University of Agricultural Sciences, Bangalore

Includes bibliographical references and index.

Machine generated contents note: SECTION I VIROIDS -- pt. I VIROIDS: ECONOMIC SIGNIFICANCE -- 1.Economic Significance of Viroids in Vegetable and Field Crops / Rosemarie W. Hammond -- Introduction -- Potato -- Tomato -- Hop -- Cucumber -- Pepper -- Disease Management -- References -- 2.Economic Significance of Fruit Tree and Grapevine Viroids / Teruo Sano -- Introduction -- Pome Fruit Viroids -- Stone Fruit Viroids -- Mulberry, Pomegranate, and Fig Viroids -- Persimmon Viroids -- Avocado Viroids -- Citrus Viroids -- Grapevine Viroids -- Acknowledgments -- References -- 3.Economic Significance of Viroids in Ornamental Crops / Giuseppe Stancanelli -- Introduction -- Viroids Infecting Ornamental Crops -- Symptoms of Viroid Infections in Ornamental Crops -- Significance of Viroids in Ornamental Crops: Direct Impact -- Significance of Viroids in Ornamental Crops: Indirect Impact -- Ornamental Crops as a Source of Viroid Infections -- References

Note continued: 4.Economic Significance of Palm Tree Viroids / John W. Randles -- Introduction -- Coconut Palm -- Oil Palm -- Conclusions -- Acknowledgments -- References -- pt. II VIROID CHARACTERISTICS -- 5.Viroid Biology / Dijana Skoric -- Introduction -- Host Range -- Symptoms -- Cytopathology -- Transmission -- Acknowledgments -- References -- 6.Viroid Structure / Jean-Pierre Perreault -- Introduction -- Structure of the Pospiviroidae -- Alternative Structures Within the Pospiviroidae -- Structure of the Avsunviroidae -- References -- 7.Viroid Replication / Kriton Kalantidis -- Introduction -- Setting the Stage: Alternative Pathways of a Replication Mechanism With One or Two Rolling Circles -- Initiation and Elongation of RNA Strands: DNA-Dependent RNA Polymerases Transcribe RNA Templates -- Cleavage of Oligomeric Strands: Host-Encoded RNAses and Viroid-Embedded Ribozymes

Note continued: Circularization of Monomeric Linear Strands: RNA Ligases and DNA Ligases Operating on RNA Substrates -- The Other Side of the Coin: Degradation of Viroid Strands -- Concluding Remarks -- Acknowledgments -- References -- 8.Viroid Movement / Gustavo Gomez -- Introduction -- Intracellular Movement -- Intercellular and Vascular Movement -- Future Prospects -- Acknowledgments -- References -- 9.Viroid Pathogenesis / Robert A. Owens -- Introduction -- Macroscopic Symptoms and Cytopathic Effects -- Biochemical Changes Accompanying Viroid Infection -- Molecular Mechanisms -- The Host Contribution to Pathogenicity Reexamined -- RNA Silencing Limits the Spread of Viroid Infection -- RNA Silencing Also Mediates Viroid Pathogenesis -- Viroid Pathogenesis Engages Multiple Regulatory Networks -- Acknowledgments -- References -- 10.Changes in the Host Proteome and Transcriptome Induced by Viroid Infection / Vicente Conejero -- Introduction

Note continued: Protein Changes Associated With Viroid Infection -- Interaction of Host Proteins With Viroids -- Transcriptional Changes Associated With Viroid Infection -- Molecular Mechanisms Underlying Transcriptional Changes -- A Glimpse Into the Future -- References -- 11.Viroids and RNA Silencing / Michael Wassenegger -- RNA Silencing in Plants -- Viroids Trigger RNA Silencing -- DCL-Processing of Viroids Into Vd-siRNAs -- Viroids as Targets for PTGS -- Viroid-Induced Trans-PTGS of Endogenes -- Viroid-Induced RdDM -- References -- 12.Origin and Evolution of Viroids / Ricardo Flores -- Introduction -- Where Do Viroids Come From? -- How Did Viroids Adapt to a Cellular Environment? -- How Did Viroids Subsequently Evolve? -- Concluding Remarks -- Acknowledgments -- References -- 13.Viroid Taxonomy / Ricardo Flores -- Introduction -- Viroid Variants and Viroid Species -- Viroid Families -- Viroid Genera -- Current Viroid Classification -- References

