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González-Pérez E, Chiquito-Almanza E, Villalobos-Reyes S, Canul-Ku J, Anaya-López JL. Diagnosis and Characterization of Plant Viruses Using HTS to Support Virus Management and Tomato Breeding. Viruses 2024; 16:888. [PMID: 38932180 PMCID: PMC11209215 DOI: 10.3390/v16060888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Viral diseases pose a significant threat to tomato crops (Solanum lycopersicum L.), one of the world's most economically important vegetable crops. The limited genetic diversity of cultivated tomatoes contributes to their high susceptibility to viral infections. To address this challenge, tomato breeding programs must harness the genetic resources found in native populations and wild relatives. Breeding efforts may aim to develop broad-spectrum resistance against the virome. To identify the viruses naturally infecting 19 advanced lines, derived from native tomatoes, high-throughput sequencing (HTS) of small RNAs and confirmation with PCR and RT-PCR were used. Single and mixed infections with tomato mosaic virus (ToMV), tomato golden mosaic virus (ToGMoV), and pepper huasteco yellow vein virus (PHYVV) were detected. The complete consensus genomes of three variants of Mexican ToMV isolates were reconstructed, potentially forming a new ToMV clade with a distinct 3' UTR. The absence of reported mutations associated with resistance-breaking to ToMV suggests that the Tm-1, Tm-2, and Tm-22 genes could theoretically be used to confer resistance. However, the high mutation rates and a 63 nucleotide insertion in the 3' UTR, as well as amino acid mutations in the ORFs encoding 126 KDa, 183 KDa, and MP of Mexican ToMV isolates, suggest that it is necessary to evaluate the capacity of these variants to overcome Tm-1, Tm-2, and Tm-22 resistance genes. This evaluation, along with the characterization of advanced lines using molecular markers linked to these resistant genes, will be addressed in future studies as part of the breeding strategy. This study emphasizes the importance of using HTS for accurate identification and characterization of plant viruses that naturally infect tomato germplasm based on the consensus genome sequences. This study provides crucial insights to select appropriate disease management strategies and resistance genes and guide breeding efforts toward the development of virus-resistant tomato varieties.
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Affiliation(s)
| | - Elizabeth Chiquito-Almanza
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
| | | | | | - José Luis Anaya-López
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Guanajuato 38110, Mexico; (E.G.-P.); (S.V.-R.); (J.C.-K.)
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Gholampour Z, Zakiaghl M, Asquini E, Moser M, Gualandri V, Mehrvar M, Si-Ammour A. Application of High-Throughput Sequencing for Comprehensive Virome Profiling in Grapevines Shows Yellows in Iran. Viruses 2024; 16:204. [PMID: 38399980 PMCID: PMC10891595 DOI: 10.3390/v16020204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
A comprehensive study on the whole spectrum of viruses and viroids in five Iranian grapevine cultivars was carried out using sRNA libraries prepared from phloem tissue. A comparison of two approaches to virus detection from sRNAome data indicated a significant difference in the results and performance of the aligners in viral genome reconstruction. The results showed a complex virome in terms of viral composition, abundance, and richness. Thirteen viruses and viroids were identified in five Iranian grapevine cultivars, among which the grapevine red blotch virus and grapevine satellite virus were detected for the first time in Iranian vineyards. Grapevine leafroll-associated virus 1 (GLRaV1) and grapevine fanleaf virus (GFLV) were highly dominant in the virome. However, their frequency and abundance were somewhat different among grapevine cultivars. The results revealed a mixed infection of GLRaV1/grapevine yellow speckle viroid 1 (GYSVd1) and GFLV/GYSVd1 in grapevines that exhibited yellows and vein banding. We also propose a threshold of 14% of complete reconstruction as an appropriate threshold for detection of grapevine viruses that can be used as indicators for reliable grapevine virome profiling or in quarantine stations and certification programs.
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Affiliation(s)
- Zahra Gholampour
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Mohammad Zakiaghl
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Elisa Asquini
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Mirko Moser
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Valeria Gualandri
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
| | - Mohsen Mehrvar
- Department of Plant Pathology, College of Agriculture, Ferdowsi University of Mashhad, Mashhad 9177948978, Iran; (Z.G.); (M.M.)
| | - Azeddine Si-Ammour
- Research and Innovation Center, Fondazione Edmund Mach, 38098 San Michele All’Adige, Italy; (E.A.); (M.M.); (V.G.)
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Rollin J, Bester R, Brostaux Y, Caglayan K, De Jonghe K, Eichmeier A, Foucart Y, Haegeman A, Koloniuk I, Kominek P, Maree H, Onder S, Posada Céspedes S, Roumi V, Šafářová D, Schumpp O, Ulubas Serce C, Sõmera M, Tamisier L, Vainio E, van der Vlugt RAA, Massart S. Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies. PeerJ 2023; 11:e15816. [PMID: 37601254 PMCID: PMC10439718 DOI: 10.7717/peerj.15816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/10/2023] [Indexed: 08/22/2023] Open
Abstract
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
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Affiliation(s)
- Johan Rollin
- Laboratory of Plant Pathology—TERRA—Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachelle Bester
- Citrus Research International, Matieland, South Africa
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Yves Brostaux
- Laboratory of Statistics, Computer Science and Modelling Applied to Bioengineering, TERRA, Gembloux Agro-Bio Tech, Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Kadriye Caglayan
- Plant Protection Department, Agricultural Faculty, Hatay Mustafa Kemal University, Hatay, Turkey
| | - Kris De Jonghe
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Ales Eichmeier
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czech Republic
| | - Yoika Foucart
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Annelies Haegeman
- Fisheries and Food (ILVO), Plant Sciences Unit, Flanders Research Institute for Agriculture, Merelbeke, Belgium
| | - Igor Koloniuk
- Biology Centre CAS, Ceske Budejovice, Czech Republic
| | | | - Hans Maree
- Citrus Research International, Matieland, South Africa
- Department of Genetics, Stellenbosch University, Matieland, South Africa
| | - Serkan Onder
- Department of Plant Protection, Faculty of Agriculture, Eskişehir Osmangazi University, Eskişehir, Turkey
| | - Susana Posada Céspedes
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | - Vahid Roumi
- Plant Protection Department, Faculty of Agriculture, University of Maragheh, Maragheh, Iran
| | - Dana Šafářová
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | | | - Cigdem Ulubas Serce
- Plant Production and Technologies Department, Ayhan Şahenk Faculty of Agricultural Science and Technologies, Niğde Ömer Halisdemir University, Niğde, Turkey
| | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Lucie Tamisier
- Pathologie Végétale, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Montfavet, France
- GAFL, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Montfavet, France
| | - Eeva Vainio
- Natural Resources Institute Finland, Helsinki, Finland
| | | | - Sebastien Massart
- Laboratory of Plant Pathology—TERRA—Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Zhou T, Gilliam NJ, Li S, Spandau S, Osborn RM, Connor S, Anderson CS, Mariani TJ, Thakar J, Dewhurst S, Mathews DH, Huang L, Sun Y. Generation and Functional Analysis of Defective Viral Genomes during SARS-CoV-2 Infection. mBio 2023; 14:e0025023. [PMID: 37074178 PMCID: PMC10294654 DOI: 10.1128/mbio.00250-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/28/2023] [Indexed: 04/20/2023] Open
Abstract
Defective viral genomes (DVGs) have been identified in many RNA viruses as a major factor influencing antiviral immune response and viral pathogenesis. However, the generation and function of DVGs in SARS-CoV-2 infection are less known. In this study, we elucidated DVG generation in SARS-CoV-2 and its relationship with host antiviral immune response. We observed DVGs ubiquitously from transcriptome sequencing (RNA-seq) data sets of in vitro infections and autopsy lung tissues of COVID-19 patients. Four genomic hot spots were identified for DVG recombination, and RNA secondary structures were suggested to mediate DVG formation. Functionally, bulk and single-cell RNA-seq analysis indicated the interferon (IFN) stimulation of SARS-CoV-2 DVGs. We further applied our criteria to the next-generation sequencing (NGS) data set from a published cohort study and observed a significantly higher amount and frequency of DVG in symptomatic patients than those in asymptomatic patients. Finally, we observed exceptionally diverse DVG populations in one immunosuppressive patient up to 140 days after the first positive test of COVID-19, suggesting for the first time an association between DVGs and persistent viral infections in SARS-CoV-2. Together, our findings strongly suggest a critical role of DVGs in modulating host IFN responses and symptom development, calling for further inquiry into the mechanisms of DVG generation and into how DVGs modulate host responses and infection outcome during SARS-CoV-2 infection. IMPORTANCE Defective viral genomes (DVGs) are generated ubiquitously in many RNA viruses, including SARS-CoV-2. Their interference activity to full-length viruses and IFN stimulation provide the potential for them to be used in novel antiviral therapies and vaccine development. SARS-CoV-2 DVGs are generated through the recombination of two discontinuous genomic fragments by viral polymerase complex, and this recombination is also one of the major mechanisms for the emergence of new coronaviruses. Focusing on the generation and function of SARS-CoV-2 DVGs, these studies identify new hot spots for nonhomologous recombination and strongly suggest that the secondary structures within viral genomes mediate the recombination. Furthermore, these studies provide the first evidence for IFN stimulation activity of de novo DVGs during natural SARS-CoV-2 infection. These findings set up the foundation for further mechanism studies of SARS-CoV-2 recombination and provide evidence to harness the immunostimulatory potential of DVGs in the development of a vaccine and antivirals for SARS-CoV-2.
