ویروس‌شناسی گیاهی کاربردی: پیشرفت‌ها، شناسایی و استراتژی‌های ضدویروسی

__Applied Plant Virology: Advances, Detection, and Antiviral Strategies__ provides an overview on recent developments and applications in the field of plant virology. The book begins with an introduction to important advances in plant virology, but then covers topics including techniques for assay detection and the diagnosis of plant viruses, the purification, isolation and characterization of plant viruses, the architecture of plant viruses, the replication of plant viruses, the physiology of virus-infected hosts, vectors of plant viruses, and the nomenclature and classification of plants. The book also discusses defense strategies by utilizing antiviral agents and management strategies of virus and viroid diseases. With contributions from an international collection of experts, this book presents a practical resource for plant virologists, plant pathologists, horticulturalists, agronomists, biotechnologists, academics and researchers interested in up-to-date technologies and information that advance the field of plant virology. Cover Applied Plant Virology: Advances, Detection, and Antiviral Strategies Copyright Dedication Contents List of Contributors About the Editor Foreword Preface Acknowledgments Part 1: Important landmarks in the history of virology 1 Major advances in the history of plant virology 1.1 Introduction 1.2 Introduction of tobacco plants to Europe from the Americas 1.3 A tobacco disease in Europe that led to the beginning of virology 1.4 Discovery of plant DNA viruses, satellites, and viroids in the 20th century 1.4.1 DNA virus discovery 1.4.2 Viral satellites discovery 1.4.3 Viroid discovery 1.5 Virus-infected plant biology, the early years (1903–52) 1.6 Virus transmission 1.6.1 Nonvector transmission 1.6.2 Vector transmission 1.6.3 Viral protein involvement in aphid or nematode vector transmission 1.6.4 Propagative transmission 1.6.5 Transmission involving helper viruses 1.6.6 Circulative nonpropagative transmission 1.7 The beginning and rise of molecular virology with tobacco mosaic virus as a model system (1935–60) 1.8 The development of biophysical virology with tobacco mosaic virus as a model system (1937–89) 1.9 Replication 1.9.1 Replication of RNA viruses 1.9.2 Replication of DNA viruses 1.9.3 Viroid replication 1.10 Methods 1.10.1 Serology 1.10.2 Electron microscopy 1.10.3 Confocal microscopy 1.10.4 Analytical and preparative ultracentrifugation 1.10.5 Density gradient ultracentrifugation 1.10.6 Gel electrophoresis 1.10.7 Protoplast systems 1.10.8 A model plant susceptible to many viruses 1.10.9 Chemotherapy 1.10.10 Hybridization 1.10.11 Polymerase chain reaction 1.10.12 Microarrays 1.10.13 Genetic engineering 1.10.14 First-generation RNA sequencing 1.10.15 First-generation DNA sequencing 1.10.16 Next-generation sequencing 1.10.17 Next-generation sequencing of ancient viruses 1.11 Resistance to virus infection 1.11.1 Pathogen-derived resistance in transgenic plants 1.11.2 RNA silencing 1.11.3 Genome editing 1.11.4 CRISPR-Cas system editing confers resistance to plant viruses 1.12 Control by exclusion References Part 2: Techniques for assay detection and diagnosis of plant viruses 2 Recent advances of virus diagnostics in horticultural crops References 3 Advance methods for the isolation and characterization of plant viruses infecting crops 3.1 Introduction 3.2 History 3.3 Methods based on biology of the virus 3.3.1 Bioassay/indicator hosts/virus indexing 3.3.2 Methods of transmission 3.3.3 Cytological studies of diseased host-plants 3.4 Methods depending on physical properties of virus particles 3.4.1 Stability and physicochemical properties 3.4.2 Electron microscopy 3.5 Methods depending on properties of viral proteins 3.5.1 ELISA-based procedures 3.5.2 Serologically specific electron microscopy 3.5.3 Immunoblotting