Note continued: pt. III VIROID DISEASES -- 14.Potato Spindle Tuber Viroid / Jacobus Th.J. Verhoeven -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- References -- 15.Other Pospiviroids Infecting Solanaceous Plants / Stephan Winter -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Host Range -- Symptoms and Economic Significance -- Transmission and Epidemiology -- Detection -- Geographical Distribution -- Control -- References -- 16.Citrus Exocortis Viroid / Nuria Duran-Vila -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References -- 17.Chrysanthemum Stunt Viroid / Peter Palukaitis -- Introduction

Note continued: Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References -- 18.Iresine Viroid 1 and a Potential New Pospiviroid From Portulaca / Pedro Serra -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Symptoms, Host Range, and Economic Significance -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References -- 19.Hop Stunt Viroid / Teruo Sano -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographic Distribution and Epidemiology -- Control -- References -- 20.Dahlia Latent Viroid / Pedro Serra -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Symptoms, Host Range, and Economic Significance -- Transmission and Control

Note continued: Detection -- Geographical Distribution and Epidemiology -- Acknowledgments -- References -- 21.Apple Scar Skin Viroid / Vipin Hallan -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Geographical Distribution and Epidemiology -- Detection -- Control -- References -- 22.Other Apscaviroids Infecting Pome Fruit Trees / Teruo Sano -- Apple Dimple Fruit Viroid (ADFVd) -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Apple Fruit Crinkle Viroid (AFCVd) -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Pear Blister Canker Viroid (PBCVd) -- Introduction -- Taxonomic Position and Nucleotide Sequence

Note continued: Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control of Apscaviroids Infecting Pome Fruit Trees -- References -- 23.Apscaviroids Infecting Citrus Trees / Matilde Tessitori -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Host Range -- Symptoms and Economic Significance -- Transmission and Epidemiology -- Detection -- Geographical Distribution -- Control -- Acknowledgments -- References -- 24.Apscaviroids Infecting Grapevine / Nuredin Habili -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms and Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Concluding Remarks -- Acknowledgments -- References -- 25.Coconut Cadang-Cadang Viroid and Coconut Tinangaja Viroid / John W. Randles -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance

Note continued: Symptoms -- Host Range -- Transmission -- Disease Identification -- Geographical Distribution and Epidemiology -- Control -- References -- 26.Other Cocadviroids / Georgios Vidalakis -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References -- 27.Coleus Blumei Viroids / Rudra P. Singh -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- References -- 28.Avocado Sunblotch Viroid / Jonathan Dixon -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References

Note continued: 29.Peach Latent Mosaic Viroid in Infected Peach / Francesco Di Serio -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References -- 30.Peach Latent Mosaic Viroid in Temperate Fruit Trees Other Than Peach / Ahmed Hadidi -- Introduction -- Taxonomic Position, Nucleotide Sequence, and Phylogeny -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References -- 31.Chrysanthemum Chlorotic Mottle Viroid / Beatriz Navarro -- Introduction -- Taxonomic Position and Nucleotide Sequence -- Economic Significance -- Symptoms -- Host Range -- Transmission -- Detection -- Geographical Distribution and Epidemiology -- Control -- Acknowledgments -- References

Note continued: 32.Eggplant Latent Viroid / Jose-Antonio Daros -- Introduction -- Nucleotide Sequence and Secondary Structure -- Taxonomic Position -- Symptoms -- Host Range -- Transmission -- Control -- Acknowledgments -- References -- pt. IV DETECTION AND IDENTIFICATION METHODS -- 33.Viroid Detection and Identification by Bioassay / Rudra P. Singh -- Introduction -- Viroid Species, Primary Hosts, and Indicator Hosts -- Factors Affecting Detection and Identification of Viroid by Bioassay -- Cross-Protection as a Means of Bioassay -- Combining Molecular and Biological Assays for Viroid Detection and Identification -- References -- 34.Gel Electrophoresis / Ganesan Vadamalai -- Introduction -- GE Systems -- Examples of Applications -- References -- 35.Molecular Hybridization Techniques for Detecting and Studying Viroids / Francesco Di Serio -- Introduction -- Dot-Blot Hybridization -- Gel-Blot Hybridization -- Polyvalent Detection Using Polyprobes

