observed in progeny variants derived from wild type PSTVd showed that most de novo mutations were lost through selection.
Collapse
Affiliation(s)
- Jian Wu
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - David M. Bisaro
- Department of Molecular Genetics, Center for Applied Plant Sciences, Center for RNA Biology, and Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
| |
Collapse
|
189
|
Abstract
Severe virus outbreaks are occurring more often and spreading faster and further than ever. Preparedness plans based on lessons learned from past epidemics can guide behavioral and pharmacological interventions to contain and treat emergent diseases. Although conventional biologics production systems can meet the pharmaceutical needs of a community at homeostasis, the COVID-19 pandemic has created an abrupt rise in demand for vaccines and therapeutics that highlight the gaps in this supply chain's ability to quickly develop and produce biologics in emergency situations given a short lead time. Considering the projected requirements for COVID-19 vaccines and the necessity for expedited large scale manufacture the capabilities of current biologics production systems should be surveyed to determine their applicability to pandemic preparedness. Plant-based biologics production systems have progressed to a state of commercial viability in the past 30 years with the capacity for production of complex, glycosylated, "mammalian compatible" molecules in a system with comparatively low production costs, high scalability, and production flexibility. Continued research drives the expansion of plant virus-based tools for harnessing the full production capacity from the plant biomass in transient systems. Here, we present an overview of vaccine production systems with a focus on plant-based production systems and their potential role as "first responders" in emergency pandemic situations.
Collapse
Affiliation(s)
- Zacharie LeBlanc
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
| | - Peter Waterhouse
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia
| | - Julia Bally
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology (QUT), Brisbane, QLD 4000, Australia;
| |
Collapse
|
190
|
Ma X, Li Z. Significantly Improved Recovery of Recombinant Sonchus Yellow Net Rhabdovirus by Expressing the Negative-Strand Genomic RNA. Viruses 2020; 12:v12121459. [PMID: 33348798 PMCID: PMC7766655 DOI: 10.3390/v12121459] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/13/2022] Open
Abstract
Generation of recombinant negative-stranded RNA viruses (NSVs) from plasmids involves in vivo reconstitution of biologically active nucleocapsids and faces a unique antisense problem where the negative-sense viral genomic RNAs can hybridize to viral messenger RNAs. To overcome this problem, a positive-sense RNA approach has been devised through expression of viral antigenomic (ag)RNA and core proteins for assembly of antigenomic nucleocapsids. Although this detour strategy works for many NSVs, the process is still inefficient. Using Sonchus yellow net rhabdovirus (SYNV) as a model; here, we develop a negative-sense genomic RNA-based approach that increased rescue efficiency by two orders of magnitude compared to the conventional agRNA approach. The system relied on suppression of double-stranded RNA induced antiviral responses by co-expression of plant viruses-encoded RNA silencing suppressors or animal viruses-encoded double-stranded RNA antagonists. With the improved approach, we were able to recover a highly attenuated SYNV mutant with a deletion in the matrix protein gene which otherwise could not be rescued via the agRNA approach. Reverse genetics analyses of the generated mutant virus provided insights into SYNV virion assembly and morphogenesis. This approach may potentially be applicable to other NSVs of plants or animals.