techniques 3.5.4 Immunosensors 3.6 Methods involving properties of the viral nucleic acid 3.6.1 Polymerase chain reaction, its variants and nucleotide sequencing 3.6.2 Hybridization-based procedures 3.6.3 DNA microarray 3.7 Conclusions References 4 Diagnosis of the casual viruses of crop plants 4.1 Detection and identification assays based on biological properties 4.1.1 Virus inoculation and symptomatology (biological indexing) 4.2 Detection and identification assays based on physical properties 4.2.1 Stability and physicochemical properties of virus 4.2.2 Structural properties of virus: electron microscopy techniques 4.3 Detection and identification assays based on biochemical properties of plants 4.4 Detection and identification assays based on serology 4.4.1 Precipitation and agglutination tests 4.4.2 Enzyme-linked immunosorbent assay 4.4.3 Immunosorbent electron microscopy 4.5 Detection and identification assays based on virus nucleic acid 4.5.1 Nucleic acid spot hybridization 4.5.2 Nucleic acid amplification methods 4.5.2.1 Polymerase chain reaction 4.5.2.2 Reverse transcription–polymerase chain reaction 4.5.2.3 Cooperational polymerase chain reaction 4.5.2.4 Simultaneous detection of multiple infections: multiplex polymerase chain reaction 4.5.2.5 Multiplex nested reverse transcription–polymerase chain reaction 4.5.2.6 Real-time polymerase chain reaction 4.6 Detection and identification assays based on isothermal amplification 4.6.1 Nucleic acid sequence–based amplification 4.6.2 Self-sustained sequence replication 4.6.3 Rolling-circle amplification 4.6.4 Loop-mediated isothermal amplification 4.7 Advanced and developing methods 4.7.1 Assays based on microarray systems 4.7.2 Assays based on biosensors 4.7.3 Assays based on high-throughput sequencing 4.8 Conclusion References 5 Modern technologies for the diagnosis and assay of plants viruses 5.1 Introduction 5.2 Diagnostics for detection of viruses 5.2.1 Conventional techniques 5.2.1.1 Biological 5.2.1.1.1 Growing-on tests 5.2.1.1.2 Infectivity assays 5.2.1.2 Biochemical (staining of inclusion bodies) 5.2.1.3 Physical (electron microscopy) 5.2.2 Modern techniques 5.2.2.1 Serological tests/immunoassays 5.2.2.1.1 Enzyme-linked immunosorbent assay 5.2.2.1.2 Dotimmunobinding assay 5.2.2.1.3 Tissue blotting immunoassay/tissue print immunoassay/tissue print immunoblotting 5.2.2.1.4 Lateral flow strip method 5.2.2.2 Nucleic acid–based methods 5.2.2.2.1 Polymerase chain reaction Multiplex polymerase chain reaction Variants of polymerase chain reaction Reverse transcription–polymerase chain reaction Immunocapture polymerase chain reaction Real-time polymerase chain reaction/real-time reverse transcription–polymerase chain reaction 5.2.2.2.2 Nucleic acid hybridization assays 5.2.2.2.3 Double-stranded RNA analysis 5.2.2.2.4 Microarrays 5.2.2.2.5 Loop-mediated isothermal amplification 5.2.2.2.6 Helicase-dependent amplification 5.2.2.2.7 Recombinase polymerase amplification 5.2.2.2.8 Next-generation sequencing 5.3 Conclusion References 6 Diagnosis of plant virus diseases 6.1 Introduction 6.2 Evolution of serodiagnosis of plant virus diseases 6.2.1 Serodiagnosis during the pre–enzyme-linked immunosorbent assay period 6.2.1.1 Chloroplast agglutination and tube-precipitin tests 6.2.1.2 Agar-gel double diffusion tests 6.2.2 Serodiagnosis by enzyme-linked immunosorbent assay 6.2.2.1 Double antibody sandwich enzyme-linked immunosorbent assay 6.2.2.2 Other commonly used forms of enzyme-linked immunosorbent assay 6.2.2.3 Affirmer protein–based enzyme-linked immunosorbent assay 6.2.2.4 Dot blot, tissue blot and lateral flow immunoassays 6.3 Electron microscopy 6.3.1 Immunosorbent electron microscopy 6.4 Nucleodiagnosis 6.4.1 Polymerase chain reaction 6.4.1.1 Nested polymerase chain reaction 6.4.1.2 Multiplex polymerase chain reaction 6.4.2 Isothermal amplification 6.4.3 Rolling-circle