Note continued: Tissue-Print Hybridization -- In Situ Hybridization -- Acknowledgments -- References -- 36.Viroid Amplification Methods: RT-PCR, Real-Time RT-PCR, and RT-LAMP / Iraklis N. Boubourakas -- Introduction -- Viroid Amplification Procedures -- Viroid RNA Preparation -- End Point RT-PCR -- Real-Time RT-PCR -- Final Considerations -- Acknowledgments -- References -- 37.Detection and Identification of Viroids by Microarrays / Marina Barba -- Introduction -- Microarray Construction -- Microarray Probe Design -- Target Preparation -- Hybridization, Washing, Scanning, and Analysis of Microarrays -- Conclusions -- References -- 38.Application of Next-Generation Sequencing Technologies to Viroids / Ahmed Hadidi -- Introduction -- Development of NGS Platforms -- Sequencing Platform Selection -- Bioinformatic Software Tools for Data Analysis -- Cost of DNA Sequencing by NGS -- Current Application of NGS Technologies to Viroids -- References

Note continued: pt. V CONTROL MEASURES FOR VIROIDS AND VIROID DISEASES -- 39.Quarantine and Certification for Viroids and Viroid Diseases / Delano James -- Introduction -- Phytosanitary Regulation in the European Union -- Phytosanitary Regulation in North America -- Quarantine -- Certification -- Conclusions -- References -- 40.Viroid Elimination by Thermotherapy, Cold Therapy, Tissue Culture, In Vitro Micrografting, or Cryotherapy / Zhibo Zhang -- Introduction -- Thermotherapy -- Cold Therapy -- Meristem Tissue Culture -- In Vitro Micrografting -- Cryotherapy -- References -- 41.Decontamination Measures to Prevent Mechanical Transmission of Viroids / Kai-Shu Ling -- Introduction -- Understanding the Means of Possible Viroid Introduction -- Disinfectants Against Mechanical Transmission of Viroids -- Integrated Disease Management Against Viroid Diseases -- Establishing General Rules of Conduct in Crop Production to Minimize Viroid Spread

Note continued: Disinfection of Greenhouse Between Crops -- Acknowledgments -- References -- 42.Strategies to Introduce Resistance to Viroids / Natalia Kovalskaya -- Introduction -- Early Molecular Methods -- Cross-Protection -- Double-Stranded RNA Interference -- Transgenic Methods for Controlling Viroid Diseases -- Future Outlook -- References -- pt. VI GEOGRAPHICAL DISTRIBUTION OF VIROIDS AND VIROID DISEASES -- 43.Geographical Distribution of Viroids in the Americas / Edward V. Podleckis -- Fruit Tree Viroids -- Grapevine Viroids -- Viroids of Ornamental Plants -- Hop Viroids -- Viroids of Solanaceous Crops and Wild Species -- Acknowledgments -- References -- 44.Geographical Distribution of Viroids in Europe / Vicente Pallas -- Fruit Tree Viroids -- Grapevine Viroids -- Pospiviroids on Ornamental and Herbaceous Crop Species -- Hop Viroids -- Coleus Viroids -- Members of the Family Avsurwiroidae in Herbaceous Crops -- References