Collapse
Affiliation(s)
- Xiaonan Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China;
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
- Correspondence: ; Tel.: +86-571-8898-2387
| |
Collapse
|
191
|
Ghoshal B, Vong B, Picard CL, Feng S, Tam JM, Jacobsen SE. A viral guide RNA delivery system for CRISPR-based transcriptional activation and heritable targeted DNA demethylation in Arabidopsis thaliana. PLoS Genet 2020; 16:e1008983. [PMID: 33315895 PMCID: PMC7769603 DOI: 10.1371/journal.pgen.1008983] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 12/28/2020] [Accepted: 11/02/2020] [Indexed: 01/01/2023] Open
Abstract
Plant RNA viruses are used as delivery vectors for their high level of accumulation and efficient spread during virus multiplication and movement. Utilizing this concept, several viral-based guide RNA delivery platforms for CRISPR-Cas9 genome editing have been developed. The CRISPR-Cas9 system has also been adapted for epigenome editing. While systems have been developed for CRISPR-Cas9 based gene activation or site-specific DNA demethylation, viral delivery of guide RNAs remains to be developed for these purposes. To address this gap we have developed a tobacco rattle virus (TRV)-based single guide RNA delivery system for epigenome editing in Arabidopsis thaliana. Because tRNA-like sequences have been shown to facilitate the cell-to-cell movement of RNAs in plants, we used the tRNA-guide RNA expression system to express guide RNAs from the viral genome to promote heritable epigenome editing. We demonstrate that the tRNA-gRNA system with TRV can be used for both transcriptional activation and targeted DNA demethylation of the FLOWERING WAGENINGEN gene in Arabidopsis. We achieved up to ~8% heritability of the induced demethylation phenotype in the progeny of virus inoculated plants. We did not detect the virus in the next generation, indicating effective clearance of the virus from plant tissues. Thus, TRV delivery, combined with a specific tRNA-gRNA architecture, provides for fast and effective epigenome editing.
Collapse
Affiliation(s)
- Basudev Ghoshal
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Brandon Vong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Colette L. Picard
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Janet M. Tam
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
| | - Steven E. Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, United States of America
- Eli and Edyth Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California, United States of America
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, California, United States of America
| |
Collapse
|
192
|
Abstract
Over a hundred years of research on plant viruses has led to a detailed understanding of viral replication, movement, and host-virus interactions. The functions of vast viral genes have also been annotated. With an increased understanding of plant viruses and plant-virus interactions, various viruses have been developed as vectors to modulate gene expressions for functional studies as well as for fulfilling the needs in biotechnology. These approaches are invaluable not only for molecular breeding and functional genomics studies related to pivotal agronomic traits, but also for the production of vaccines and health-promoting carotenoids. This review summarizes the latest progress in these forefronts as well as the available viral vectors for economically important crops and beyond.
Collapse
Affiliation(s)
- Mo Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Shilei Gao
- Fujian University Key Laboratory for Plant-Microbe Interaction, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Wenzhi Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Yongqing Yang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Junfei Ma
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39759, USA;
| | - Ying Wang
- Department of Biological Sciences, Mississippi State University, Starkville, MS 39759, USA;
| |
Collapse
|
193
|
Abstract
Infection by multiple pathogens of the same host is ubiquitous in both natural and managed habitats. While intraspecific variation in disease resistance is known to affect pathogen occurrence, how differences among host genotypes affect the assembly of pathogen communities remains untested. In our experiment using cloned replicates of naive Plantago lanceolata plants as sentinels during a seasonal virus epidemic, we find non-random co-occurrence patterns of five focal viruses. Using joint species distribution modelling, we attribute the non-random virus occurrence patterns primarily to differences among host genotypes and local population context. Our results show that intraspecific variation among host genotypes may play a large, previously unquantified role in pathogen community structure.
Collapse
Affiliation(s)
- Suvi Sallinen
- Organismal and Evolutionary Biology Research Programme, Viikinkaari 1 (PO box 65), FI-00014, University of Helsinki, Helsinki, Finland.
