Fundamentals of Viroid Biology

1st Edition - November 16, 2023
Editors: Charith Raj Adkar-Purushothama, Teruo Sano, Jean-Pierre Perreault, Sreenivasa Marikunte Yanjarappa, Francesco Di Serio, José-Antonio Daròs
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 6 8 8 - 4
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 9 6 8 9 - 1

Fundamentals of Viroid Biology provides a comprehensive introduction to emerging research on viroids and their biology. The book is organized into three parts, with sections… Read more

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Fundamentals of Viroid Biology provides a comprehensive introduction to emerging research on viroids and their biology. The book is organized into three parts, with sections that discuss historical perspectives as well as information on classifications, structure, life cycle and replication and viroid movement. The book goes on to discuss viroid diseases and their geographic distributions across Asia, Europe, Africa, Australia, North and South America. Viroid pathogenesis and viroid-host interaction rounds out the coverage which includes viroid associated disease symptoms and viroid regions associated and viroid-host protein and translations. Detection and disease control strategies are also covered.

Contributed by an international group of renown contributors in viroid research, this book is a useful introductory reference to advanced undergraduates and graduate and postgraduate students. It is also ideal for early career researchers and scientists engaged in the study of viroid biology, virology, plant virology and microbiology.

Cover image
Title page
Table of Contents
Copyright
Dedication
Contributors
Foreword
Preface
Introduction
Section A: Introduction
Chapter 1 Milestones in viroid research
Abstract
Graphical representation
Acknowledgments
Definitions
Learning objectives
Fundamental introduction
Viroid conformation(s)
Replication
Pathogenicity
Movement
Origin/evolution
Epidemiology/control
Questions for the reader
Further reading
References
Chapter 2 Viroid taxonomy
Graphical representation
Abstract
Definitions
Chapter outline
Learning objectives
Fundamental introduction
History of viroid classification
Demarcation criteria of viroid families
Demarcation criteria of viroid genera
Species demarcation criteria
Current viroid classification
Protocols/procedures/methods
Assigning a name to novel viroid species
Prospective and future implications
Chapter summary
Study question
References
Chapter 3 Structure of viroids
Abstract
Graphical representation
Acknowledgments
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Avsunviroidae
Pospiviroidae
Perspective
Questions for the reader
References
Chapter 4 Replication and movement of viroids in host plants
Abstract
Graphical representation
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Viroid replication occurs through a rolling circle mechanism
Replication of nuclear viroids
Replication of chloroplastic viroids
How viroid RNAs reach the organelles where they replicate
Intercellular and vascular movement
Prospective and future implications
Chapter summary
Study question
References
Section B: Prospecting for viroid
Chapter 5 Viroids diseases and its distribution in Asia
Graphical representation
Abstract
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Viroid diseases of vegetable crops
Viroids infecting ornamental plants
Viroids infecting pome fruits
Viroids infecting avocado
Viroids infecting citrus
Viroid infecting coconut palm
Viroids infecting grapevine
Viroids of hop
Viroids infecting other fruit trees and weeds
Prospective
Future implications
Chapter summary
Study questions
Further reading
References
Chapter 6 Viroid-associated plant diseases in Europe
Abstract
Graphical representation
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Viroids of herbaceous plants
Viroids of specialized crops
Viroids of woody plants
Procedures
Prospective
Future implications
Chapter summary
Study questions
Further reading
References
Chapter 7 Naturally occurring viroid diseases of economically important plants in Africa
Abstract
Graphical representation
Acknowledgment
Definitions
Chapter outline
Learning objectives
Introduction
Occurrence of Avsunviroidae members in fruits trees in Africa
Occurrence of Pospiviroidae members in fruits trees in Africa
Occurrence of viroids in herbaceous plants
Procedure
Prospective
Future implications
Chapter summary
Study questions
Further reading
References
Chapter 8 Finding the coconut cadang-cadang and tinangaja viroids, naturally occurring pathogens of tropical monocotyledons of Oceania
Graphical representation
Abstract
Acknowledgments
Definitions
Chapter outline
Learning objectives
Fundamental introduction
A short history of cadang-cadang disease
Discovery of coconut cadang-cadang viroid in the Philippines
CCCVd beyond the Philippines
Prospective: Are there viroid sequences in progenitors of the palms?
Chapter summary
Study question
Further reading
References
Chapter 9 Viroids and their distribution in North America
Graphical representation
Abstract
Definitions
Chapter outline
Learning objectives
Introduction