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Affiliation(s)
- Terry Zhou
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Nora J. Gilliam
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sizhen Li
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Simone Spandau
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - Raven M. Osborn
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Translational Biomedical Sciences PhD Program, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Sarah Connor
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Christopher S. Anderson
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Thomas J. Mariani
- Department of Pediatrics and Center for Children’s Health Research, University of Rochester, Rochester, New York, USA
| | - Juilee Thakar
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Department of Biomedical Genetics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Stephen Dewhurst
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York, USA
| | - Liang Huang
- School of Electrical Engineering & Computer Science, Oregon State University, Corvallis, Oregon, USA
| | - Yan Sun
- Department of Immunology and Microbiology, University of Rochester Medical Center, Rochester, New York, USA
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5
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Sotcheff S, Zhou Y, Yeung J, Sun Y, Johnson JE, Torbett BE, Routh AL. ViReMa: a virus recombination mapper of next-generation sequencing data characterizes diverse recombinant viral nucleic acids. Gigascience 2023; 12:giad009. [PMID: 36939008 PMCID: PMC10025937 DOI: 10.1093/gigascience/giad009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 11/30/2022] [Accepted: 02/03/2023] [Indexed: 03/21/2023] Open
Abstract
BACKGROUND Genetic recombination is a tremendous source of intrahost diversity in viruses and is critical for their ability to rapidly adapt to new environments or fitness challenges. While viruses are routinely characterized using high-throughput sequencing techniques, characterizing the genetic products of recombination in next-generation sequencing data remains a challenge. Viral recombination events can be highly diverse and variable in nature, including simple duplications and deletions, or more complex events such as copy/snap-back recombination, intervirus or intersegment recombination, and insertions of host nucleic acids. Due to the variable mechanisms driving virus recombination and the different selection pressures acting on the progeny, recombination junctions rarely adhere to simple canonical sites or sequences. Furthermore, numerous different events may be present simultaneously in a viral population, yielding a complex mutational landscape. FINDINGS We have previously developed an algorithm called ViReMa (Virus Recombination Mapper) that bootstraps the bowtie short-read aligner to capture and annotate a wide range of recombinant species found within virus populations. Here, we have updated ViReMa to provide an "error density" function designed to accurately detect recombination events in the longer reads now routinely generated by the Illumina platforms and provide output reports for multiple types of recombinant species using standardized formats. We demonstrate the utility and flexibility of ViReMa in different settings to report deletion events in simulated data from Flock House virus, copy-back RNA species in Sendai viruses, short duplication events in HIV, and virus-to-host recombination in an archaeal DNA virus.
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Affiliation(s)
- Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jason Yeung
- John Sealy School of Medicine, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Yan Sun
- Department of Microbiology and Immunology, The University of Rochester Medical Center, Rochester, NY 14642, USA
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA 98105, USA
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98105, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA
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Lombardi EM, Peters J, Jacob L, Power AG. Wild and weedy Hesperis matronalis hosts turnip mosaic virus across heterogeneous landscapes in upstate New York. Virus Res 2023; 323:199011. [PMID: 36511291 DOI: 10.1016/j.virusres.2022.199011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022]
Abstract
Turnip mosaic virus (TuMV) is a widespread and economically important pathogen in agricultural crops and has the widest known host range in the virus family Potyviridae. While management of the virus and its aphid vectors in agricultural fields decreases virus incidence, many alternative wild hosts for TuMV may serve as source populations for crop infection through spillover. Over thirty years ago, research demonstrated that the introduced brassica, Dame's Rocket (Hesperis matronalis) hosts several viruses, including TuMV. Here, we use both enzyme-linked immunosorbent assays (ELISA) and next generation sequencing to document the frequent infection by TuMV of Dame's Rocket, which is common and widespread in disturbed areas around crop fields in upstate New York. Deep sequencing of multiple tissue types of symptomatic hosts indicate that the infection is systemic and causes diagnostic, visible symptoms. In a common garden experiment using host populations from across upstate New York, we found evidence for genetic tolerance to TuMV infection in H. matronalis. Field surveys show that TuMV prevalence varies across populations, but is generally higher in agricultural areas. Examining disease dynamics in this and other common alternative hosts will enhance our understanding of TuMV epidemiology and, more broadly, virus distribution in wild plants.
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Affiliation(s)
- Elizabeth M Lombardi
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA.
| | - Jasmine Peters
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA
| | - Lukin Jacob
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA
| | - Alison G Power
- Cornell University, Department of Ecology and Evolutionary Biology, E145 Corson Hall, Ithaca, New York 14853, USA
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Plant Virus Adaptation to New Hosts: A Multi-scale Approach. Curr Top Microbiol Immunol 2023; 439:167-196. [PMID: 36592246 DOI: 10.1007/978-3-031-15640-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Viruses are studied at each level of biological complexity: from within-cells to ecosystems. The same basic evolutionary forces and principles operate at each level: mutation and recombination, selection, genetic drift, migration, and adaptive trade-offs. Great efforts have been put into understanding each level in great detail, hoping to predict the dynamics of viral population, prevent virus emergence, and manage their spread and virulence. Unfortunately, we are still far from this. To achieve these ambitious goals, we advocate for an integrative perspective of virus evolution. Focusing in plant viruses, we illustrate the pervasiveness of the above-mentioned principles. Beginning at the within-cell level, we describe replication modes, infection bottlenecks, and cellular contagion rates. Next, we move up to the colonization of distal tissues, discussing the fundamental role of random events. Then, we jump beyond the individual host and discuss the link between transmission mode and virulence. Finally, at the community level, we discuss properties of virus-plant infection networks. To close this review we propose the multilayer network theory, in which elements at different layers are connected and submit to their own dynamics that feed across layers, resulting in new emerging properties, as a way to integrate information from the different levels.
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Bhoi TK, Samal I, Majhi PK, Komal J, Mahanta DK, Pradhan AK, Saini V, Nikhil Raj M, Ahmad MA, Behera PP, Ashwini M. Insight into aphid mediated Potato Virus Y transmission: A molecular to bioinformatics prospective. Front Microbiol 2022; 13:1001454. [PMID: 36504828 PMCID: PMC9729956 DOI: 10.3389/fmicb.2022.1001454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/28/2022] [Indexed: 11/25/2022] Open
Abstract
Potato, the world's most popular crop is reported to provide a food source for nearly a billion people. It is prone to a number of biotic stressors that affect yield and quality, out of which Potato Virus Y (PVY) occupies the top position. PVY can be transmitted mechanically and by sap-feeding aphid vectors. The application of insecticide causes an increase in the resistant vector population along with detrimental effects on the environment; genetic resistance and vector-virus control are the two core components for controlling the deadly PVY. Using transcriptomic tools together with differential gene expression and gene discovery, several loci and genes associated with PVY resistance have been widely identified. To combat this virus we must increase our understanding on the molecular response of the PVY-potato plant-aphid interaction and knowledge of genome organization, as well as the function of PVY encoded proteins, genetic diversity, the molecular aspects of PVY transmission by aphids, and transcriptome profiling of PVY infected potato cultivars. Techniques such as molecular and bioinformatics tools can identify and monitor virus transmission. Several studies have been conducted to understand the molecular basis of PVY resistance/susceptibility interactions and their impact on PVY epidemiology by studying the interrelationship between the virus, its vector, and the host plant. This review presents current knowledge of PVY transmission, epidemiology, genome organization, molecular to bioinformatics responses, and its effective management.
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Affiliation(s)
- Tanmaya Kumar Bhoi
- Forest Protection Division, ICFRE-Arid Forest Research Institute (AFRI), Jodhpur, Rajasthan, India
| | - Ipsita Samal
- Department of Entomology, Sri Sri University, Cuttack, Odisha, India
| | - Prasanta Kumar Majhi
- Department of Plant Breeding and Genetics, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - J. Komal
- Department of Entomology, Navsari Agricultural University, Navsari, Gujarat, India,J. Komal
| | - Deepak Kumar Mahanta
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, India,*Correspondence: Deepak Kumar Mahanta
| | - Asit Kumar Pradhan
- Social Science Division, ICAR-National Rice Research Institute (NRRI), Cuttack, Odisha, India
| | - Varun Saini
- Division of Entomology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - M. Nikhil Raj
- Division of Entomology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Mohammad Abbas Ahmad
- Department of Entomology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, India
| | | | - Mangali Ashwini
- Department of Entomology, Navsari Agricultural University, Navsari, Gujarat, India
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9
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Analysis of the Contribution of Intrinsic Disorder in Shaping Potyvirus Genetic Diversity. Viruses 2022; 14:v14091959. [PMID: 36146764 PMCID: PMC9504506 DOI: 10.3390/v14091959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 12/30/2022] Open
Abstract
Intrinsically disordered regions (IDRs) are abundant in the proteome of RNA viruses. The multifunctional properties of these regions are widely documented and their structural flexibility is associated with the low constraint in their amino acid positions. Therefore, from an evolutionary stand point, these regions could have a greater propensity to accumulate non-synonymous mutations (NS) than highly structured regions (ORs, or 'ordered regions'). To address this hypothesis, we compared the distribution of non-synonymous mutations (NS), which we relate here to mutational robustness, in IDRs and ORs in the genome of potyviruses, a major genus of plant viruses. For this purpose, a simulation model was built and used to distinguish a possible selection phenomenon in the biological datasets from randomly generated mutations. We analyzed several short-term experimental evolution datasets. An analysis was also performed on the natural diversity of three different species of potyviruses reflecting their long-term evolution. We observed that the mutational robustness of IDRs is significantly higher than that of ORs. Moreover, the substitutions in the ORs are very constrained by the conservation of the physico-chemical properties of the amino acids. This feature is not found in the IDRs where the substitutions tend to be more random. This reflects the weak structural constraints in these regions, wherein an amino acid polymorphism is naturally conserved. In the course of evolution, potyvirus IDRs and ORs follow different evolutive paths with respect to their mutational robustness. These results have forced the authors to consider the hypothesis that IDRs and their associated amino acid polymorphism could constitute a potential adaptive reservoir.