| | - Anna Norberg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, CH-8067, Zürich, Switzerland
| | - Hanna Susi
- Organismal and Evolutionary Biology Research Programme, Viikinkaari 1 (PO box 65), FI-00014, University of Helsinki, Helsinki, Finland
| | - Anna-Liisa Laine
- Organismal and Evolutionary Biology Research Programme, Viikinkaari 1 (PO box 65), FI-00014, University of Helsinki, Helsinki, Finland
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, CH-8067, Zürich, Switzerland
| |
Collapse
|
194
|
Sá Antunes TF, Maurastoni M, Madroñero LJ, Fuentes G, Santamaría JM, Ventura JA, Abreu EF, Fernandes AAR, Fernandes PMB. Battle of Three: The Curious Case of Papaya Sticky Disease. Plant Dis 2020; 104:2754-2763. [PMID: 32813628 DOI: 10.1094/pdis-12-19-2622-fe] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Among the most serious problems in papaya production are the viruses associated with papaya ringspot and papaya sticky disease (PSD). PSD concerns producers worldwide because its symptoms are extremely aggressive and appear only after flowering. As no resistant cultivar is available, several disease management strategies have been used in affected countries, such as the use of healthy seeds, exclusion of the pathogen, and roguing. In the 1990s, a dsRNA virus, papaya meleira virus (PMeV), was identified in Brazil as the causal agent of PSD. However, in 2016 a second virus, papaya meleira virus 2 (PMeV2), with an ssRNA genome, was also identified in PSD plants. Only PMeV is detected in asymptomatic plants, whereas all symptomatic plants contain both viral RNAs separately packaged in particles formed by the PMeV capsid protein. PSD also affects papaya plants in Mexico, Ecuador, and Australia. PMeV2-like viruses have been identified in the affected plants, but the partner virus(es) in these countries are still unknown. In Brazil, PMeV and PMeV2 reside in laticifers that promote spontaneous latex exudation, resulting in the affected papaya fruit's sticky appearance. Genes modulated in plants affected by PSD include those involved in reactive oxygen species and salicylic acid signaling, proteasomal degradation, and photosynthesis, which are key plant defenses against PMeV complex infection. However, the complete activation of the defense response is impaired by the expression of negative effectors modulated by the virus. This review presents a summary of the current knowledge of the Carica papaya-PMeV complex interaction and management strategies.
Collapse
Affiliation(s)
- Tathiana F Sá Antunes
- Nucleo de Biotecnologia Universidade Federal do Espírito Santo, Vitória, Espírito Santo 29040-090, Brazil
| | - Marlonni Maurastoni
- Nucleo de Biotecnologia Universidade Federal do Espírito Santo, Vitória, Espírito Santo 29040-090, Brazil
| | - L Johana Madroñero
- Nucleo de Biotecnologia Universidade Federal do Espírito Santo, Vitória, Espírito Santo 29040-090, Brazil
- Universidad El Bosque, Vicerrectoría de Investigaciones, Bogota, Colombia
| | - Gabriela Fuentes
- Centro de Investigación Científica de Yucatán, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
| | - Jorge M Santamaría
- Centro de Investigación Científica de Yucatán, Col. Chuburná de Hidalgo, 97200 Mérida, Yucatán, Mexico
| | - José Aires Ventura
- Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural, Vitória 29050790, Espírito Santo, Brazil
| | - Emanuel F Abreu
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, 70770-900, Brazil
| | - A Alberto R Fernandes
- Nucleo de Biotecnologia Universidade Federal do Espírito Santo, Vitória, Espírito Santo 29040-090, Brazil
| | - Patricia M B Fernandes
- Nucleo de Biotecnologia Universidade Federal do Espírito Santo, Vitória, Espírito Santo 29040-090, Brazil
| |
Collapse
|
195
|
Liu H, Zhou Y, Xu Q, Wong SM. Selection of DNA Aptamers for Subcellular Localization of RBSDV P10 Protein in the Midgut of Small Brown Planthoppers by Emulsion PCR-Based SELEX. Viruses 2020; 12:v12111239. [PMID: 33143344 PMCID: PMC7692627 DOI: 10.3390/v12111239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 12/31/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV), classified under the Reoviridae, Fijivirus genus, caused an epidemic in the eastern provinces of China and other East Asian countries and resulted in severe yield loss in rice and wheat production. RBSDV is transmitted by the small brown planthopper (SBPH, Laodelphax striatellus Fallén) in a persistent manner. In order to provide a stable and cost-effective detection probe, in this study we selected three DNA aptamers (R3, R5 and R11) by an optimized, standardized and time saving emulsion PCR-based SELEX, for the detection of RBSDV outer-shell P10 protein for in situ localization studies in the midgut of SBPH. The specificity of these three DNA aptamers was tested through detection of the P10 protein using an enzyme-linked oligonucleotide assay (ELONA) and aptamer-based dot-blot ELISA. All three DNA aptamers can be used to detect RBSDV P10 protein by immunofluorescent labeling in the midgut of RBSDV-infected SBPH. These data show that the selected aptamers can be used for the detection of RBSDV P10 protein in vitro and in vivo. This is the first report of aptamers being selected for detection of a rice virus capsid protein.