amplification 6.4.3.1 Microarray and next-generation sequencing 6.5 Emerging technologies based on physicochemical changes 6.6 Conclusion Acknowledgements References 7 Advances in protein-based diagnostic tools of plant viruses 7.1 Introduction 7.2 Methods based on properties of viral proteins 7.3 Serology-based detection 7.3.1 Enzyme-linked immunosorbent assay 7.3.2 Immunoblotting 7.3.2.1 Dot immunoblotting assay 7.3.2.2 Tissue immunoblotting assay 7.3.2.3 Immunosorbent electron microscopy 7.3.3 Lateral-flow immunochromatographic assay 7.3.4 Immunocapture assay 7.3.4.1 Immunocapture polymerase chain reaction 7.3.4.2 Immunocapture loop-mediated isothermal amplification 7.3.5 Fluorescence polarization immunoassay 7.3.6 Microparticle enzyme immunoassay 7.3.7 Chemiluminescent immunoassay 7.3.8 Radioimmunoassay 7.3.9 Protein fingerprinting: a novel virus identification system 7.3.10 Applications of gold nanoparticles in virus detection 7.3.11 Quartz crystal microbalance immunosensors 7.4 Limitations 7.5 Conclusion References Further reading 8 Rapid detection of plant viruses and viroids 8.1 Plant viral diseases and rapid diagnosis 8.2 Rapid detection methods for plant viruses and viroids 8.2.1 Enzyme-linked immunosorbent assay 8.2.2 Immunochromatographic assay 8.2.3 Thermal cycling–based amplification–polymerase chain reaction 8.2.4 Isothermal nucleic acid amplification 8.2.5 Other rapid detection methods 8.3 Recombinase polymerase amplification — a rapid detection tool 8.3.1 Recombinase polymerase amplification basics 8.3.1.1 Recombinant polymerase amplification proteins and enzymes 8.3.1.2 Recombinant polymerase amplification primers and probes 8.3.1.3 Recombinant polymerase amplification reaction conditions 8.3.1.4 Amplicon detection 8.3.2 Recombinant polymerase amplification performance 8.3.3 Rapid detection of viruses and viroids in plants via recombinant polymerase amplification 8.3.3.1 Detection of plant RNA viruses 8.3.3.2 Detection of plant DNA viruses 8.3.3.3 Detection of viroids 8.3.4 Pros, cons, and potential applications of recombinant polymerase amplification 8.4 Rapid detection and plant viral disease control 8.4.1 Considerations in choosing rapid detection methods 8.4.2 Importance and potential application of rapid detection technologies Acknowledgment References Part 3: Architecture of important viruses 9 Architecture of important plant viruses: the role of capsid protein—its assembly and architecture 9.1 Introduction 9.2 Methods for structure determination 9.3 Arrangement of capsid proteins 9.4 Icosahedral symmetry 9.5 Quasi-equivalence and other structure theories 9.6 The structure of capsid proteins 9.7 Bacilliform particles 9.8 Helical symmetry 9.9 Rod-shaped and flexuous filamentous viruses 9.9.1 Strong intersubunit interactions in tobamovirus virions 9.9.2 Flexible intersubunit contacts in potexviruses 9.10 Architecture and assembly of capsid proteins 9.11 Intrinsically disordered domain 9.12 Conclusion Acknowledgment References Part 4: Plant molecular virology 10 Next-generation sequencing technologies and plant molecular virology: a practical perspective 10.1 Introduction 10.2 Next-generation sequencing 10.2.1 Genesis of platforms available for next-generation sequencing 10.2.1.1 First-generation sequencing technology 10.2.1.2 Second-generation sequencing technologies 10.2.1.3 Third-generation sequencing technologies 10.3 Discovery of novel viruses 10.4 Identification of virus-specific noncoding RNAs 10.5 Viral diagnostics 10.6 Metagenomics of viruses (metaviromics) 10.7 Concluding remarks References 11 Molecular responses of plants to viruses with emphasis on small RNAs 11.1 Plant immune response 11.2 Plant–virus interactions 11.3 Endogenous small RNAs in plant–virus interactions 11.3.1 sRNA biogenesis and action 11.3.2 Short RNA regulation in PTI 11.3.3 Small RNA regulation in effector-triggered