Plant Virus Evolution (eBook)

Preface 5
Contents 6
Contributors 8
1 Questions and Concepts in Plant Virus Evolution: a Historical Perspective 10
1.1 Introduction 11
1.2 The Early Period 11
1.3 The Analysis of Viral Genomes and Its Impact on Virus Evolution Research: Quasispecies and Phylogenetics 12
1.4 The Challenge to the Dogma: Viruses Might Be Not So Variable nor Might Their Populations Be So Big 15
1.5 Recent Times: New Concepts and New Challenges 17
1.6 Final Comments 19
References 19
2 Community Ecology of Plant Viruses 24
2.1 Introduction 25
2.2 Patterns of Host and Vector Specialization 26
2.3 Virus Interactions Within and Among Hosts 28
2.4 Virus Spread in a Community Context 29
2.5 Viruses and Plant Invasions 31
2.6 Summary 32
References 33
3 Emerging Plant Viruses: a Diversity of Mechanisms and Opportunities 36
3.1 Introduction 37
3.2 What are Some Plant Viruses that Presently are Considered as Emergent? 38
3.3 What Factor(s) Lead to the Emergence of a Plant Virus? 39
3.4 Reassortment and Recombination: Effective Mechanisms of Variability for DNA Viruses 46
3.5 Tripartite Begomovirus Complexes: A Way for Bipartite Begomoviruses To Fight Host Defense Responses? 48
3.6 Acquisition of Novel Viruslike Entities: Monopartite Begomoviruses and their Satellite DNAs 49
3.7 Emergence of Diseases Caused by Novel Viruslike Agents 51
3.8 Multiple Mechanisms often Underlie the Emergence of Plant Viruses 51
3.9 Bringing Them All Together: Tomato Yellow Leaf Curl/ Leaf Curl Disease in West Africa 52
3.10 Emergence of a New Virus is not always Catastrophic: Failure of New Viral Diseases to Emerge Following a Major Change in the Whitefly Vector Population 53
3.11 Conclusions 56
References 57
4 Evolution of Integrated Plant Viruses 61
4.1 Introduction 62
4.2 Plant DNA Viruses 63
4.3 Detection of Integrated Plant DNA Virus Sequences 65
4.4 EPRVs Identified in Plant Genomes 67
4.5 Integration of DNA Copies of RNA Viruses and Viroids 70
4.6 Evolution 71
4.7 Conclusions 83
References 84
5 Viroids 90
5.1 Introduction 91
5.2 Genome Structure and Replication Strategy 91
5.3 Evolutionary Relationships Among Subviral RNAs 95
5.4 Possible Roles of Conserved Sequence Motifs in Viroid Evolution 97
5.5 Structure of Viroid Quasispecies 98
5.6 Origin and Evolution of Viroids 109
5.7 Concluding Remarks 111
References 112
6 Virus Populations, Mutation Rates and Frequencies 116
6.1 Introduction 117
6.2 Mutation Sources and Mutagenic Agents 117
6.3 Quantifying Methods 119
6.4 Mutational Spectrum 119
6.5 Mutation Rates Versus Adaptation 120
6.6 Intrahost Versus Interhost Diversity of Plant Virus Population 121
6.7 Replication Strategy 122
6.8 RNA Versus DNA Viruses 123
6.9 Virus Populations 124
6.10 Conclusion 124
References 125
7 Genetic Bottlenecks 129
7.1 Introduction 130
7.2 Bottlenecks During Systemic Infections 131
7.3 Bottlenecks During Horizontal Transmission 132
7.4 Bottlenecks During Vertical Transmission 132
7.5 Genetic Drift Versus Selection 133
7.6 Effective Population Size 133
7.7 Muller’s Ratchet in Plant Viruses 134
7.8 Bottlenecks and Speciation 135
7.9 Conclusions 135
References 135
8 Recombination in Plant RNA Viruses 138
8.1 Introduction 139
8.2 The Benefit of RNA Recombination to RNA Virus Evolution 139
8.3 The Role of RNA Recombination in Plant Virus Variability 141
8.4 Experimental Approaches to Study Viral RNA Recombination 143
8.5 Mechanisms of RNA Recombination 144
8.6 Classification of RNA Recombinants 145
8.7 The Role of Viral Replication Proteins in RNA Recombination 148
8.8 Viral RNA Sequences Form Recombination Hotspots and Coldspots 150
8.9 The Role of the Host Genes in RNA Recombination 152
8.10 Conclusions 154
References 155
9 Symbiosis, Mutualism and Symbiogenesis 162
9.1 Introduction 162
9.2 Virus–Host Symbiosis 163
9.3 Virus–Host Symbiogenesis 164
9.4 Virus–Virus Symbiosis 164
9.5 Virus–Virus Symbiogenesis 165
9.6 Conclusions 166
References 166
10 Methods for Analyzing Viral Evolution 170
10.1 Introduction 171
10.2 Alignment Strategies 171
10.3 Model Selection: Beyond Kimura 2-Parameter 176
10.4 Phylogenetic Inference: Picking Trees from the Forest 181
10.5 Population Inference 188
10.6 Summary 200
References 200
11 Virus Evolution and Taxonomy 210
11.1 Brief Overview of Virus Taxonomy 211
11.2 Elements Dictating Taxonomy 211
11.3 Taxonomy and Evolution 212
11.4 The Problems of Plant Virus Taxonomy 215
11.5 Concluding Remarks 219
References 221
Index 223