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Villamor DEV, Keller KE, Martin RR, Tzanetakis IE. Comparison of High Throughput Sequencing to Standard Protocols for Virus Detection in Berry Crops. PLANT DISEASE 2022; 106:518-525. [PMID: 34282931 DOI: 10.1094/pdis-05-21-0949-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We completed a comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium, and eight Rubus) with known virus profiles. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, reverse transcription (RT) PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared with RT-PCR on a wide spectrum of variants and discovery of novel viruses. More importantly, in most cases in which the two protocols showed parallel virus detection, 11 viruses in 16 selections were not consistently detected by both methods at all sampling points. Based on these data, we propose a testing requirement of four sampling times over two growing seasons for berry and potentially other crops, to ensure that no virus remains undetected independent of titer, distribution, or other virus-virus or virus-host interactions.
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Affiliation(s)
- D E V Villamor
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - K E Keller
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - R R Martin
- U.S. Department of Agriculture Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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11
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Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops. Microorganisms 2021; 9:microorganisms9051043. [PMID: 34066188 PMCID: PMC8150983 DOI: 10.3390/microorganisms9051043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
We used high-throughput sequencing to identify viruses on tomato samples showing virus-like symptoms. Samples were collected from crops in the Iberian Peninsula. Either total RNA or double-stranded RNA (dsRNA) were used as starting material to build the cDNA libraries. In total, seven virus species were identified, with pepino mosaic virus being the most abundant one. The dsRNA input provided better coverage and read depth but missed one virus species compared with the total RNA input. By performing in silico analyses, we determined a minimum sequencing depth per sample of 0.2 and 1.5 million reads for dsRNA and rRNA-depleted total RNA inputs, respectively, to detect even the less abundant viruses. Primers and TaqMan probes targeting conserved regions in the viral genomes were designed and/or used for virus detection; all viruses were detected by qRT-PCR/RT-PCR in individual samples, with all except one sample showing mixed infections. Three virus species (Olive latent virus 1, Lettuce ring necrosis virus and Tomato fruit blotch virus) are herein reported for the first time in tomato crops in Spain.
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12
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Kutnjak D, Tamisier L, Adams I, Boonham N, Candresse T, Chiumenti M, De Jonghe K, Kreuze JF, Lefebvre M, Silva G, Malapi-Wight M, Margaria P, Mavrič Pleško I, McGreig S, Miozzi L, Remenant B, Reynard JS, Rollin J, Rott M, Schumpp O, Massart S, Haegeman A. A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses. Microorganisms 2021; 9:841. [PMID: 33920047 PMCID: PMC8071028 DOI: 10.3390/microorganisms9040841] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing (HTS) technologies have become indispensable tools assisting plant virus diagnostics and research thanks to their ability to detect any plant virus in a sample without prior knowledge. As HTS technologies are heavily relying on bioinformatics analysis of the huge amount of generated sequences, it is of utmost importance that researchers can rely on efficient and reliable bioinformatic tools and can understand the principles, advantages, and disadvantages of the tools used. Here, we present a critical overview of the steps involved in HTS as employed for plant virus detection and virome characterization. We start from sample preparation and nucleic acid extraction as appropriate to the chosen HTS strategy, which is followed by basic data analysis requirements, an extensive overview of the in-depth data processing options, and taxonomic classification of viral sequences detected. By presenting the bioinformatic tools and a detailed overview of the consecutive steps that can be used to implement a well-structured HTS data analysis in an easy and accessible way, this paper is targeted at both beginners and expert scientists engaging in HTS plant virome projects.
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Affiliation(s)
- Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Lucie Tamisier
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Ian Adams
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Neil Boonham
- Institute for Agri-Food Research and Innovation, Newcastle University, King’s Rd, Newcastle Upon Tyne NE1 7RU, UK;
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Michela Chiumenti
- Institute for Sustainable Plant Protection, National Research Council, Via Amendola, 122/D, 70126 Bari, Italy;
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
| | - Jan F. Kreuze
- International Potato Center (CIP), Avenida la Molina 1895, La Molina, Lima 15023, Peru;
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, INRA, University of Bordeaux, 33140 Villenave d’Ornon, France; (T.C.); (M.L.)
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK;
| | - Martha Malapi-Wight
- Biotechnology Risk Analysis Programs, Biotechnology Regulatory Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Riverdale, MD 20737, USA;
| | - Paolo Margaria
- Leibniz Institute-DSMZ, Inhoffenstrasse 7b, 38124 Braunschweig, Germany;
| | - Irena Mavrič Pleško
- Agricultural Institute of Slovenia, Hacquetova Ulica 17, 1000 Ljubljana, Slovenia;
| | - Sam McGreig
- Fera Science Limited, York YO41 1LZ, UK; (I.A.); (S.M.)
| | - Laura Miozzi
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy;
| | - Benoit Remenant
- ANSES Plant Health Laboratory, 7 Rue Jean Dixméras, CEDEX 01, 49044 Angers, France;
| | | | - Johan Rollin
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
- DNAVision, 6041 Charleroi, Belgium
| | - Mike Rott
- Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Rd, North Saanich, BC V8L 1H3, Canada;
| | - Olivier Schumpp
- Agroscope, Route de Duillier 50, 1260 Nyon, Switzerland; (J.-S.R.); (O.S.)
| | - Sébastien Massart
- Plant Pathology Laboratory, Université de Liège, Gembloux Agro-Bio Tech, TERRA, Passage des Déportés, 2, 5030 Gembloux, Belgium; (L.T.); (J.R.); (S.M.)
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (A.H.)
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13
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Vetukuri RR, Kalyandurg PB, Saripella GV, Sen D, Gil JF, Lukhovitskaya NI, Grenville-Briggs LJ, Savenkov EI. Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species. Arch Virol 2020; 165:2953-2959. [PMID: 33040310 PMCID: PMC7588395 DOI: 10.1007/s00705-020-04832-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/01/2020] [Indexed: 10/31/2022]
Abstract
Chrysanthemum virus B encodes a multifunctional p12 protein that acts as a transcriptional activator in the nucleus and as a suppressor of RNA silencing in the cytoplasm. Here, we investigated the impact of p12 on accumulation of major classes of small RNAs (sRNAs). The results show dramatic changes in the sRNA profiles characterised by an overall reduction in sRNA accumulation, changes in the pattern of size distribution of canonical siRNAs and in the ratio between sense and antisense strands, lower abundance of siRNAs with a U residue at the 5'-terminus, and changes in the expression of certain miRNAs, most of which were downregulated.
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Affiliation(s)
- Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Pruthvi B Kalyandurg
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden
| | | | - Diya Sen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Jose Fernando Gil
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden
| | - Nina I Lukhovitskaya
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden.,Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Laura J Grenville-Briggs
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eugene I Savenkov
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Linnean Center for Plant Biology, Uppsala, Sweden.
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14
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Nigam D, LaTourrette K, Garcia-Ruiz H. Mutations in virus-derived small RNAs. Sci Rep 2020; 10:9540. [PMID: 32533016 PMCID: PMC7293216 DOI: 10.1038/s41598-020-66374-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/18/2020] [Indexed: 02/03/2023] Open
Abstract
RNA viruses exist as populations of genome variants. Virus-infected plants accumulate 21–24 nucleotide small interfering RNAs (siRNAs) derived from viral RNA (virus-derived siRNAs) through gene silencing. This paper describes the profile of mutations in virus-derived siRNAs for three members of the family Potyviridae: Turnip mosaic virus (TuMV), Papaya ringspot virus (PRSV) and Wheat streak mosaic virus (WSMV). For TuMV in Arabidopsis thaliana, profiles were obtained for mechanically inoculated rosette leaves and systemically infected cauline leaves and inflorescence. Results are consistent with selection pressure on the viral genome imposed by local and systemic movement. By genetically removing gene silencing in the plant and silencing suppression in the virus, our results showed that antiviral gene silencing imposes selection in viral populations. Mutations in siRNAs derived from a PRSV coat protein transgene in the absence of virus replication showed the contribution of cellular RNA-dependent RNA polymerases to the generation of mutations in virus-derived siRNAs. Collectively, results are consistent with two sources of mutations in virus-derived siRNAs: viral RNA-dependent RNA polymerases responsible for virus replication and cellular RNA-dependent RNA polymerases responsible for gene silencing amplification.
