plant virology || preface

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vii The first three editions of Plant Virology (1970, 1981, and 1991) were written by R.E.F. (Dick) Matthews, and I dedi- cated the fourth edition (2002) to his memory. Thus, new editions of Plant Virology have been published at approxi- mately 10-year intervals, and this fifth edition follows this timing. As was noted in the prefaces for previous edi- tions, each has chronicled ever-increasing major advances in the subject. The last decade has been no exception—if anything, the rate of progress has increased even more remarkably. This is illustrated in the graph of annual num- bers of publications on the subject shown in Figure 1.2. I consider that there have been more advances in the under- standing of plant virus functions in the last 10–15 years than in the previous forty. As well as studies on viruses causing important crop diseases leading to new control approaches, there has been a sea change in the applica- tion of genomics and other “omics” to the understanding of how viruses function. This is beginning to lead to infor- mation on the interactions of the genomes of viruses, their hosts, and their vectors which I am terming “plant viro- mics” and which is illustrated in the cover design. We are just starting to unravel the complexities of plant viromics, and I consider that this will be an area that will provide opportunities for major advances over the next decade or more. However, as far as trying to describe the subject of Plant Virology in this book, these developments have pre- sented major challenges. To fully unravel the interactions between, say, a virus and its host, one has to understand the normal functioning of not only the relatively simple virus but also the very complex host at the biochemical, molecular, and genomic and other “omic” levels; many of the details of host functions would be the subject of one or more textbooks on their own. I have included references to reviews (where available) on some host topics that are likely to be of significance. Also one has to have informa- tion on vector “omics” which is very limited at present. The sixteen chapters in this new edition are divided into four major sections that form a logical progression in gaining an understanding of the subject. In the chapters in Section I, I outline some of the basic features of plant virology starting with an introductory chapter giving the history of the subject and definitions of a virus. This leads into a description of the classification and taxonomy of 92 genera and more than 1300 recognized and tentative spe- cies of plant viruses (compared with 977 species in 70 genera recognized 10 years ago); further details of these are given in various appendices. However, the increase of taxonomic information has led to and is continuing to raise difficulties of definition, which the International Committee on the Taxonomy of Viruses will have to resolve. For instance, should there be different criteria for discriminating between species in the various genera or should there be a commonality for most, if not all, gen- era? In Chapter 3, the structure and assembly of the vari- ous types of plant virus particles are discussed; even in this seemingly well-established subject there are new concepts and ideas. The other two chapters in this section describe the symptoms and host ranges of plant viruses, and various other agents that induce virus-like diseases, together with some of the practicalities of working on biological aspects of these pathogens. In the seven chapters in Section II, molecular mecha- nisms involved in the various stages of the virus infection cycle are discussed. This has presented another challenge as it is becoming increasingly apparent that most, if not all, of the stages are closely integrated with each other. For ease of presentation and understanding, each of the stages (gene expression, replication, interactions with permissive and non-permissive hosts, and with vectors) is presented in a separate chapter; one chapter is devoted to RNA silenc- ing which plays a pivotal role in many of these stages. A further chapter in this section discusses the origins and evolution of viruses, which, through coevolution, is related to the evolution of the host and the vector. The three chapters in Section III deal with applied aspects of plant virology and cover the detection and diagnosis of plant viruses, their ecology, epidemiology and control, and their technological uses. The latter high- lights one of the “spin-offs” of plant virology, namely the application of their relatively simple genomes and simple organized capsid structures to the pharmacology and nano- technology industries. In Section IV, I attempt to look to the future by discuss- ing the integration of the processes in the viral infection cycle leading on to the interactions between the viral, host, and vector genomes (plant viromics). Preface