Viroids of solanaceous plants
Viroids of ornamentals
Viroids of Humulus plants
Viroids of fruit trees
Viroids in pome and stone fruit trees
Viroids in citrus
Viroids in grapevine
Chapter summary
Study questions
Further reading
References
Chapter 10 Viroid-associated plant diseases in South America
Graphical representation
Abstract
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Herbaceous ornamentals
Horticultural plants
Fruit trees and grapevine
Prospective
Future implications
Chapter summary
Study questions
Further reading
References
Section C: Viroid pathogenesis and viroid-host interaction
Chapter 11 Viroid pathogenicity
Abstract
Graphical representation
Definitions
Chapter outline
Learning objectives
Introduction
Viroid-associated symptoms in host plants
Structural motifs and nucleotides modulating viroid pathogenicity
Role of the host components in viroid pathogenicity
Viroid-induced biochemical changes
Effect of viroids on host gene expression and the host response to viroid infection
Role of gene silencing in viroid pathogenesis
Prospective
Future implications
Chapter summary
Protocols/procedures/methods
Study questions
Further reading
References
Chapter 12 Viroids and protein translation
Abstract
Graphical representation
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Non-coding nature of viroids
Changes in protein expression associated with viroid infection
Interaction of viroids with host proteins
Alterations in the translational machinery caused by viroids
Revisiting viroid translation capacity: are negative results conclusive?
Chapter summary
Study questions
Further reading
References
Chapter 13 Viroid infection and host epigenetic alterations
Graphical representation
Abstract
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Discovery of RNA directed DNA methylation
Viroid infection and host epigenetic changes
Potential ways of promoting viroid-associated host epigenetic changes
Remarks and future perspectives
Simplified strategy to analyze epigenetic changes induced by viroid infection*
Study questions
Further reading
References
Chapter 14 Transcriptomic analyses provide insights into plant-viroid interactions
Graphical representation
Abstract
Acknowledgment
Chapter outline
Learning objectives
Fundamental introduction
Transcriptomic studies of viroid-infected samples
Gene expression profiles underlying plant-viroid interactions
Methods for transcriptomic analyses
Prospective
Future implications
Chapter summary
Study questions
Further reading
References
Chapter 15 Viroid-induced RNA silencing and its secondary effect on the host transcriptome
Graphical representation
Abstract
Definitions
Chapter outline
Learning objectives
Introduction
RNA silencing
Viroid induced RNA silencing
Direct effect of viroid derived small RNAs on the host transcriptome
Generation of secondary siRNAs triggered by viroid infection and their global effect on both the transcriptome and the phenotype—A working hypothesis
Protocols/procedures/methods
Perspective
Future implications
Chapter summary
Study questions
Further reading
References
Chapter 16 Detection of viroids
Abstract
Graphical representation
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Sample collection and preparation
Detection methods
Method selection
Prospective
Chapter summary
Study questions
Further reading
References
Chapter 17 Viroid disease control and strategies
Abstract
Graphical representation
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Viroid replication and spread—Control of viroid diseases
Conventional methods of control
Transgenic methods of control
Perspective/future implications
Questions for the reader
References
Chapter 18 Policies, regulations, and production of viroid-free propagative plant materials for sustainable agriculture
Graphical representation
Abstract
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Chapter
Protocols/procedures/methods
Prospective
Future implications
Chapter summary
Study questions
References
Chapter 19 Bioinformatic approaches for the identification and discovery of viroid-like genomes
Abstract
Graphical representation
Definitions
Chapter outline
Learning objectives
Introduction
The discovery of viroid-like RNAs
Initial approaches to identify viroid-like RNAs through bioinformatics
De novo discovery of viroid-like genomes
Perspective
Study questions
Further reading
References
Chapter 20 Contributions of viroid research to methods for RNA purification, diagnostics, and secondary structure prediction
Abstract
Graphical abstract
Definitions
Chapter outline
Learning objectives
Fundamental introduction
Chapter
Protocols/procedures/methods
Future implications
Study questions
Further reading
References
Chapter 21 Future perspectives in viroid research
Abstract
Graphical representation
Acknowledgments
Chapter outline
Learning objectives
Fundamental introduction
Do viroids infect hosts other than flowering plants?
How do viroid RNAs survive in the hostile environment of an infected cell?
Do viroids contain auto-catalytic motifs other than hammerhead?
May viroids still encode proteins?
Are viroids useful for biotechnology?
Questions for the reader
References
Index