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Affiliation(s)
- Deepti Nigam
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Nebraska, United States of America
| | - Katherine LaTourrette
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Nebraska, United States of America
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Nebraska, United States of America.
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15
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Della Bartola M, Byrne S, Mullins E. Characterization of Potato Virus Y Isolates and Assessment of Nanopore Sequencing to Detect and Genotype Potato Viruses. Viruses 2020; 12:E478. [PMID: 32340210 PMCID: PMC7232445 DOI: 10.3390/v12040478] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 02/06/2023] Open
Abstract
Potato virus Y (PVY) is the most economically important virus infecting cultivated potato (Solanum tuberosum L.). Accurate diagnosis is crucial to regulate the trade of tubers and for the sanitary selection of plant material for propagation. However, high genetic diversity of PVY represents a challenge for the detection and classification of isolates. Here, the diversity of Irish PVY isolates from a germplasm collection and commercial sites was investigated using conventional molecular and serological techniques. Recombinant PVY isolates were prevalent, with PVYNTNa being the predominant genotype. In addition, we evaluated Nanopore sequencing to detect and reconstruct the whole genome sequence of four viruses (PVY, PVX, PVS, PLRV) and five PVY genotypes in a subset of eight potato plants. De novo assembly of Nanopore sequencing reads produced single contigs covering greater than 90% of the viral genome and sharing greater than 99.5% identity to the consensus sequences obtained with Illumina sequencing. Interestingly, single near full genome contigs were obtained for different isolates of PVY co-infecting the same plant. Mapping reads to available reference viral genomes enabled us to generate near complete genome sequences sharing greater than 99.90% identity to the Illumina-derived consensus. This is the first report describing the use of Oxford Nanopore's MinION to detect and genotype potato viruses. We reconstructed the genome of PVY and other RNA viruses; indicating the technologies potential for virus detection in potato production systems, and for the study of genetic diversity of highly heterogeneous viruses such as PVY.
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Affiliation(s)
| | | | - Ewen Mullins
- Crop Science Department, Teagasc, Oak Park, R93XE12 Carlow, Ireland; (M.D.B.); (S.B.)
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16
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Gibbs AJ, Hajizadeh M, Ohshima K, Jones RA. The Potyviruses: An Evolutionary Synthesis Is Emerging. Viruses 2020; 12:E132. [PMID: 31979056 PMCID: PMC7077269 DOI: 10.3390/v12020132] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/28/2022] Open
Abstract
In this review, encouraged by the dictum of Theodosius Dobzhansky that "Nothing in biology makes sense except in the light of evolution", we outline the likely evolutionary pathways that have resulted in the observed similarities and differences of the extant molecules, biology, distribution, etc. of the potyvirids and, especially, its largest genus, the potyviruses. The potyvirids are a family of plant-infecting RNA-genome viruses. They had a single polyphyletic origin, and all share at least three of their genes (i.e., the helicase region of their CI protein, the RdRp region of their NIb protein and their coat protein) with other viruses which are otherwise unrelated. Potyvirids fall into 11 genera of which the potyviruses, the largest, include more than 150 distinct viruses found worldwide. The first potyvirus probably originated 15,000-30,000 years ago, in a Eurasian grass host, by acquiring crucial changes to its coat protein and HC-Pro protein, which enabled it to be transmitted by migrating host-seeking aphids. All potyviruses are aphid-borne and, in nature, infect discreet sets of monocotyledonous or eudicotyledonous angiosperms. All potyvirus genomes are under negative selection; the HC-Pro, CP, Nia, and NIb genes are most strongly selected, and the PIPO gene least, but there are overriding virus specific differences; for example, all turnip mosaic virus genes are more strongly conserved than those of potato virus Y. Estimates of dN/dS (ω) indicate whether potyvirus populations have been evolving as one or more subpopulations and could be used to help define species boundaries. Recombinants are common in many potyvirus populations (20%-64% in five examined), but recombination seems to be an uncommon speciation mechanism as, of 149 distinct potyviruses, only two were clear recombinants. Human activities, especially trade and farming, have fostered and spread both potyviruses and their aphid vectors throughout the world, especially over the past five centuries. The world distribution of potyviruses, especially those found on islands, indicates that potyviruses may be more frequently or effectively transmitted by seed than experimental tests suggest. Only two meta-genomic potyviruses have been recorded from animal samples, and both are probably contaminants.
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Affiliation(s)
- Adrian J. Gibbs
- Emeritus Faculty, Australian National University, Canberra, ACT 2601, Australia
| | - Mohammad Hajizadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
| | - Kazusato Ohshima
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga 840-8502, Japan;
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-2410 Korimoto, Kagoshima 890-0065, Japan
| | - Roger A.C. Jones
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
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17
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Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches. J Virol 2019; 94:JVI.01462-19. [PMID: 31597769 DOI: 10.1128/jvi.01462-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/01/2019] [Indexed: 12/29/2022] Open
Abstract
Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components of ecosystems, there is a need to explore the diversity and richness of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and virion-associated nucleic acids (VANA), have been used and compared here for the description of the virome of complex plant pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. A novel bioinformatics strategy was used to assess viral richness not only at the family level but also by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. A large viral diversity dominated by novel dsRNA viruses was detected in all sites, while a large between-site variability limited the ability to draw a clear conclusion on the impact of cultivation. A trend for a higher diversity of dsRNA viruses was nevertheless detected in unmanaged sites (118 versus 77 unique OTUs). The dsRNA-based approach consistently revealed a broader and more comprehensive diversity for RNA viruses than the VANA approach, whatever the assessment criterion. In addition, dissimilarity analyses indicated both approaches to be largely reproducible but not necessarily convergent. These findings illustrate features of phytoviromes in various ecosystems and a novel strategy for precise virus richness estimation. These results allow us to reason methodological choices in phytovirome studies and likely in other virome studies where RNA viruses are the focal taxa.IMPORTANCE There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them but also on the comparative performance-methodological approaches for their study. We used and compared two viral sequence enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA), for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining operational taxonomic units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing us to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is recommended because it consistently provided a more comprehensive description of the analyzed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.
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18
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Stare T, Ramšak Ž, Križnik M, Gruden K. Multiomics analysis of tolerant interaction of potato with potato virus Y. Sci Data 2019; 6:250. [PMID: 31673114 PMCID: PMC6823367 DOI: 10.1038/s41597-019-0216-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/11/2019] [Indexed: 12/21/2022] Open
Abstract
Potato virus Y (PVY) is the most economically important viral pathogen of potato worldwide. Different potato cultivars react to the pathogen differently, resulting in resistant, tolerant or disease outcome of the interaction. Here we focus on tolerant interaction between potato cv. Désirée and PVYNTN. To capture the response in its full complexity, we analyzed the dynamic changes on multiple molecular levels, including transcriptomics, sRNAomics, degradomics, proteomics and hormonomics. The analysis was complemented by the measurements of viral accumulation, photosynthetic activity and phenotypisation of the symptoms. Besides cv. Désirée we also studied its transgenic counterpart depleted for the accumulation of salicylic acid (NahG-Désirée). This multiomics analysis provides better insights into the mechanisms leading to tolerant response of potato to viral infection and can be used as a base in further studies of plant immunity regulation.
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Affiliation(s)
- Tjaša Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Jamova 39, 1000, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
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19
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Vivek AT, Zahra S, Kumar S. From current knowledge to best practice: A primer on viral diagnostics using deep sequencing of virus-derived small interfering RNAs (vsiRNAs) in infected plants. Methods 2019; 183:30-37. [PMID: 31669354 DOI: 10.1016/j.ymeth.2019.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 01/05/2023] Open
Abstract
Plants have evolved many defense strategies for combating viral infections. One major surveillance strategy adopted by them is manipulating viral sequences to generate distinct small RNA products via Dicer-like enzymes (DCL), and thereby restricting virus multiplication through the RNA interference (RNAi) mechanism. The power of high-throughput sequencing technologies, with diverse computational tools to handle small RNA sequencing (sRNA-Seq) data, bestows unprecedented opportunities to answer fundamental questions in plant virology. Here, we present some basic concepts of virus-derived, small interfering RNA (vsiRNA) biogenesis in plants, optimization strategies, caveats, and best practices for efficient discovery and diagnosis of known as well as novel plant viruses/viroids using deep sequencing of small RNA (sRNA) pools.
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Affiliation(s)
- A T Vivek
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shafaque Zahra
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India.