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vii

The first three editions of Plant Virology (1970, 1981, and 1991) were written by R.E.F. (Dick) Matthews, and I dedi-cated the fourth edition (2002) to his memory. Thus, new editions of Plant Virology have been published at approxi-mately 10-year intervals, and this fifth edition follows this timing. As was noted in the prefaces for previous edi-tions, each has chronicled ever-increasing major advances in the subject. The last decade has been no exception—if anything, the rate of progress has increased even more remarkably. This is illustrated in the graph of annual num-bers of publications on the subject shown in Figure 1.2. I consider that there have been more advances in the under-standing of plant virus functions in the last 10–15 years than in the previous forty. As well as studies on viruses causing important crop diseases leading to new control approaches, there has been a sea change in the applica-tion of genomics and other “omics” to the understanding of how viruses function. This is beginning to lead to infor-mation on the interactions of the genomes of viruses, their hosts, and their vectors which I am terming “plant viro-mics” and which is illustrated in the cover design. We are just starting to unravel the complexities of plant viromics, and I consider that this will be an area that will provide opportunities for major advances over the next decade or more. However, as far as trying to describe the subject of Plant Virology in this book, these developments have pre-sented major challenges. To fully unravel the interactions between, say, a virus and its host, one has to understand the normal functioning of not only the relatively simple virus but also the very complex host at the biochemical, molecular, and genomic and other “omic” levels; many of the details of host functions would be the subject of one or more textbooks on their own. I have included references to reviews (where available) on some host topics that are likely to be of significance. Also one has to have informa-tion on vector “omics” which is very limited at present.

The sixteen chapters in this new edition are divided into four major sections that form a logical progression in gaining an understanding of the subject. In the chapters in Section I, I outline some of the basic features of plant virology starting with an introductory chapter giving the history of the subject and definitions of a virus. This leads into a description of the classification and taxonomy of 92

genera and more than 1300 recognized and tentative spe-cies of plant viruses (compared with 977 species in 70 genera recognized 10 years ago); further details of these are given in various appendices. However, the increase of taxonomic information has led to and is continuing to raise difficulties of definition, which the International Committee on the Taxonomy of Viruses will have to resolve. For instance, should there be different criteria for discriminating between species in the various genera or should there be a commonality for most, if not all, gen-era? In Chapter 3, the structure and assembly of the vari-ous types of plant virus particles are discussed; even in this seemingly well-established subject there are new concepts and ideas. The other two chapters in this section describe the symptoms and host ranges of plant viruses, and various other agents that induce virus-like diseases, together with some of the practicalities of working on biological aspects of these pathogens.

In the seven chapters in Section II, molecular mecha-nisms involved in the various stages of the virus infection cycle are discussed. This has presented another challenge as it is becoming increasingly apparent that most, if not all, of the stages are closely integrated with each other. For ease of presentation and understanding, each of the stages (gene expression, replication, interactions with permissive and non-permissive hosts, and with vectors) is presented in a separate chapter; one chapter is devoted to RNA silenc-ing which plays a pivotal role in many of these stages. A further chapter in this section discusses the origins and evolution of viruses, which, through coevolution, is related to the evolution of the host and the vector.

The three chapters in Section III deal with applied aspects of plant virology and cover the detection and diagnosis of plant viruses, their ecology, epidemiology and control, and their technological uses. The latter high-lights one of the “spin-offs” of plant virology, namely the application of their relatively simple genomes and simple organized capsid structures to the pharmacology and nano-technology industries.

In Section IV, I attempt to look to the future by discuss-ing the integration of the processes in the viral infection cycle leading on to the interactions between the viral, host, and vector genomes (plant viromics).

Preface

viii Preface

The rapid developments over the past decade have necessitated not just a revision of the fourth edition but a substantial rewriting of it. However, I consider it important to retain material from previous editions giving descrip-tions of phenomena studied over the years as these can, and do, form the basis of understanding newly recognized mechanisms. I hope to have expressed the dynamism of the subject, and I have tried in various places to point to future directions that may prove to be scientifically profit-able. There will be new technologies arising in the future, for example virtual cell biology (Karr et al., 2012) which should be applicable to further unraveling of viral genom-ics. However, older approaches and observations should not be forgotten.

I am greatly indebted to a large number of colleagues for their helpful discussion and advice on various topics

and for access to prepublication material. These are too numerous to name individually and I hope that they will accept my apologies for not giving them individual recog-nition. My eternal gratitude goes to my wife, Jennifer, who has tolerated the “piles of papers” all over the house and disruptions to social schedules, and who has given me con-tinuous encouragement.

Roger HullMay 2013

REFERENCE

Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., et al., 2012. The dawn of virtual cell biology. Cell 150, 248–250.