Charith Raj Adkar-Purushothama

Dr. Charith Raj Adkar-Purushothama PhD has more than 19 years of research experience in molecular biology, bioinformatics, viroid-host interactions, RNA biology and metagenomics. He earned his master’s degree in microbiology from the University of Mysore, India and a doctorate from the University of Milano, Italy. He did his first postdoctoral training with Prof. Teruo Sano at Hirosaki University, Japan, where he worked on the RNA silencing strategies against viroid diseases. He completed his second postdoctoral training in the laboratory of Prof. Jean-Pierre Perreault in the Université de Sherbrooke, Canada, in the field of plant-viroid interaction using biochemistry, molecular biology and bioinformatics tools. He has published over 60 original research articles, four review articles, two book chapters, presented in 30 international scientific conferences, and is a Associate Editor of Fundamental Virology (Frontiers in Virology,) and a Topic Editor for the journal, Viruses. He hold a patent issued by the Government of India.

Affiliations and expertise

Adjunct Professor, Department of Biochemistry, Universite de Sherbrooke, Canada

Teruo Sano

Prof. Teruo Sano PhD is a plant virologist with more than 40 years of research experience in viroid biology, viroid-host interaction, and biotechnology. After obtaining a PhD from Hokkaido University, Japan, he did his postdoctoral studies in Microbiology and Plant Pathology Laboratory, USDA-ARS, Beltsville, the USA, for two years. He joined Hirosaki University as an associate professor in 1992 and became a professor in the year 2005. He received 35 research grants and has published more than 140 original scientific articles, 32 scientific reports, 18 book chapters, and three review articles. He has also holds three patents issued by the Government of Japan. He is an invited speaker for more than 25 scientific meetings. He is one of the virologists who well-balanced both fundamental and applied research. He is one of the pioneering researchers who showed transgenic potato plants expressing a double-strand RNA ribonuclease is resistant to potato spindle tuber viroid. He is a recipient of the 2020 Japan Academy Prize for his studies detecting and isolating viroid's, that causes disease in plants.

Affiliations and expertise

Professor Emeritus, Hirosaki University, Hirosaki, Japan

Jean-Pierre Perreault

Prof. Jean-Pierre Perreault completed in BA, MA, and PhD in biochemistry at the University of Montreal, Canada. Under Dr. Robert J. Cedergren, he participated in synthesizing the first mixed RNA/DNA polymers. This pioneering work allowed him to receive the Prix d'Excellence de l'Académie des Grands Montréalais for the biomedical sector's best thesis in 1991. He then completed postdoctoral training at Yale University. Under Professor Sidney Altman's direction, he worked on RNase P's characterization, an enzyme essential for life. Currently, he is the Vice-President, Research and Graduate Studies at the University of Sherbrooke. He was the first director of the RNA Biology Research Center and a co-founder of RiboClub, the Canadian group of researchers interested in studying RNAs. He also chaired the Canadian Society for Biochemistry, Molecular and Cellular Biology. He has more than 25 years of teaching and research experience in Biochemistry, RNA biology, viroid structure and cancer biology.