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20
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Fuentes S, Jones RAC, Matsuoka H, Ohshima K, Kreuze J, Gibbs AJ. Potato virus Y; the Andean connection. Virus Evol 2019; 5:vez037. [PMID: 31559020 PMCID: PMC6755682 DOI: 10.1093/ve/vez037] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Potato virus Y (PVY) causes disease in potatoes and other solanaceous crops. The appearance of its necrogenic strains in the 1980s made it the most economically important virus of potatoes. We report the isolation and genomic sequences of 32 Peruvian isolates of PVY which, together with 428 published PVY genomic sequences, gave an alignment of 460 sequences. Of these 190 (41%) were non-recombinant, and 162 of these provided a dated phylogeny, that corresponds well with the likely history of PVY, and show that PVY originated in South America which is where potatoes were first domesticated. The most basal divergences of the PVY population produced the N and C: O phylogroups; the origin of the N phylogroup is clearly Andean, but that of the O and C phylogroups is unknown, although they may have been first to establish in European crops. The current PVY population originated around 156 CE. PVY was probably first taken from South America to Europe in the 16th century in tubers. Most of the present PVY diversity emerged in the second half of the 19th century, after the Phytophthora infestans epidemics of the mid-19th century destroyed the European crop and stimulated potato breeding. Imported breeding lines were shared, and there was no quarantine. The early O population was joined later by N phylogroup isolates and their recombinants generated the R1 and R2 populations of damaging necrogenic strains. Our dating study has confirmed that human activity has dominated the phylodynamics of PVY for the last two millennia.
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Affiliation(s)
- Segundo Fuentes
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Roger A C Jones
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
- Institute of Agriculture, University of Western Australia, 35 Stirling Highway, Crawley, WA
| | - Hiroki Matsuoka
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
| | - Kazusato Ohshima
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA, Australia
| | - Jan Kreuze
- Crop and System Sciences Division, International Potato Center (CIP), Apartado 1558, Lima 12, Peru
| | - Adrian J Gibbs
- Laboratory of Plant Virology, Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, 1-banchi, Honjo-machi, Saga, Japan
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21
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Knierim D, Menzel W, Winter S. Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences. PLoS One 2019; 14:e0216713. [PMID: 31071169 PMCID: PMC6542260 DOI: 10.1371/journal.pone.0216713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/26/2019] [Indexed: 12/21/2022] Open
Abstract
Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus.
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Affiliation(s)
- Dennis Knierim
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
| | - Wulf Menzel
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
- * E-mail:
| | - Stephan Winter
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
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22
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Villamor DEV, Ho T, Al Rwahnih M, Martin RR, Tzanetakis IE. High Throughput Sequencing For Plant Virus Detection and Discovery. PHYTOPATHOLOGY 2019; 109:716-725. [PMID: 30801236 DOI: 10.1094/phyto-07-18-0257-rvw] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists' utility in their research.
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Affiliation(s)
- D E V Villamor
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - T Ho
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
| | - M Al Rwahnih
- 2 Department of Plant Pathology, University of California, Davis 95616; and
| | - R R Martin
- 3 Horticulture Crops Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Corvallis, OR 97330
| | - I E Tzanetakis
- 1 Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701
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23
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Chikh-Ali M, Rodriguez-Rodriguez M, Green KJ, Kim DJ, Chung SM, Kuhl JC, Karasev AV. Identification and Molecular Characterization of Recombinant Potato Virus Y (PVY) in Potato from South Korea, PVY NTN Strain. PLANT DISEASE 2019; 103:137-142. [PMID: 30412456 DOI: 10.1094/pdis-05-18-0715-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Potato is an important source of food in South Korea, and viruses represent a significant threat to sustainable and profitable potato production. However, information about viruses affecting the potato crop in South Korea is limited. In 2017, potato plants of five cultivars exhibiting foliar mosaic, crinkling, and mottle were collected in two seed potato production areas, in Gangwon-do and Jeollabuk-do Provinces, and subjected to virus testing and characterization. Potato virus Y (PVY) was found associated with mosaic symptoms, and samples were characterized using reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing. All analyzed PVY-positive samples were found to represent the same recombinant PVY strain: PVYNTN. Three PVY isolates were subjected to whole genome sequencing using overlapping RT-PCR fragments and Sanger methodology, and all three were confirmed to represent strain PVYNTNa after a recombination analysis of the complete genomes. In phylogenetic analysis, the three South Korean isolates were placed most closely to several PVYNTNa isolates reported from Japan and Vietnam, suggesting a common source of infection. This is the first report and complete molecular characterization of a PVYNTN strain present in the country, and because this strain induces tuber necrotic ringspot disease in susceptible cultivars of potato, appropriate management tools need to be implemented to mitigate potential tuber quality losses.
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Affiliation(s)
- Mohamad Chikh-Ali
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, 83844-2329
| | | | - Kelsie J Green
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, 83844-2329
| | - Dong-Jun Kim
- Inno Seed Co., Dong-myeon Chuncheon-si Gangwon-do, 24210, South Korea
| | - Sang-Min Chung
- Life Science Department, Dongguk University-Seoul, Seoul, 04620, South Korea
| | - Joseph C Kuhl
- Department of Plant Science, University of Idaho, Moscow, 83844-2333
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, 83844-2329, and Bioinformatics and Computational Biology Program, University of Idaho, Moscow, 83844-3050
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24
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Pooggin MM. Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization. Front Microbiol 2018; 9:2779. [PMID: 30524398 PMCID: PMC6256188 DOI: 10.3389/fmicb.2018.02779] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/30/2018] [Indexed: 11/13/2022] Open
Abstract
RNA interference (RNAi)-based antiviral defense generates small interfering RNAs that represent the entire genome sequences of both RNA and DNA viruses as well as viroids and viral satellites. Therefore, deep sequencing and bioinformatics analysis of small RNA population (small RNA-ome) allows not only for universal virus detection and genome reconstruction but also for complete virome reconstruction in mixed infections. Viral infections (like other stress factors) can also perturb the RNAi and gene silencing pathways regulating endogenous gene expression and repressing transposons and host genome-integrated endogenous viral elements which can potentially be released from the genome and contribute to disease. This review describes the application of small RNA-omics for virus detection, virome reconstruction and antiviral defense characterization in cultivated and non-cultivated plants. Reviewing available evidence from a large and ever growing number of studies of naturally or experimentally infected hosts revealed that all families of land plant viruses, their satellites and viroids spawn characteristic small RNAs which can be assembled into contigs of sufficient length for virus, satellite or viroid identification and for exhaustive reconstruction of complex viromes. Moreover, the small RNA size, polarity and hotspot profiles reflect virome interactions with the plant RNAi machinery and allow to distinguish between silent endogenous viral elements and their replicating episomal counterparts. Models for the biogenesis and functions of small interfering RNAs derived from all types of RNA and DNA viruses, satellites and viroids as well as endogenous viral elements are presented and discussed.
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Affiliation(s)
- Mikhail M. Pooggin
- Institut National de la Recherche Agronomique, UMR BGPI, Montpellier, France
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25
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Xu T, Lei L, Shi J, Wang X, Chen J, Xue M, Sun S, Zhan B, Xia Z, Jiang N, Zhou T, Lai J, Fan Z. Characterization of maize translational responses to sugarcane mosaic virus infection. Virus Res 2018; 259:97-107. [PMID: 30355529 DOI: 10.1016/j.virusres.2018.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Revised: 10/14/2018] [Accepted: 10/18/2018] [Indexed: 10/28/2022]
Abstract
Sugarcane mosaic virus (SCMV) frequently causes dramatic losses in maize production as the main pathogen of maize dwarf mosaic disease. It is important to understand the translational responses in maize to SCMV infection since viruses have to recruit host translation apparatus to express their proteins. However, due to technical limitations, research on virus translation lags far behind that on transcription. Here, we studied the relationship between systemic symptom expression and virus accumulation and found that both SCMV RNA and proteins accumulated rapidly during the systemic infection process in which varying degrees of chlorosis to mosaic symptoms developed on non-inoculated leaves. In addition, we applied ribosome profiling, which couples polysomal mRNA isolation with high-throughput sequencing, on the symptomatic leaves infected with SCMV to unravel the translational responses of maize to viral infection on a genome-wide scale. The results showed that only the genomic positive-stranded RNA of SCMV was involved in translation, and SCMV only occupied a small amount of translational resources of host plant at the early stage of infection. Further analyses on a global gene expression and gene ontology (GO) enrichment revealed that photosynthesis and metabolism were dramatically repressed at both transcriptional and translational levels. Altogether, our results laid a foundation for dissecting the molecular mechanism of plant translational responses to viral infection.
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Affiliation(s)
- Tengzhi Xu
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Lei Lei
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China; Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Junpeng Shi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Xin Wang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Mingshuo Xue
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Silong Sun
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Binhui Zhan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Zihao Xia
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Na Jiang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Tao Zhou
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, PR China
| | - Zaifeng Fan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Pest Monitoring and Green Management-MOA, China Agricultural University, Beijing 100193, PR China.