Collapse
Affiliation(s)
- Haoqiu Liu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
- National University of Singapore (Suzhou) Research Institute, Suzhou 215123, China
| | - Yijun Zhou
- Key Laboratory of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Qiufang Xu
- Key Laboratory of Food Quality and Safety of Jiangsu Province, State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- Correspondence: (Q.X.); (S.-M.W.); Tel.: +86-25-84390394 (Q.X.); +65-65162976 (S.-M.W.); Fax: +86-25-84390391 (Q.X.); +65-67792486 (S.-M.W.)
| | - Sek-Man Wong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore;
- National University of Singapore (Suzhou) Research Institute, Suzhou 215123, China
- Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604, Singapore
- Correspondence: (Q.X.); (S.-M.W.); Tel.: +86-25-84390394 (Q.X.); +65-65162976 (S.-M.W.); Fax: +86-25-84390391 (Q.X.); +65-67792486 (S.-M.W.)
| |
Collapse
|
196
|
Zhang Z, Xia C, Matsuda T, Taneda A, Murosaki F, Hou W, Owens RA, Li S, Sano T. Effects of Host-Adaptive Mutations on Hop Stunt Viroid Pathogenicity and Small RNA Biogenesis. Int J Mol Sci 2020; 21:ijms21197383. [PMID: 33036282 PMCID: PMC7582576 DOI: 10.3390/ijms21197383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/29/2020] [Accepted: 10/04/2020] [Indexed: 01/02/2023] Open
Abstract
Accidental transmission of hop stunt viroid (HSVd) from grapevine to hop has led to several epidemics of hop stunt disease with convergent evolution of HSVd-g(rape) into HSVd-h(op) containing five mutations. However, the biological function of these five mutations remains unknown. In this study, we compare the biological property of HSVd-g and HSVd-h by bioassay and analyze HSVd-specific small RNA (HSVd-sRNA) using high-throughput sequencing. The bioassay indicated an association of these five mutations with differences in infectivity, replication capacity, and pathogenicity between HSVd-g and HSVd-h, e.g., HSVd-g induced more severe symptoms than HSVd-h in cucumber. Site-directed mutagenesis of HSVd-g showed that the mutation at position 54 increased pathogenicity. HSVd-sRNA analysis of cucumber and hop plants infected with different HSVd variants showed that several sRNA species containing adaptive nucleotides were specifically down-regulated in plants infected with HSVd-h. Several HSVd-sRNAs containing adaptive mutations were predicted to target cucumber genes, but changes in the levels of these genes were not directly correlated with changes in symptom expression. Furthermore, expression levels of two other cucumber genes targeted by HSVd-RNAs, encoding ethylene-responsive transcription factor ERF011, and trihelix transcription factor GTL2, were altered by HSVd infection. The possible relationship between these two genes to HSVd pathogenicity is discussed.
Collapse
Affiliation(s)
- Zhixiang Zhang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Changjian Xia
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Takahiro Matsuda
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan;
| | - Fumiko Murosaki
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
| | - Wanying Hou
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
| | - Robert A. Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA;
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.Z.); (C.X.); (W.H.)
- Environment and Plant Protection Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (S.L.); (T.S.)
| | - Teruo Sano
- Plant Pathology Laboratory, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki 036-8561, Japan; (T.M.); (F.M.)