immunity 11.3.4 Role of small RNAs in epigenetic responses 11.3.5 Small RNAs in plant–virus interactions 11.4 Conclusion References 12 Protein preparation from virus-infected plants for protoplast–chloroplast proteomics 12.1 Introduction 12.2 Materials 12.2.1 Plant growth 12.2.2 Virus infection 12.2.3 Protoplast isolation 12.2.4 Chloroplast isolation 12.2.5 Protein extraction 12.3 Methods 12.3.1 Plant growth 12.3.2 Virus inoculation 12.3.3 Protoplast isolation 12.3.4 Chloroplast isolation 12.3.5 Protein extraction Acknowledgments References Part 5: Replication of plant viruses 13 DNA plant viruses: biochemistry, replication, and molecular genetics 13.1 Introduction 13.1.1 Plant viruses 13.1.1.1 Geminiviruses 13.1.2 Gemini viruses classification 13.1.2.1 Begomoviruses 13.1.3 Bipartite Begomoviruses 13.1.4 Potential functions of begomovirus-encoded proteins 13.1.5 Monopartite begomoviruses and associated complexes 13.1.6 Betasatellite 13.1.7 Deltasatellite 13.1.8 Alphasatellite 13.1.8.1 Capulavirus 13.1.8.2 Curtovirus 13.1.8.3 Eragrovirus 13.1.8.4 Becurtovirus 13.1.8.5 Grablovirus 13.1.8.6 Mastrevirus 13.1.8.7 Topocuvirus 13.1.8.8 Turncurtovirus 13.2 Family Caulimoviridae (dsDNA viruses) 13.2.1 Structure of virus particle 13.2.2 Replication and biosynthesis of viral proteins 13.2.3 Caulimovirus 13.2.4 Petuvirus 13.2.5 Cavemovirus 13.2.6 Soymovirus 13.2.7 Badnavirus 13.2.8 Tungrovirus References 14 RNA plant viruses: biochemistry, replication and molecular genetics 14.1 Introduction 14.2 RNA replication and translation of plant viruses 14.2.1 Initial infection 14.3 A case study of tobamovirus replication 14.4 Cellular mechanisms involved in viral replication complex formation 14.4.1 Recruitment of red clover necrotic mosaic virus movement protein to viral replication complexes organized by a repli... 14.4.2 Formation of viral replication complex and potato virus X movement protein 14.4.3 Replication and movement of turnip mosaic virus 14.5 Virus interaction with plant cytoskeleton 14.6 Positive-sense single-stranded RNA virus replication: role of host factors 14.6.1 Host proteins regulate viral genome replication in chloroplasts 14.7 How is replication of virus affected by host silencing? 14.8 Molecular approaches to study host factors and virus replication 14.9 Conclusion References Part 6: Physiology of virus infected hosts 15 Physiology of virus-infected plants 15.1 Introduction 15.2 Changes in photosynthetic activity in virus-infected hosts 15.3 Chlorophyll content 15.4 The rate of photosynthesis 15.5 Changes in starch metabolism in virus-infected plants 15.6 Changes in respiration in virus-infected plants 15.7 Changes in nitrogen metabolism and proteins in virus-infected plants 15.8 Changes in water content and transpiration of virus-infected plants 15.9 Changes in hormone metabolism of virus-infected plants 15.10 Conclusion References Part 7: Viroids 16 Viroids: small entities with a mean punch 16.1 Introduction 16.2 Structure and taxonomy 16.2.1 Family Pospiviroidae 16.2.2 Family Avsunviroidae 16.3 Replication of viroids 16.4 Movement of viroids 16.5 Symptoms and host–pathogen interaction 16.6 Transmission of viroids 16.7 Detection of viroids 16.8 Control of viroids References Further reading Part 8: Viruses of cryptogamic plants 17 Fungal viruses: an unlikely ally 17.1 Introduction 17.2 The birth of mycovirology 17.3 Symptoms of mycoviruses 17.4 Natural and experimental transmission of mycoviruses 17.5 Classification of mycoviruses 17.6 Double-stranded RNA mycoviruses 17.6.1 Floating genus: Botybirnavirus 17.7 Positive-sense single-stranded RNA mycoviruses 17.8 Reverse-transcribing positive-sense RNA mycoviruses 17.9 Negative-sense RNA mycoviruses 17.10 Single-stranded DNA (ssDNA) mycoviruses 17.11 Hypovirulence of mycoviruses 17.12 Conclusions Acknowledgments References Further reading 18 Algal viruses 18.1 The