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26
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Turco S, Golyaev V, Seguin J, Gilli C, Farinelli L, Boller T, Schumpp O, Pooggin MM. Small RNA-Omics for Virome Reconstruction and Antiviral Defense Characterization in Mixed Infections of Cultivated Solanum Plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:707-723. [PMID: 29424662 DOI: 10.1094/mpmi-12-17-0301-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In plants, RNA silencing-based antiviral defense generates viral small RNAs (sRNAs) faithfully representing the viral genomes. We employed sRNA sequencing and bioinformatics (sRNA-omics) to characterize antiviral defense and to reconstruct the full genomic sequences and their variants in the evolving viral quasispecies in cultivated solanaceous plants carrying mixed infections. In naturally infected Solanum tuberosum (potato), one case study revealed a virome comprising Potato virus Y (genus Potyvirus) and Potato virus X (genus Potexvirus), which was reconstructed by de novo-assembling separate genome-size sRNA contigs. Another case study revealed a virome comprising NTN and O strains of Potato virus Y, whose sRNAs assembled in chimeric contigs, which could be disentangled on the basis of reference genome sequences. Both viromes were stable in vegetative potato progeny. In a cross-protection trial of Solanum lycopersicum (tomato), the supposedly protective mild strain CH2 of Pepino mosaic virus (genus Potexvirus) was tested for protection against strain LP of the same virus. Reciprocal mechanical inoculations eventually resulted in co-infection of all individual plants with CH2 and LP strains, reconstructed as separate sRNA contigs. LP invasions into CH2-preinfected plants and vice versa were accompanied by alterations of consensus genome sequences in viral quasispecies, indicating a potential risk of cross-protection measures. Additionally, the study also revealed, by reconstruction from sRNAs, the presence of the mechanically nontransmissible Southern tomato virus (genus Amalgavirus) in some plants. Our in-depth analysis of sRNA sizes, 5'-nucleotide frequencies and hotspot maps revealed similarities in sRNA-generating mechanisms in potato and tomato, differential silencing responses to virome components and potential for sRNA-directed cross-targeting between viral strains which could not, however, prevent the formation of stable viromes.
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Affiliation(s)
- Silvia Turco
- 1 Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland
| | - Victor Golyaev
- 1 Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland
| | - Jonathan Seguin
- 1 Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland
| | | | | | - Thomas Boller
- 1 Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland
| | | | - Mikhail M Pooggin
- 1 Department of Environmental Sciences, Botany, Zurich-Basel Plant Science Center, University of Basel, Hebelstrasse 1, 4056 Basel, Switzerland
- 5 INRA, UMR BGPI, 34398 Montpellier, France
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27
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Gutiérrez-Aguirre I, Kutnjak D, Rački N, Rupar M, Ravnikar M. Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples. Methods Mol Biol 2018; 1746:63-75. [PMID: 29492887 DOI: 10.1007/978-1-4939-7683-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Viruses exist in aquatic media and many of them use this media as transmission route. Next-generation sequencing (NGS) technologies have opened new doors in virus research, allowing also to reveal a hidden diversity of viral species in aquatic environments. Not surprisingly, many of the newly discovered viruses are found in environmental fresh and marine waters. One of the problems in virome research can be the low amount of viral nucleic acids present in the sample in contrast to the background ones (host, eukaryotic, prokaryotic, environmental). Therefore, virus enrichment prior to NGS is necessary in many cases. In water samples, an added problem resides in the low concentration of viruses typically present in aquatic media. Different concentration strategies have been used to overcome such limitations. CIM monoliths are a new generation of chromatographic supports that due to their particular structural characteristics are very efficient in concentration and purification of viruses. In this chapter, we describe the use of CIM monolithic chromatography for sample preparation step in NGS studies targeting viruses in fresh or marine water. The step-by-step protocol will include a case study where CIM concentration was used to study the virome of a wastewater sample using NGS.
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Affiliation(s)
- Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Nejc Rački
- Lek Pharmaceuticals d.d., Menges, Slovenia
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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28
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Križnik M, Petek M, Dobnik D, Ramšak Ž, Baebler Š, Pollmann S, Kreuze JF, Žel J, Gruden K. Salicylic Acid Perturbs sRNA-Gibberellin Regulatory Network in Immune Response of Potato to Potato virus Y Infection. FRONTIERS IN PLANT SCIENCE 2017; 8:2192. [PMID: 29312421 PMCID: PMC5744193 DOI: 10.3389/fpls.2017.02192] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/12/2017] [Indexed: 05/19/2023]
Abstract
Potato virus Y is the most economically important potato viral pathogen. We aimed at unraveling the roles of small RNAs (sRNAs) in the complex immune signaling network controlling the establishment of tolerant response of potato cv. Désirée to the virus. We constructed a sRNA regulatory network connecting sRNAs and their targets to link sRNA level responses to physiological processes. We discovered an interesting novel sRNAs-gibberellin regulatory circuit being activated as early as 3 days post inoculation (dpi) before viral multiplication can be detected. Two endogenous sRNAs, miR167 and phasiRNA931 were predicted to regulate gibberellin biosynthesis genes GA20-oxidase and GA3-oxidase. The increased expression of phasiRNA931 was also reflected in decreased levels of GA3-oxidase transcripts. Moreover, decreased concentration of gibberellin confirmed this regulation. The functional relation between lower activity of gibberellin signaling and reduced disease severity was previously confirmed in Arabidopsis-virus interaction using knockout mutants. We further showed that this regulation is salicylic acid-dependent as the response of sRNA network was attenuated in salicylic acid-depleted transgenic counterpart NahG-Désirée expressing severe disease symptoms. Besides downregulation of gibberellin signaling, regulation of immune receptor transcripts by miR6022 as well as upregulation of miR164, miR167, miR169, miR171, miR319, miR390, and miR393 in tolerant Désirée, revealed striking similarities to responses observed in mutualistic symbiotic interactions. The intertwining of different regulatory networks revealed, shows how developmental signaling, disease symptom development, and stress signaling can be balanced.
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Affiliation(s)
- Maja Križnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- JoŽef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Marko Petek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid UPM - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Jan F. Kreuze
- Global Program of Integrated Crop and Systems Research, International Potato Center (CIP), Lima, Peru
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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29
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Pecman A, Kutnjak D, Gutiérrez-Aguirre I, Adams I, Fox A, Boonham N, Ravnikar M. Next Generation Sequencing for Detection and Discovery of Plant Viruses and Viroids: Comparison of Two Approaches. Front Microbiol 2017; 8:1998. [PMID: 29081770 PMCID: PMC5645528 DOI: 10.3389/fmicb.2017.01998] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/28/2017] [Indexed: 01/19/2023] Open
Abstract
Next generation sequencing (NGS) technologies are becoming routinely employed in different fields of virus research. Different sequencing platforms and sample preparation approaches, in the laboratories worldwide, contributed to a revolution in detection and discovery of plant viruses and viroids. In this work, we are presenting the comparison of two RNA sequence inputs (small RNAs vs. ribosomal RNA depleted total RNA) for the detection of plant viruses by Illumina sequencing. This comparison includes several viruses, which differ in genome organization and viroids from both known families. The results demonstrate the ability for detection and identification of a wide array of known plant viruses/viroids in the tested samples by both approaches. In general, yield of viral sequences was dependent on viral genome organization and the amount of viral reads in the data. A putative novel Cytorhabdovirus, discovered in this study, was only detected by analysing the data generated from ribosomal RNA depleted total RNA and not from the small RNA dataset, due to the low number of short reads in the latter. On the other hand, for the viruses/viroids under study, the results showed higher yields of viral sequences in small RNA pool for viroids and viruses with no RNA replicative intermediates (single stranded DNA viruses).
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Affiliation(s)
- Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ian Adams
- Fera Science Ltd., York, United Kingdom
| | | | - Neil Boonham
- Fera Science Ltd., York, United Kingdom
- Institute for Agri-Food Research and Innovation, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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30
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Li L, Andika IB, Xu Y, Zhang Y, Xin X, Hu L, Sun Z, Hong G, Chen Y, Yan F, Yang J, Li J, Chen J. Differential Characteristics of Viral siRNAs between Leaves and Roots of Wheat Plants Naturally Infected with Wheat Yellow Mosaic Virus, a Soil-Borne Virus. Front Microbiol 2017; 8:1802. [PMID: 28979249 PMCID: PMC5611437 DOI: 10.3389/fmicb.2017.01802] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/05/2017] [Indexed: 01/09/2023] Open
Abstract
RNA silencing is an important innate antiviral defense in plants. Soil-borne plant viruses naturally infect roots via soil-inhabiting vectors, but it is unclear how antiviral RNA silencing responds to virus infection in this particular tissue. In this study, viral small interfering RNA (siRNA) profiles from leaves and roots of wheat plants naturally infected with a soil-borne virus, wheat yellow mosaic virus (WYMV, genus Bymovirus), were analyzed by deep sequencing. WYMV siRNAs were much more abundant in roots than leaves, which was positively correlated with the accumulation of viral RNA. WYMV siRNAs in leaves and roots were predominantly 21- and 22-nt long and equally derived from the positive- and negative-strands of the viral genome. WYMV siRNAs from leaves and roots differed in distribution pattern along the viral genome. Interestingly, compared to siRNAs from leaves (and most other reports), those from roots obviously had a lower A/U bias at the 5'-terminal nucleotide. Moreover, the expression of Dicer-like genes upon WYMV infection were differently regulated between leaves and roots. Our data suggest that RNA silencing in roots may operate differently than in leaves against soil-borne virus invasion.
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Affiliation(s)
- Linying Li
- College of Plant Protection, Nanjing Agricultural UniversityNanjing, China
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Ida Bagus Andika
- Group of Plant-Microbe Interactions, Institute of Plant Science and Resources, Okayama UniversityKurashiki, Japan
| | - Yu Xu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yan Zhang
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xiangqi Xin
- Institute of Plant Protection, Shandong Academy of Agricultural SciencesJinan, China
| | - Lifeng Hu
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Zongtao Sun
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Gaojie Hong
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yang Chen
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Fei Yan
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jian Yang
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Junmin Li
- College of Plant Protection, Nanjing Agricultural UniversityNanjing, China
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jianping Chen
- College of Plant Protection, Nanjing Agricultural UniversityNanjing, China
- The State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
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31
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Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y. J Virol 2017; 91:JVI.00690-17. [PMID: 28592544 PMCID: PMC5533922 DOI: 10.1128/jvi.00690-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/28/2017] [Indexed: 11/20/2022] Open
Abstract
RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.