- Correspondence: (S.L.); (T.S.)
| |
Collapse
|
197
|
Umber M, Filloux D, Gélabale S, Gomez RM, Marais A, Gallet S, Gamiette F, Pavis C, Teycheney PY. Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange. Viruses 2020; 12:v12101101. [PMID: 33003342 PMCID: PMC7650539 DOI: 10.3390/v12101101] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 01/25/2023] Open
Abstract
Yam (Dioscorea spp.) is an important crop in tropical and subtropical regions. Many viruses have been recently identified in yam, hampering genetic conservation and safe international exchanges of yam germplasm. We report on the implementation of reliable and cost-effective PCR-based detection tools targeting eight different yam-infecting viruses. Viral indexing of the in vitro yam collection maintained by the Biological Resources Center for Tropical Plants (BRC-TP) in Guadeloupe (French West Indies) unveiled a high prevalence of potyviruses, badnaviruses, Dioscorea mosaic associated virus (DMaV) and yam asymptomatic virus 1 (YaV1) and a high level of coinfections. Infected yam accessions were subjected to a combination of thermotherapy and meristem culture. Sanitation levels were monitored using PCR-based and high-throughput sequencing-based diagnosis, confirming the efficacy and reliability of PCR-based detection tools. Sanitation rates were highly variable depending on viruses. Sixteen accessions were successfully sanitized, paving the way to safe yam germplasm exchanges and the implementation of clean seed production programs worldwide.
Collapse
Affiliation(s)
- Marie Umber
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
- Correspondence: ; Tel.: +590-590-25-59-29
| | - Denis Filloux
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche—Biologie et Génétique des Interactions Plante-Parasite, F-34398 Montpellier, France;
- Biologie et Génétique des Interactions Plante-Parasite, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, Montpellier SupAgro, F-34060 Montpellier, France
| | - Suzia Gélabale
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Rose-Marie Gomez
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Armelle Marais
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Université de Bordeaux, Unité Mixte de Recherche Biologie du Fruit et Pathologie, F-33882 Villenave d’Ornon, France;
| | - Séverine Gallet
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Franciane Gamiette
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Claudie Pavis
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Unité de Recherche Agrosystèmes Tropicaux, F-97170 Petit-Bourg, France; (S.G.); (R.-M.G.); (S.G.); (F.G.); (C.P.)
| | - Pierre-Yves Teycheney
- Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, F-97130 Capesterre Belle-Eau, France;
- Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales, Univ. Montpellier, Centre de Coopération Internationale en Recherche Agronomique Pour le Développement, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Institut Agro, F-97130 Capesterre Belle-Eau, France
| |
Collapse
|
198
|
Herath V, Romay G, Urrutia CD, Verchot J. Family Level Phylogenies Reveal Relationships of Plant Viruses within the Order Bunyavirales. Viruses 2020; 12:v12091010. [PMID: 32927652 PMCID: PMC7551631 DOI: 10.3390/v12091010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
Bunyavirales are negative-sense segmented RNA viruses infecting arthropods, protozoans, plants, and animals. This study examines the phylogenetic relationships of plant viruses within this order, many of which are recently classified species. Comprehensive phylogenetic analyses of the viral RNA dependent RNA polymerase (RdRp), precursor glycoprotein (preGP), the nucleocapsid (N) proteins point toward common progenitor viruses. The RdRp of Fimoviridae and Tospoviridae show a close evolutional relationship while the preGP of Fimoviridae and Phenuiviridae show a closed relationship. The N proteins of Fimoviridae were closer to the Phasmaviridae, the Tospoviridae were close to some Phenuiviridae members and the Peribunyaviridae. The plant viral movement proteins of species within the Tospoviridae and Phenuiviridae were more closely related to each other than to members of the Fimoviridae. Interestingly, distal ends of 3′ and 5′ untranslated regions of species within the Fimoviridae shared similarity to arthropod and vertebrate infecting members of the Cruliviridae and Peribunyaviridae compared to other plant virus families. Co-phylogeny analysis of the plant infecting viruses indicates that duplication and host switching were more common than co-divergence with a host species.
Collapse
Affiliation(s)
- Venura Herath
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
- Department of Agriculture Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya 20400, Sri Lanka
| | - Gustavo Romay
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
| | - Cesar D. Urrutia
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
| | - Jeanmarie Verchot
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX 77802, USA; (V.H.); (G.R.); (C.D.U.)