diversity of algal viruses 18.2 Applications of algal viruses in advancement of molecular biology and for enhancement of biofuel production 18.3 Environmental factors affecting growth and development of algae and viruses 18.3.1 Temperature 18.3.2 Salinity 18.3.3 Ultraviolet radiation 18.3.4 Photosynthetic active radiation 18.3.5 Nutrients 18.3.6 Inorganic particles 18.3.7 Organic particles 18.3.8 Carbon dioxide concentration 18.3.9 pH References Part 9: Transmission of plant viruses 19 The role of heat-shock proteins, in vector-virus transmission 19.1 Introduction 19.2 Endosymbionts 19.3 GroEL-homologue protein 19.3.1 GroEL-homologue protein specificity 19.4 Virus coat protein 19.5 Other heat-shock proteins References Further reading Part 10: Vectors of plant viruses/virus, vector relationship 20 Mite (Acari Acarina) vectors involved in transmission of plant viruses 20.1 Introduction 20.2 Virus transmissions 20.3 Mites-borne plant viruses 20.3.1 Tetranychoidea (Raphignathina) mites 20.3.1.1 Tenuipalpidae mites 20.3.1.2 Brevipalpus mites 20.3.1.2.1 Red and black flat mite Brevipalpus phoenicis (Geijskes) 20.3.2 Tetranychidae mites 20.3.2.1 Two-spotted spider mite Tetranychus urticae Koch 20.3.2.2 Brown wheat mite Petrobia latens (Muller) 20.3.3 Eriophyidae mites 20.3.3.1 Dry-bulb mite Aceria tulipae (Keifer) 20.3.3.2 Phyllocoptes fructiphilus Keifer 20.3.3.3 Wheat curl mite Aceria tosichella (Keifer) 20.3.4 Tarsonemid mites 20.3.4.1 Broad mite Polyphagotarsonemus latus (Banks) 20.4 Management of mite-vectored viruses 20.5 Conclusions References Further reading 21 Different nematodes and plasmodiophorids as vectors of plant viruses 21.1 Introduction 21.2 Nematodes 21.2.1 Feeding behavior of nematodes 21.2.2 Virus ingestion activity of nematodes 21.2.3 Virus retention and transmission by nematodes 21.2.4 Plant viruses vectored by nematodes 21.2.4.1 Stubby-root nematode Paratrichodorus minor 21.2.4.2 Needle Nematode Paralongidorus maximus (Butschli) 21.2.5 Management of nematode-transmitted viruses 21.2.5.1 Detection and identification 21.2.5.2 Exclusion 21.2.5.3 Natural resistance to vector nematodes and their viruses 21.2.5.4 Cultural control 21.2.5.5 Transgenic resistance 21.2.5.6 Chemical products 21.3 Plasmodiophorids 21.3.1 Plasmodiophorid-transmitted viruses 21.3.2 Polymyxa graminis Ledingham 21.3.3 Diseases caused by plasmodiophorid-transmitted viruses 21.3.4 Mechanisms of virus acquisition and transmission 21.3.5 Controlling of plasmodiophorid-transmitted viruses 21.4 Conclusion References 22 Transmission of plant viruses through soil-inhabiting nematode vectors 22.1 Introduction 22.2 Transmission through nematodes 22.2.1 Transmission of nepoviruses 22.2.2 Transmission of tobraviruses 22.3 Virus-nematode–vector relationship 22.3.1 Ingestion 22.3.2 Acquisition 22.3.3 Adsorption 22.3.4 Retention 22.3.5 Release 22.3.6 Transfer and establishment 22.4 Transmission efficiency 22.5 Mode of virus transmission by nematode References 23 New advances in insect vector biology and virus epidemiology 23.1 Introduction 23.2 Insect vector biology 23.3 Elucidating complex interactions between viruses and vectors 23.3.1 Virus impacts on biology and behavior of vector 23.3.2 Using basic research in insect biology to fight disease 23.3.2.1 Genetic control of insects 23.3.2.1.1 Genetic suppression of the vectors ability to transmit pathogens 23.3.2.1.2 Genetic suppression of insect populations 23.3.2.2 New avenues for the behavioral manipulation of disease vector 23.4 Viral epidemiology 23.5 Integrated control measures against viruses and their vectors 23.6 Conclusion References 24 Transmission of plant viruses in fields through various vectors 24.1 Introduction 24.2 Pathway of plant-virus transmission 24.2.1 Horizontal transmission 24.2.2 Vertical transmission 24.3 Methods of transmission 24.3.1 Noninsect transmission 24.3.1.1 Transmission