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32
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Krajacic M, Ravnikar M, Štrancar A, Gutiérrez-Aguirre I. Application of monolithic chromatographic supports in virus research. Electrophoresis 2017; 38:2827-2836. [DOI: 10.1002/elps.201700152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Mladen Krajacic
- Department of Biology; Faculty of Science; University of Zagreb; Zagreb Croatia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology; National Institute of Biology; Ljubljana Slovenia
| | | | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology; National Institute of Biology; Ljubljana Slovenia
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33
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Jo Y, Choi H, Kim SM, Kim SL, Lee BC, Cho WK. The pepper virome: natural co-infection of diverse viruses and their quasispecies. BMC Genomics 2017; 18:453. [PMID: 28595635 PMCID: PMC5465472 DOI: 10.1186/s12864-017-3838-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 06/01/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host. RESULTS Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host. CONCLUSIONS Taken together, we provide the first evidence that the host plant resistant to viruses has an unrevealed antiviral system, affecting viral quasispecies, not replication.
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Affiliation(s)
- Yeonhwa Jo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hoseong Choi
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Min Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Sun-Lim Kim
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Bong Choon Lee
- Crop Foundation Division, National Institute of Crop Science, RDA, Wanju, 55365, South Korea
| | - Won Kyong Cho
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,The Taejin Genome Institute, Gadam-gil 61, Hoeongseong, 25239, Republic of Korea.
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Xu C, Sun X, Taylor A, Jiao C, Xu Y, Cai X, Wang X, Ge C, Pan G, Wang Q, Fei Z, Wang Q. Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing. J Virol 2017; 91:e00173-17. [PMID: 28331089 PMCID: PMC5432854 DOI: 10.1128/jvi.00173-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/09/2017] [Indexed: 12/16/2022] Open
Abstract
Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here, we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified, including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with cold spots and hot spots. Most samples were coinfected by multiple viruses, and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data have enabled us to identify several unreported viruses in tomato, including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in the genus Cytorhabdovirus Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance, and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases.IMPORTANCE Tomato is an important source of micronutrients in the human diet and is extensively consumed around the world. Virus is among the major constraints on tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast-evolving biological entities. Here, we report the landscape of the tomato virome in China, the leading country in tomato production. We identified dozens of viruses present in tomato, including both well-documented and completely new viruses. Some newly emerged viruses in tomato were found to spread fast, and therefore, prompt attention is needed to control them. Moreover, we show that the virus genomes exhibit considerable degree of polymorphisms and recombination, and the virus-derived small interfering RNA (vsiRNA) sequences indicate distinct vsiRNA biogenesis mechanisms for different viruses. The Chinese tomato virome that we developed provides valuable information to facilitate the management of tomato viral diseases.
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Affiliation(s)
- Chenxi Xu
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xuepeng Sun
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Angela Taylor
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Chen Jiao
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Yimin Xu
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
| | - Xiaofeng Cai
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Xiaoli Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Chenhui Ge
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Guanghui Pan
- Chongqing Academy of Agricultural Science, Chongqing, China
| | - Quanxi Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
| | - Zhangjun Fei
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, USA
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, USA
| | - Quanhua Wang
- Development and Collaborative Innovation Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, China
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Nordenstedt N, Marcenaro D, Chilagane D, Mwaipopo B, Rajamäki ML, Nchimbi-Msolla S, Njau PJR, Mbanzibwa DR, Valkonen JPT. Pathogenic seedborne viruses are rare but Phaseolus vulgaris endornaviruses are common in bean varieties grown in Nicaragua and Tanzania. PLoS One 2017; 12:e0178242. [PMID: 28542624 PMCID: PMC5444779 DOI: 10.1371/journal.pone.0178242] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 05/10/2017] [Indexed: 12/29/2022] Open
Abstract
Common bean (Phaseolus vulgaris) is an annual grain legume that was domesticated in Mesoamerica (Central America) and the Andes. It is currently grown widely also on other continents including Africa. We surveyed seedborne viruses in new common bean varieties introduced to Nicaragua (Central America) and in landraces and improved varieties grown in Tanzania (eastern Africa). Bean seeds, harvested from Nicaragua and Tanzania, were grown in insect-controlled greenhouse or screenhouse, respectively, to obtain leaf material for virus testing. Equal amounts of total RNA from different samples were pooled (30-36 samples per pool), and small RNAs were deep-sequenced (Illumina). Assembly of the reads (21-24 nt) to contiguous sequences and searches for homologous viral sequences in databases revealed Phaseolus vulgaris endornavirus 1 (PvEV-1) and PvEV-2 in the bean varieties in Nicaragua and Tanzania. These viruses are not known to cause symptoms in common bean and are considered non-pathogenic. The small-RNA reads from each pool of samples were mapped to the previously characterized complete PvEV-1 and PvEV-2 sequences (genome lengths ca. 14 kb and 15 kb, respectively). Coverage of the viral genomes was 87.9-99.9%, depending on the pool. Coverage per nucleotide ranged from 5 to 471, confirming virus identification. PvEV-1 and PvEV-2 are known to occur in Phaseolus spp. in Central America, but there is little previous information about their occurrence in Nicaragua, and no information about occurrence in Africa. Aside from Cowpea mild mosaic virus detected in bean plants grown from been seeds harvested from one region in Tanzania, no other pathogenic seedborne viruses were detected. The low incidence of infections caused by pathogenic viruses transmitted via bean seeds may be attributable to new, virus-resistant CB varieties released by breeding programs in Nicaragua and Tanzania.
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Affiliation(s)
- Noora Nordenstedt
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Delfia Marcenaro
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Nicaraguan Institute of Agricultural Technology (CNIAB-INTA), Managua, Nicaragua
| | - Daudi Chilagane
- Sokoine University of Agriculture, Morogoro, Tanzania
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | - Beatrice Mwaipopo
- Sokoine University of Agriculture, Morogoro, Tanzania
- Mikocheni Agricultural Research Institute, Dar es Salaam, Tanzania
| | | | | | | | | | - Jari P. T. Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
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36
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Viral small RNAs reveal the genomic variations of three grapevine vein clearing virus quasispecies populations. Virus Res 2017; 229:24-27. [PMID: 28012998 DOI: 10.1016/j.virusres.2016.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 11/23/2022]
Abstract
Viral small RNAs (vsRNAs) include viral small interfering RNAs (vsiRNAs) that are initiators and products of RNA silencing, and small RNAs that are derived from viral RNAs with function still unknown. Sequencing of vsRNAs allows assembling of viral genomes and revelation of viral population variations at genomic levels. Grapevine vein clearing virus (GVCV) is a new member of the family Caulimoviridae whose DNA genome is replicated by reverse transcription of pre-genomic RNA molecules. In this short report, three genomic sequences of GVCV were assembled from vsRNAs that were isolated and sequenced from three individual grapevines in commercial vineyards and compared to the GVCV-CHA reference genome. Profiles of single nucleotide polymorphism among three viral populations indicated a closer relatedness between two populations in different grape cultivars at the same location than those in the same grape cultivar at different locations, suggesting the spread of GVCV populations among vineyards of close proximity. Classic types of vsiRNAs (21-nt, 22-nt, and 24-nt) were found in the three GVCV vsiRNA populations, but these did not produce alignment hotspots on the GVCV-CHA reference genome. The number of 36-nt reads is the highest among vsRNAs, the role of these vsRNAs remains unclear. The analysis of vsRNAs provides a first holistic picture of genomic variations among GVCV viral quasispecies populations that help monitor epidemics and evolution of GVCV populations, an emerging virus that is becoming a threat to grape production in the Midwest region of the USA.
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37
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Deep sequencing for discovery and evolutionary analysis of plant viruses. Virus Res 2016; 239:82-86. [PMID: 27876625 DOI: 10.1016/j.virusres.2016.11.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/18/2016] [Indexed: 11/21/2022]
Abstract
The advent of next generation sequencing (NGS), or deep sequencing, has allowed great advances to be made in discovery, diagnostics, and evolutionary studies in plant viruses. Various methods have been used for enrichment for virus-specific nucleic acids, each of which have some drawbacks. Many novel viruses have been discovered in plants by NGS technologies, and there is a good deal of promise for more comprehensive studies in virus evolution. However, each aspect of using NGS has its caveats that need to be considered, and there is still a need for better tools of analysis, as well as method for validation of sequence variation.