- Correspondence: ; Tel.: +1-979-845-1788
| |
Collapse
|
199
|
Zhang T, Liang Q, Li C, Fu S, Kundu JK, Zhou X, Wu J. Transcriptome Analysis of Rice Reveals the lncRNA-mRNA Regulatory Network in Response to Rice Black-Streaked Dwarf Virus Infection. Viruses 2020; 12:v12090951. [PMID: 32867233 PMCID: PMC7552052 DOI: 10.3390/v12090951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 01/05/2023] Open
Abstract
The plant genome can produce long non-coding RNAs (lncRNAs), some of which have been identified as important regulators of gene expression. To better understand the response mechanism of rice plants to Rice black-streaked dwarf virus (RBSDV) infection, we performed a comparative transcriptome analysis between the RBSDV-infected and non-infected rice plants. A total of 1342 mRNAs and 22 lncRNAs were identified to be differentially expressed after RBSDV infection. Most differentially expressed transcripts involved in the plant–pathogen interaction pathway were upregulated after RBSDV infection, indicating the activation of rice defense response by RBSDV. A network of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) was then constructed. In this network, there are 56 plant–pathogen interaction-related DEmRNAs co-expressing with 20 DElncRNAs, suggesting these DElncRNAs and DEmRNAs may play essential roles in rice innate immunity against RBSDV. Moreover, some of the lncRNA–mRNA regulatory relationships were experimentally verified in rice calli by a quick and effective method established in this study. Three DElncRNAs were selected to be tested, and the results indicated that five mRNAs were found to be regulated by them. Together, we give a whole landscape of rice mRNAs and lncRNAs in response to RBSDV infection, and a feasible method to rapidly verify the lncRNA–mRNA regulatory relationship in rice.
Collapse
Affiliation(s)
- Tianze Zhang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Qian Liang
- Key Laboratory of microorganism technology and bioinformatics research of Zhejiang Province, NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang TianKe High-Technology Development Co. Ltd., Hangzhou 310023, China;
| | - Chenyang Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
| | | | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.Z.); (C.L.); (S.F.)
- Correspondence: (X.Z.); (J.W.); Tel.: +86-571-88982250 (J.W.)
| |
Collapse
|
200
|
Gaafar YZA, Ziebell H. Comparative study on three viral enrichment approaches based on RNA extraction for plant virus/viroid detection using high-throughput sequencing. PLoS One 2020; 15:e0237951. [PMID: 32841302 PMCID: PMC7447037 DOI: 10.1371/journal.pone.0237951] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing (HTS) has become increasingly popular as virus diagnostic tool. It has been used to detect and identify plant viruses and viroids in different types of matrices and tissues. A viral sequence enrichment method prior to HTS is required to increase the viral reads in the generated data to ease the bioinformatic analysis of generated sequences. In this study, we compared the sensitivity of three viral enrichment approaches, i.e. double stranded RNA (dsRNA), ribosomal RNA depleted total RNA (ribo-depleted totRNA) and small RNA (sRNA) for plant virus/viroid detection, followed by sequencing on MiSeq and NextSeq Illumina platforms. The three viral enrichment approaches used here enabled the detection of all viruses/viroid used in this study. When the data was normalised, the recovered viral/viroid nucleotides and depths were depending on the viral genome and the enrichment method used. Both dsRNA and ribo-depleted totRNA approaches detected a divergent strain of Wuhan aphid virus 2 that was not expected in this sample. Additionally, Vicia cryptic virus was detected in the data of dsRNA and sRNA approaches only. The results suggest that dsRNA enrichment has the highest potential to detect and identify plant viruses and viroids. The dsRNA approach used here detected all viruses/viroid, consumed less time, was lower in cost, and required less starting material. Therefore, this approach appears to be suitable for diagnostics laboratories.
Collapse
Affiliation(s)
- Yahya Zakaria Abdou Gaafar
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
| | - Heiko Ziebell
- Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Braunschweig, Germany
- * E-mail:
| |
Collapse
|