Note continued: 45.Geographical Distribution of Viroids in Africa and the Middle East / Ahmed Hadidi -- Avsunviroidae; Avsunviroid; Avocado Sunblotch Viroid -- Avsunviroidae; Pelamoviroid; Peach Latent Mosaic Viroid -- Pospiviroidae; Pospiviroid; Potato Spindle Tuber Viroid -- Pospiviroidae; Pospiviroid; Tomato Chlorotic Dwarf Viroid -- Pospiviroidae; Pospiviroid; Tomato Apical Stunt Viroid -- Pospiviroidae; Pospiviroid; Columnea Latent Viroid -- Pospiviroidae; Pospiviroid; Chrysanthemum Stunt Viroid -- Pospiviroidae; Pospiviroid; Citrus Exocortis Viroid and Citrus Viroid Complexes -- Pospiviroidae; Hostuviroid; Hop Stunt Viroid -- Pospiviroidae; Apscaviroid; Pear Blister Canker Viroid, Apple Dimple Fruit Viroid, Apple Scar Skin Viroid -- Pospiviroidae; Apscaviroid; Australian Grapevine Viroid, Grapevine Yellow Speckle Viroid I, Grapevine Yellow Speckle Viroid 2 -- Pospiviroidae; Apscaviroid; Citrus Bent Leaf Viroid, Citrus Dwarfing Viroid

Note continued: Pospiviroidae; Apscaviroid; Citrus Viroid V -- Pospiviroidae; Cocadviroid; Citrus Bark Cracking Viroid -- Acknowledgments -- References -- 46.Geographical Distribution of Viroids in Oceania / Andrew D.W. Geering -- Avocado Sunblotch Viroid (ASBVd) -- Citrus Viroids -- Grapevine Viroids -- Hop Viroids -- Chrysanthemum Viroids -- Palm Viroids -- Pear Blister Canker Viroid (PBCVd) -- Peach Latent Mosaic Viroid (PLMVd) -- Solanaceous Plant Viroids -- Acknowledgments -- References -- 47.Geographical Distribution of Viroids in South, Southeast, and East Asia / Teruo Sano -- Fruit Tree Viroids -- Grapevine Viroids -- Ornamental Viroids -- Palm Tree Viroids -- Hop Viroids -- Solanaceous Crop Viroids -- Acknowledgments -- References -- pt. VII SPECIAL TOPICS -- 48.Seed, Pollen, and Insect Transmission of Viroids / Rosemarie W. Hammond -- Seed and Pollen Transmission in Members of the Family Pospiviroidae

Note continued: Seed and Pollen Transmission in Members of the Family Avsunviroidae -- Detection Methods and Decontamination of Seed -- Seed Health and the Impact of Viroid Seed Transmission on Growers and International Seed Trade -- Insect Transmission -- References -- 49.Genome Editing by CRISPR-Based Technology: Potential Applications for Viroids / Ricardo Flores -- Introduction -- CRISPR/Cas9 Editing Confers Resistance to Plant Viruses -- Introducing Viroid Resistance in Plants -- Targeting Viroid Specific Nucleotide Sites for Genome Editing -- Final Remarks -- Acknowledgments -- References -- SECTION II SATELLITES -- pt. VIII INTRODUCTION -- 50.Satellite Viruses and Satellite Nucleic Acids / Peter Palukaitis -- Introduction -- Detection and Identification of Satellites -- Overview -- Acknowledgments -- References -- pt. IX IMPACT OF SATELLITES -- 51.Economic Significance of Satellites / Donato Gallitelli -- Introduction -- Begomovirus Betasatellites

Note continued: The Cotton and Okra Leaf Curl Diseases -- The African Cassava Mosaic Disease Pandemic -- Satellites Associated With RNA Viruses -- References -- pt. X SATELLITE CHARACTERISTICS -- 52.Biology of Satellites / Luisa Rubino -- Introduction -- Geographical Distribution, Host Range, and Transmission -- Satellite Affinity for the Helper Virus -- Effects on Symptoms -- Cytopathology -- References -- 53.Replication of Satellites / Na-Sheng Lin -- Introduction -- Satellite Virus Replication -- Large satRNA Replication -- Small Linear satRNA Replication -- Small Circular satRNA Replication -- satDNA Replication -- Acknowledgments -- References -- 54.Satellite RNAs: Their Involvement in Pathogenesis and RNA Silencing / Hanako Shimura -- Introduction -- Symptom Alterations by Satellite Nucleic Acids -- Pathogenicity Involving RNA Silencing Machinery in Satellite Nucleic Acids -- sat-siRNAs