by sap inoculation or mechanical transmission 24.3.1.2 Factors affecting mechanical transmission 24.3.1.2.1 Effect of source of inoculum 24.3.1.2.2 Effect of concentration of inoculum 24.3.1.2.3 Effect of extraction medium 24.3.1.2.4 Effect of metal ions and ionic strength 24.3.1.2.5 Effect of substances protecting against phenolics 24.3.1.2.6 Effect of charcoal 24.3.1.2.7 Effect of enzymes 24.3.1.2.8 Effect of detergents 24.3.1.3 Transmission through seed 24.3.1.4 Transmission through vegetative propagation 24.3.1.5 Transmission by dodder 24.3.1.6 Transmission through fungi 24.3.1.7 Transmission through nematodes 24.3.1.8 Nepoviruses 24.3.1.9 Tobraviruses 24.3.1.10 Virus–nematode relationships 24.3.2 Insect transmission 24.3.2.1 Virus–vector relationships 24.3.2.1.1 Nonpersistent transmission 24.3.2.1.2 Noncirculative, semipersistent transmission 24.3.2.1.3 Circulative, nonpropagative transmission 24.3.2.1.4 Circulative, propagative transmission 24.3.2.2 Insect vectors of plant viruses 24.3.2.2.1 Transmission through aphids 24.3.2.2.2 Transmission by whiteflies 24.3.2.2.3 Transmission through leafhopper/planthopper 24.3.2.2.4 Transmission by mite 24.3.2.2.5 Transmission thrips 24.3.2.2.6 Transmission by beetle References Further reading 25 Bemisia tabaci (Gennadius) as vector of plant viruses 25.1 Introduction 25.2 Economic importance 25.3 Biology 25.4 Biotypes 25.5 Host plant–vector–virus interaction 25.6 Vector–virus 25.7 Effect of ICMV on vector 25.8 Management 25.9 Virus–vector interactions and designing management tactics for plant viruses—future strategies and research needs 25.9.1 Transmission research 25.9.2 Strategic vector research References 26 Arthropod vectors of plant viruses 26.1 Introduction 26.2 Nonpersistent transmission 26.3 Family Potyviridae (genera Potyvirus and Macluravirus) 26.4 Family Bromoviridae (genera Alfamovirus and Cucumovirus) 26.5 Family Betaflexiviridae (genus Carlavirus) 26.6 Family Secoviridae (genus Fabavirus) 26.7 Semipersistent transmission 26.8 Family Closteroviridae (genera Ampelovirus, Closterovirus, and Crinivirus) 26.9 Family Potyviridae (genus Ipomovirus) 26.10 Family Secoviridae (genera Sequivirus, Torradovirus, and Waikavirus) 26.11 Family Betaflexiviridae (genera Trichovirus and Vitivirus) 26.12 Family Caulimoviridae (genera Badnavirus and Caulimovirus) 26.13 Persistent-circulative transmission 26.14 Family Geminiviridae (genera Becurtovirus, Begomovirus, Capulavirus, Curtovirus, Eragrovirus, Grablovirus, Mastreviru... 26.15 Family Luteoviridae (genera Enamovirus, Luteovirus and Polerovirus) 26.16 Family Nanoviridae (genera Babuvirus and Nanovirus) 26.17 Persistent-propagative transmission 26.18 Family Tospoviridae (genus Orthotospovirus) 26.19 Family Phenuiviridae (genus Tenuivirus) 26.20 Family Rhabdoviridae (genera Cytorhabdovirus and Nucleorhabdovirus) 26.21 Family Tymoviridae (genus Marafivirus) 26.22 Family Reoviridae (genera Phytoreovirus, Fijivirus, and Oryzavirus) 26.23 Beetle transmission 26.24 Unassigned family (genus Sobemovirus) 26.25 Family Tombusviridae (genera Machlomovirus, Betacarmovirus, and Gammacarmovirus) 26.26 Family Tymoviridae (genus Tymovirus) 26.27 Family Secoviridae (genus Comovirus) 26.28 Family Bromoviridae (genus Bromovirus) 26.29 Mite transmission 26.30 Aceria mites 26.31 Potyviridae (genera Poacevirus, Rymovirus and Tritimovirus) 26.32 Fimoviridae (genus Emaravirus) 26.33 Alphaflexiviridae (genus Allexivirus) 26.34 Secoviridae (genus Nepovirus) 26.35 Betaflexiviridae (genus Trichovirus) 26.36 Brevipalpus mites 26.37 Family Rhabdoviridae (genus Dichorhavirus) 26.38 Unassigned family (genus Cilevirus) 26.39 Pollenborne insect-aided transmission 26.40 Family Bromoviridae (genus Ilarvirus) 26.41 Family Tombusviridae (genus Alphacarmovirus) 26.42 Unassigned family (genus Sobemovirus) 26.43 Conclusions References 27 Insects as transport