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38
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Li J, Zheng H, Zhang C, Han K, Wang S, Peng J, Lu Y, Zhao J, Xu P, Wu X, Li G, Chen J, Yan F. Different Virus-Derived siRNAs Profiles between Leaves and Fruits in Cucumber Green Mottle Mosaic Virus-Infected Lagenaria siceraria Plants. Front Microbiol 2016; 7:1797. [PMID: 27881977 PMCID: PMC5101232 DOI: 10.3389/fmicb.2016.01797] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/25/2016] [Indexed: 01/24/2023] Open
Abstract
RNA silencing is an evolutionarily conserved antiviral mechanism, through which virus-derived small interfering RNAs (vsiRNAs) playing roles in host antiviral defense are produced in virus-infected plant. Deep sequencing technology has revolutionized the study on the interaction between virus and plant host through the analysis of vsiRNAs profile. However, comparison of vsiRNA profiles in different tissues from a same host plant has been rarely reported. In this study, the profiles of vsiRNAs from leaves and fruits of Lagenaria siceraria plants infected with Cucumber green mottle mosaic virus (CGMMV) were comprehensively characterized and compared. Many more vsiRNAs were present in infected leaves than in fruits. vsiRNAs from both leaves and fruits were mostly 21- and 22-nt in size as previously described in other virus-infected plants. Interestingly, vsiRNAs were predominantly produced from the viral positive strand RNAs in infected leaves, whereas in infected fruits they were derived equally from the positive and negative strands. Many leaf-specific positive vsiRNAs with lengths of 21-nt (2058) or 22-nt (3996) were identified but only six (21-nt) and one (22-nt) positive vsiRNAs were found to be specific to fruits. vsiRNAs hotspots were only present in the 5'-terminal and 3'-terminal of viral positive strand in fruits, while multiple hotspots were identified in leaves. Differences in GC content and 5'-terminal nucleotide of vsiRNAs were also observed in the two organs. To our knowledge, this provides the first high-resolution comparison of vsiRNA profiles between different tissues of the same host plant.
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Affiliation(s)
- Junmin Li
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Hongying Zheng
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Chenhua Zhang
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Kelei Han
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Shu Wang
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jiejun Peng
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Yuwen Lu
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jinping Zhao
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Pei Xu
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xiaohua Wu
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Guojing Li
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Institute of Vegetable, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jianping Chen
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Fei Yan
- State Key Laboratory Breeding Base for Sustainable Control of Pest and Disease, Zhejiang Academy of Agricultural SciencesHangzhou, China
- Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural SciencesHangzhou, China
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Bertran A, Ciuffo M, Margaria P, Rosa C, Oliveira Resende R, Turina M. Host-specific accumulation and temperature effects on the generation of dimeric viral RNA species derived from the S-RNA of members of the Tospovirus genus. J Gen Virol 2016; 97:3051-3062. [PMID: 27600541 DOI: 10.1099/jgv.0.000598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Polygonum ringspot virus (PolRSV) is a recently characterized Tospovirus reported in Italy. Northern blot analyses of PolRSV infections in Nicotiana benthamiana and tomato plants showed that a viral RNA species with nearly twice the length of the Small genomic RNA (S-RNA) accumulated abundantly in the former host, but was not detected in the latter. Additional assays confirmed that biogenesis of this novel RNA species was common to all PolRSV isolates tested and also to an isolate of Tomato spotted wilt virus (TSWV). Given its size, we hypothesized that the novel RNA species was a dimer molecule and we confirmed this hypothesis by RNA sequencing (RNAseq) analysis and reverse transcription (RT)-PCR of putative predicted dimer junction sites in RNA extracts of N. benthamiana challenged with PolRSV isolates Plg6 and Plg13/2. We also confirmed that these molecules are derived from head-to-tail dimers and often contain deletions at their junction sites. We named these novel molecules imperfect dimer RNAs (IMPD-RNAs). PolRSV IMPD-RNAs systemic accumulation in a range of host plants was restricted to N. benthamiana and Nicotiana occidentalis. Notably, IMPD-RNAs accumulation was modulated by temperature and their generation was restricted to late stages of systemic infection (12 days post-inoculation) in N. benthamiana. Differently from all other PolRSV isolates used in this study, Plg13/2 generated more IMPD-RNAs coupled with low amounts of genomic S-RNA and maintained them even at 18 °C, besides having lost the ability to infect tomato plants. This is the first characterization of S-RNA dimers for Tospovirus, and of occurrence of dimers of genomic segments at the whole organism level for Bunyaviridae.
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Affiliation(s)
- André Bertran
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
- Plant Virology Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - Marina Ciuffo
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
| | - Paolo Margaria
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Cristina Rosa
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, USA
| | - Renato Oliveira Resende
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
- Plant Virology Laboratory, Institute of Biological Sciences, University of Brasília, Brazil
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Turin, Piemonte, Italy
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40
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Seguin J, Otten P, Baerlocher L, Farinelli L, Pooggin MM. MISIS-2: A bioinformatics tool for in-depth analysis of small RNAs and representation of consensus master genome in viral quasispecies. J Virol Methods 2016; 233:37-40. [PMID: 26994965 DOI: 10.1016/j.jviromet.2016.03.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 11/19/2022]
Abstract
In most eukaryotes, small RNA (sRNA) molecules such as miRNAs, siRNAs and piRNAs regulate gene expression and repress transposons and viruses. AGO/PIWI family proteins sort functional sRNAs based on size, 5'-nucleotide and other sequence features. In plants and some animals, viral sRNAs are extremely diverse and cover the entire viral genome sequences, which allows for de novo reconstruction of a complete viral genome by deep sequencing and bioinformatics analysis of viral sRNAs. Previously, we have developed a tool MISIS to view and analyze sRNA maps of viruses and cellular genome regions which spawn multiple sRNAs. Here we describe a new release of MISIS, MISIS-2, which enables to determine and visualize a consensus sequence and count sRNAs of any chosen sizes and 5'-terminal nucleotide identities. Furthermore we demonstrate the utility of MISIS-2 for identification of single nucleotide polymorphisms (SNPs) at each position of a reference sequence and reconstruction of a consensus master genome in evolving viral quasispecies. MISIS-2 is a Java standalone program. It is freely available along with the source code at the website http://www.fasteris.com/apps.
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Affiliation(s)
- Jonathan Seguin
- University of Basel, Department of Environmental Sciences, Botany, Hebelstrasse 1, 4056 Basel, Switzerland; Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland
| | - Patricia Otten
- Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland
| | - Loïc Baerlocher
- Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland
| | - Laurent Farinelli
- Fasteris SA, Ch. du Pont-du-Centenaire 109, 1228 Plan-les-Ouates, Switzerland
| | - Mikhail M Pooggin
- University of Basel, Department of Environmental Sciences, Botany, Hebelstrasse 1, 4056 Basel, Switzerland.
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Using Small RNA Deep Sequencing Data to Detect Human Viruses. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2596782. [PMID: 27066498 PMCID: PMC4811048 DOI: 10.1155/2016/2596782] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Revised: 01/13/2016] [Accepted: 02/03/2016] [Indexed: 01/08/2023]
Abstract
Small RNA sequencing (sRNA-seq) can be used to detect viruses in infected hosts without the necessity to have any prior knowledge or specialized sample preparation. The sRNA-seq method was initially used for viral detection and identification in plants and then in invertebrates and fungi. However, it is still controversial to use sRNA-seq in the detection of mammalian or human viruses. In this study, we used 931 sRNA-seq runs of data from the NCBI SRA database to detect and identify viruses in human cells or tissues, particularly from some clinical samples. Six viruses including HPV-18, HBV, HCV, HIV-1, SMRV, and EBV were detected from 36 runs of data. Four viruses were consistent with the annotations from the previous studies. HIV-1 was found in clinical samples without the HIV-positive reports, and SMRV was found in Diffuse Large B-Cell Lymphoma cells for the first time. In conclusion, these results suggest the sRNA-seq can be used to detect viruses in mammals and humans.
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42
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Zhang C, Wu Z, Li Y, Wu J. Biogenesis, Function, and Applications of Virus-Derived Small RNAs in Plants. Front Microbiol 2015; 6:1237. [PMID: 26617580 PMCID: PMC4637412 DOI: 10.3389/fmicb.2015.01237] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
RNA silencing, an evolutionarily conserved and sequence-specific gene-inactivation system, has a pivotal role in antiviral defense in most eukaryotic organisms. In plants, a class of exogenous small RNAs (sRNAs) originating from the infecting virus called virus-derived small interfering RNAs (vsiRNAs) are predominantly responsible for RNA silencing-mediated antiviral immunity. Nowadays, the process of vsiRNA formation and the role of vsiRNAs in plant viral defense have been revealed through deep sequencing of sRNAs and diverse genetic analysis. The biogenesis of vsiRNAs is analogous to that of endogenous sRNAs, which require diverse essential components including dicer-like (DCL), argonaute (AGO), and RNA-dependent RNA polymerase (RDR) proteins. vsiRNAs trigger antiviral defense through post-transcriptional gene silencing (PTGS) or transcriptional gene silencing (TGS) of viral RNA, and they hijack the host RNA silencing system to target complementary host transcripts. Additionally, several applications that take advantage of the current knowledge of vsiRNAs research are being used, such as breeding antiviral plants through genetic engineering technology, reconstructing of viral genomes, and surveying viral ecology and populations. Here, we will provide an overview of vsiRNA pathways, with a primary focus on the advances in vsiRNA biogenesis and function, and discuss their potential applications as well as the future challenges in vsiRNAs research.
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Affiliation(s)
- Chao Zhang
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Zujian Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China
| | - Yi Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
| | - Jianguo Wu
- Key Laboratory of Plant Virology of Fujian Province, Institute of Plant Virology, Fujian Agriculture and Forestry University Fuzhou, China ; Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University Beijing, China
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