Note continued: Mechanisms by Which satRNAs Reduce CMV Genomic RNAs and Attenuate Symptoms -- Molecular Mechanisms Underlying the Distinct Symptoms Induced by CMV satRNA -- Other Examples of Small Linear satRNAs: TCV satC and Cymbidium Ringspot Virus (CymRSV) satRNA -- Concluding Remarks -- Acknowledgments -- References -- 55.Development and Application of Satellite-Based Vectors / Yau-Heiu Hsu -- Introduction -- In Planta Expression of Foreign Gene -- Gene Silencing Vector -- Concluding Remarks: Current Challenges and Future Perspectives of Satellite-Based Vectors -- Acknowledgments -- References -- 56.Origin and Evolution of Satellites / Aurora Fraile -- Introduction -- Origin of Satellite Nucleic Acids -- Experimental Evolution of Satellite Nucleic Acids -- Genetic Variation and Structure of Natural Populations of Satellite Nucleic Acids -- Concluding Remarks -- Acknowledgments -- References -- 57.Satellite Taxonomy / Peter Palukaitis -- Introduction

Note continued: Satellite Viruses -- Satellite DNAs -- Large Linear ss Satellite RNAs -- Small Linear ss Satellites RNAs -- Small Circular ss Satellite RNAs -- Satellite-Like RNAs -- Acknowledgments -- References -- pt. XI TYPES OF SATELLITES -- A.Satellite Viruses -- 58.Biology and Pathogenesis of Satellite Viruses / Karen-Beth G. Scholthof -- Introduction -- Biological and Molecular Properties of STNV -- Biological and Molecular Properties of STMV -- Biological and Molecular Properties of SMWLMV -- Biological and Molecular Properties SPMV -- Plant Satellite Virus Structures -- Acknowledgments -- References -- B.Satellite Nucleic Acids -- 59.Large Satellite RNAs / Na-Sheng Lin -- Introduction -- Roles and Phylogeny of the Proteins Encoded by the Large Secovirid-satRNAs -- Effects of Secovirid-satRNAs on HV Accumulation -- satBaMV -- Roles of the satBaMV P20 Protein -- Effects of satBaMV on HV Accumulation -- Acknowledgments -- References

Note continued: 60.Small Linear Satellite RNAs / Marilyn J. Roossinck -- Introduction -- Nucleotide Sequence and Classification -- Structure and Replication -- Effects on Helper Viruses and Hosts -- Evolution and Origins -- Conclusions -- Acknowledgments -- References -- 61.Small Circular Satellite RNAs / Francesco Di Serio -- Introduction -- Structural Properties -- Biological Properties -- Role of Self-Cleavage in Rolling-Cycle Replication -- Structure of the Hammerhead and Hairpin Ribozymes of sc-satRNAs -- Do sc-satRNAs Code for Functional Proteins? -- Other Putative sc-Satellite RNAs -- Acknowledgments -- References -- 62.Betasatellites of Begomoviruses / Xueping Zhou -- Introduction -- Genome Organization of Betasatellites -- Betasatellite -- Begomovirus Interaction -- Biological Functions of Betasatellites -- Conclusions -- Acknowledgments -- References -- pt. XII APPLICATION TO CONTROL OF VIRUSES -- 63.Satellites as Viral Biocontrol Agents / Donato Gallitelli

Note continued: Introduction -- Strategies to Use CMV satRNA as a Biocontrol Agent -- Mechanisms and Potential Risks -- References.

Viroids and Satellites describes plant diseases and their causal agents while also addressing the economic impact of these diseases. The book discusses various strategies for state-of-the-art methods for the detection and control of pathogens in their infected hosts and provides pivotal information from the discovery of viroids through the analysis of their molecular and biological properties, to viroid pathogenesis, host interactions, and RNA silencing pathways. Students, researchers and regulators will find this to be a comprehensive resource on the topics presented.