devices of plant viruses 27.1 Introduction 27.2 Plant pathogen spread by vectors 27.3 Types of virus transmission 27.4 Categories of vectors 27.5 Insect-transmitted plant-virus diseases 27.5.1 Homoptera 27.5.1.1 Aphids (Homoptera: Aphididae) 27.5.1.2 Whiteflies (Homoptera: Aleyrodidae) 27.5.1.3 Leafhoppers, planthoppers, and treehoppers (Homoptera) 27.5.1.3.1 Planthoppers (Homoptera: Delphacidae) 27.5.1.3.2 Leafhoppers (Homoptera: Cicadellidae) 27.5.1.3.3 Treehoppers (Homoptera: Membracidae) 27.5.1.4 Mealybugs and soft scales (Homoptera) 27.5.2 Hemiptera 27.5.3 Thrips (Thysanoptera: Thripidae) 27.5.4 Diptera 27.5.5 Coleoptera 27.5.6 Orthoptera 27.5.7 Lepidoptera 27.5.8 Dermaptera 27.6 Virus control 27.6.1 Virus control by interfering vectors and transmission 27.6.1.1 Reducing vector populations 27.6.1.2 Reducing virus sources 27.6.1.3 Interference with vector landing on crops 27.6.1.4 Interference with the transmission process 27.6.2 Host-plant resistance 27.6.3 Cultural control 27.6.4 Biological control 27.6.5 Chemical control 27.6.6 Regulatory measures 27.6.7 Integrated management 27.7 Conclusion References Part 11: Epidemiology and evolution of viruses 28 Epidemiology and evolution of poytviruses infecting cucurbits 28.1 Cucurbits 28.2 Viruses of cucurbits 28.3 Papaya ring spot virus 28.4 Watermelon mosaic virus 28.5 Zucchini yellow mosaic virus 28.6 Zucchini tigre mosaic virus 28.7 Evolution of papaya ringspot virus type W, watermelon mosaic virus, zucchini yellow mosaic virus, and zucchini tigre m... 28.1.1 Natural variation 28.1.2 Recombination Conclusions Acknowledgments References Further reading Part 12: Nomenclature and classification of plant viruses 29 Plant virus taxonomy 29.1 Introduction 29.2 Plant viruses 29.3 The diversity and classification of viruses 29.4 International committee on taxonomy of viruses taxonomy 29.4.1 The taxa of viruses 29.5 Database and website 29.5.1 Virus classification 29.5.2 Virus taxonomy 29.5.3 The International Committee on Taxonomy of Viruses database of virus taxonomy 29.6 Nomenclature and classification of plant viruses 29.6.1 Use of virus names 29.6.2 Baltimore system of virus classification 29.6.2.1 Latest classification 29.7 The international code of nomenclature 29.7.1 Names 29.7.2 Name stems 29.7.3 Derivation of species names 29.7.4 Typography 29.7.5 Virus names and the biocode 29.8 Principles of virus taxonomy 29.8.1 Stability 29.8.2 Utility 29.8.3 Acceptability 29.8.4 Flexibility 29.9 Plant virus biodiversity 29.10 Current taxonomy of viruses 29.11 Conclusions References Further reading Part 13: Viral diseases of crops 30 Interspecific and intraspecific interactions among plant viruses in mixed infections 30.1 Introduction 30.2 General overview of interactions among viruses 30.3 Interspecific interactions 30.3.1 Most famous synergy 30.3.2 Another couples in a synergistic marriage 30.3.3 Genes involved in synergistic interactions 30.3.4 Synergy as a driving force in the spread of viral diseases 30.4 Intraspecific interactions 30.4.1 Superinfection exclusion: viruses on a war footing 30.4.2 Why exclusion? 30.4.3 The extraordinary case of Citrus tristeza virus 30.4.4 Spatial separation: move over, and leave room for others 30.5 Interspecific and intraspecific helper dependence 30.5.1 Get neighborly help 30.5.2 Transport media used by potyviruses 30.5.3 Transport media used by umbraviruses 30.6 Implications of interspecific and intraspecific interactions 30.6.1 Recombination: give a part of yourself to others 30.6.2 Helper-dependent vector transmission: a multicomponent process 30.7 Conclusion References 31 Begomovirus research in Oman: a critical appraisal and the way ahead 31.1 Introduction 31.2 Begomovirus research in Oman 31.3 Conclusion References Further reading 32 Papaya ringspot virus–Carica papaya pathosystem 32.1 Introduction 32.1.1 Origin, taxonomy, and