Affiliations and expertise

Vice-President, Research and Graduate Studies RNA Group/Groupe ARN, Département de Biochimie, Faculté de Médecine des Sciences de la Santé, Pavillon de Recherche Appliquée au Cancer, Université de Sherbrooke, Sherbrooke, Canada

Sreenivasa Marikunte Yanjarappa

Dr. M. Y. Sreenivasa PhD currently working as Professor and Chairman at Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysore, India. He is actively involved in research for more than 19 years in the field of mycology, myco-toxicology and Plant pathology. He is also engaged in viroid diseases of the economical plant in India. He has published more than 100 international/national scientific papers, including 15 book chapters and editorial articles. He is a principal and co-investigator for funded research grants. He has an Indian patent issued by the Govt. of India. In recognition of his research outputs, he was awarded Indo-USA Raman postdoctoral fellowship to visit USA for his post doctoral studies, the International Faculty Development award by the Kennesaw State University, Kennesaw, USA, Indo-Canada Shastri Fellow to visit Ottawa university, Canada. He is an Associate Editor for Frontiers in Microbiology, editing three research topics, member of the review editorial boards of several international journals. He has been invited as Keynote Speakers and Experts in various Plant pathology, microbiology, mycology and Life Sciences-based conferences and workshops.

Affiliations and expertise

Professor and Chairman, Department of studies in Microbiology, University of Mysore, Manasagangotri, Mysore, India

Francesco Di Serio

Francesco Di Serio PhD is Research Director at the Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione Sostenibile delle Piante (IPSP), SS Bari, Italy. He obtained his PhD degree in Plant Virology at the University of Naples Federico II. His PhD and early postdoctoral research focused on viroids' characterization in the laboratory directed by Prof. Ricardo Flores (CSIC-Universidad Politécnica de Valencia, Spain). His second postdoc was carried out in the laboratory directed by Prof. Frederick Meins (Friedrich Miescher Institute, Basel, Switzerland), where he studied RNA silencing and virus movement in tobacco. Currently, Dr.. Di Serio is a Member and Vice-Chair of the Plant Health Panel of the European Food Safety Authority (EFSA). He is Member of Accademico aggregato) of the Georgofili Accademy. Since 2011, he has chaired the Viroid Study Group of the International Committee on Taxonomy of Viruses. In 2014, F. Di Serio obtained the Italian National Scientific Habilitation as a full professor in Plant Pathology and Entomology. He has more than 25 years of teaching and research experience in viroid characterization, taxonomy, characterization of novel viroid-like RNAs and viruses and has published in a hundred research articles in refereed journals.

Affiliations and expertise

Research Director at the Consiglio Nazionale delle Ricerche (CNR), Istituto per la Protezione Sostenibile delle Piante (IPSP), SS Bari, Italy

José-Antonio Daròs

José-Antonio Daròs PhD is a Research Professor at the Institute for Plant Molecular and Cell Biology (IBMCP) where he supervises the research group "Plant Virus Biotechnology." Dr. Daròs obtained his degree in Biological Sciences at the University of Valencia (Spain) and his PhD in this same University, with research work about viroid replication. He gained postdoctoral experience working in potyvirus molecular biology for three years and a half in the laboratory of Prof. James C. Carrington at Texas A&M University and Washington State University in the USA. He joined the laboratory of Prof. Ricardo Flores at IBMCP in 1998, investigating the viroid-plant interaction. In 2004, he obtained his own CSIC permanent position as a Scientist in this same Institute. Dr. Daròs has more than 25 years of teaching and research experience and authored more than one hundred research, review articles and book chapters about various aspects of plant virus, viroid biology, and biotechnology.

Affiliations and expertise

Research Professor, Institute for Plant Molecular and Cell Biology (IBMCP), Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València, Valencia, Spain