distribution of papaya 32.1.2 Papaya genome 32.1.3 Global production 32.1.4 Papaya ringspot virus 32.1.4.1 Taxonomy 32.1.4.2 Symptom description 32.1.4.3 Epidemiology 32.1.4.3.1 Host plants 32.1.4.3.2 Transmission Host selection by aphids 32.1.4.4 Detection methods 32.1.4.5 Genetic diversity 32.1.4.6 Origin and dispersal 32.1.4.7 Disease management 32.1.5 Conclusion References 33 Viral diseases of crops: a critical review References 34 Molecular diversity of begomoviruses and DNA satellite molecules infecting ornamental plants in India 34.1 Introduction 34.2 Indian begomoviruses and satellite molecules in ornamental plants 34.3 Phylogenetics and recombinations among the viruses and satellites 34.4 Conclusion Acknowledgments References 35 Recent advances in begomovirus research in India 35.1 Introduction 35.2 Detection of begomoviruses 35.2.1 Enzyme-linked immunosorbent assay 35.2.2 Dot-immunobinding assay 35.2.3 Nucleic acid hybridization method 35.2.4 Dot-blot hybridization (nucleic acid spot hybridization) 35.2.5 Southern blot 35.2.6 Polymerase chain reaction–based assay 35.2.6.1 Polymerase chain reaction detection of geminivirus using degenerate primer 35.2.6.2 Reverse transcription–polymerase chain reaction 35.2.6.3 Real-time polymerase chain reaction 35.2.6.4 Rolling-circle amplification–polymerase chain reaction assay 35.2.7 Rolling-circle amplification 35.2.8 Microarray/DNA chip 35.3 Molecular characterization of begomoviruses 35.3.1 Mung bean yellow mosaic virus 35.3.2 Black gram yellow mosaic virus 35.3.3 Bhendi yellow vein mosaic virus 35.3.4 Chilli leaf curl virus 35.3.5 Cotton leaf curl virus 35.3.6 Pumpkin yellow vein mosaic virus 35.3.7 Tomato leaf curl New Delhi virus 35.3.8 Tobacco leaf curl virus 35.3.9 Tomato yellow leaf curl virus 35.3.10 Papaya leaf curl virus 35.4 Management of begomoviruses 35.4.1 Pathogen-derived resistance 35.4.2 RNA interference–mediated resistance 35.4.3 Ribozyme-mediated resistance 35.4.4 Small interfering RNA–mediated 35.4.5 Artificial trans-acting short, interfering RNA References 36 Begomovirus research in Saudi Arabia: current status and future prospects 36.1 Introduction 36.2 Begomovirus infection in Saudi Arabia 36.2.1 Amaranthus 36.2.2 Beans 36.2.3 Cucumber 36.2.4 Corchorus 36.2.5 Okra 36.2.6 Ridge gourd 36.2.7 Squash 36.2.8 Tomato 36.3 Conclusion Acknowledgements References 37 Beet curly top virus transmission, epidemiology, and management 37.1 Beet curly top virus strains 37.2 Leafhopper transmission of beet curly top virus 37.3 Beet curley top virus epidemiology 37.4 Management of curly top 37.5 Conclusion References Part 14: Economic losses due to infection by plant viruses 38 Overview of yield losses due to plant viruses 38.1 Introduction 38.2 Yield losses in different crops 38.3 Cereals and millets 38.3.1 Rice 38.3.2 Wheat 38.3.3 Barley 38.3.4 Maize 38.4 Sorghum and pearl millet 38.4.1 Oats 38.5 Legumes 38.5.1 Common bean (Phaseolus vulgaris) 38.5.2 Pea 38.5.3 Chickpea 38.5.4 Cowpea 38.5.5 Greengram/mung bean 38.5.6 Blackgram/urdbean 38.5.7 Broad bean/faba bean 38.5.8 Redgram/pigeonpea 38.5.9 Lentil 38.6 Vegetables 38.6.1 Potato 38.6.2 Tomato 38.6.3 Chilli/pepper 38.6.4 Eggplant/brinjal 38.6.5 Ladies finger (bhendi) 38.6.6 Cucurbits 38.6.7 Carrot 38.6.8 Crucifers 38.6.9 Lettuce 38.6.10 Tuber crops 38.6.11 Sweet potato 38.6.12 Cassava 38.6.13 Aroids 38.6.14 Yam and elephant foot yam 38.7 Fruit crops 38.7.1 Citrus 38.7.2 Banana 38.7.3 Grapes 38.7.4 Papaya 38.7.5 Watermelon 38.8 Stone fruits (Prunus spp.) 38.9 Pome fruits 38.9.1 Apple 38.9.2 Strawberry 38.9.3 Pineapple 38.10 Industrial crops 38.10.1 Sugarcane 38.10.2 Sugar beet 38.10.3 Cotton 38.10.4 Tobacco 38.10.5 Cacao 38.10.6 Jatropha 38.11 Edible oil seed crops 38.11.1 Groundnut/peanut 38.11.2 Soybean 38.11.3 Brassicas 38.11.4 Sunflower 38.12 Spice crops 38.12.1 Onion and garlic 38.12.2 Cardamoms 38.12.3 Pepper 38.1