{"title":"Plant Virus Vectors 3.0: Transitioning into Synthetic Genomics.","authors":"Will B Cody, Herman B Scholthof","doi":"10.1146/annurev-phyto-082718-100301","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100301","url":null,"abstract":"<p><p>Plant viruses were first implemented as heterologous gene expression vectors more than three decades ago. Since then, the methodology for their use has varied, but we propose it was the merging of technologies with virology tools, which occurred in three defined steps discussed here, that has driven viral vector applications to date. The first was the advent of molecular biology and reverse genetics, which enabled the cloning and manipulation of viral genomes to express genes of interest (vectors 1.0). The second stems from the discovery of RNA silencing and the development of high-throughput sequencing technologies that allowed the convenient and widespread use of virus-induced gene silencing (vectors 2.0). Here, we briefly review the events that led to these applications, but this treatise mainly concentrates on the emerging versatility of gene-editing tools, which has enabled the emergence of virus-delivered genetic queries for functional genomics and virology (vectors 3.0).</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"211-230"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100301","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37317483","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mark L Gleason, Rong Zhang, Jean C Batzer, Guangyu Sun
{"title":"Stealth Pathogens: The Sooty Blotch and Flyspeck Fungal Complex.","authors":"Mark L Gleason, Rong Zhang, Jean C Batzer, Guangyu Sun","doi":"10.1146/annurev-phyto-082718-100237","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100237","url":null,"abstract":"<p><p>Sooty blotch and flyspeck (SBFS) fungi produce superficial, dark-colored colonies on fruits, stems, and leaves of many plant genera. These blemishes are economically damaging on fruit, primarily apple and pear, because they reduce the sale price of fresh fruit. Fungicide spray programs can control SBFS but are costly and impair human and environmental health; thus, less chemically intensive management strategies are needed. Although the scientific study of SBFS fungi began nearly 200 years ago, recent DNA-driven studies revealed an unexpectedly diverse complex: more than 100 species in 30 genera of Ascomycota and Basidiomycota. Analysis of evolutionary phylogenetics and phylogenomics indicates that the evolution of SBFS fungi from plant-penetrating ancestors to noninvasive ectophytic parasites was accompanied by a massive contraction of pathogenicity-related genes, including plant cell wall-degrading enzymes and effectors, and an expansion of cuticle-degradation genes. This article reviews progress in understanding SBFS taxonomy and ecology and improving disease management. We also highlight recent breakthroughs in reconstructing the evolutionary origins of these unusual plant pathogens and delineating adaptations to their ectophytic niche.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"135-164"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100237","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37295547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Min Zhu, Irene Louise van Grinsven, Richard Kormelink, Xiaorong Tao
{"title":"Paving the Way to Tospovirus Infection: Multilined Interplays with Plant Innate Immunity.","authors":"Min Zhu, Irene Louise van Grinsven, Richard Kormelink, Xiaorong Tao","doi":"10.1146/annurev-phyto-082718-100309","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100309","url":null,"abstract":"<p><p>Tospoviruses are among the most important plant pathogens and cause serious crop losses worldwide. Tospoviruses have evolved to smartly utilize the host cellular machinery to accomplish their life cycle. Plants mount two layers of defense to combat their invasion. The first one involves the activation of an antiviral RNA interference (RNAi) defense response. However, tospoviruses encode an RNA silencing suppressor that enables them to counteract antiviral RNAi. To further combat viral invasion, plants also employ intracellular innate immune receptors (e.g., Sw-5b and Tsw) to recognize different viral effectors (e.g., NSm and NSs). This leads to the triggering of a much more robust defense against tospoviruses called effector-triggered immunity (ETI). Tospoviruses have further evolved their effectors and can break Sw-5b-/Tsw-mediated resistance. The arms race between tospoviruses and both layers of innate immunity drives the coevolution of host defense and viral genes involved in counter defense. In this review, a state-of-the-art overview is presented on the tospoviral life cycle and the multilined interplays between tospoviruses and the distinct layers of defense.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"41-62"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100309","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37075521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Activity and Phylogenetics of the Broadly Occurring Family of Microbial Nep1-Like Proteins.","authors":"Michael F Seidl, Guido Van den Ackerveken","doi":"10.1146/annurev-phyto-082718-100054","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100054","url":null,"abstract":"<p><p>Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLP) have an extremely broad taxonomic distribution; they occur in bacteria, fungi, and oomycetes. NLPs come in two forms, those that are cytotoxic to eudicot plants and those that are noncytotoxic. Cytotoxic NLPs bind to glycosyl inositol phosphoryl ceramide (GIPC) sphingolipids that are abundant in the outer leaflet of plant plasma membranes. Binding allows the NLP to become cytolytic in eudicots but not monocots. The function of noncytotoxic NLPs remains enigmatic, but the expansion of <i>NLP</i> genes in oomycete genomes suggests they are important. Several plant species have evolved the capacity to recognize NLPs as molecular patterns and trigger plant immunity, e.g., <i>Arabidopsis thaliana</i> detects nlp peptides via the receptor-like protein RLP23. In this review, we provide a historical perspective from discovery to understanding of molecular mechanisms and describe the latest developments in the NLP field to shed light on these fascinating microbial proteins.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"367-386"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100054","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37140338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Lessons from a Life in Time and Space.","authors":"Jeremy J Burdon","doi":"10.1146/annurev-phyto-082718-095938","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-095938","url":null,"abstract":"<p><p>A research career investigating epidemiological and evolutionary patterns in both natural and crop host-pathogen systems emphasizes the need for flexibility in thinking and a willingness to adopt ideas from a wide diversity of subdisciplines. Here, I reflect on the pivotal issues, research areas, and interactions, including the role of science management, that shaped my career in the hope of demonstrating that career paths and collaborations in science can be as diverse and unpredictable as the natural world in which we study our organisms of choice.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"1-13"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-095938","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37411443","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Boxwood Blight: Threat to Ornamentals.","authors":"Margery L Daughtrey","doi":"10.1146/annurev-phyto-082718-100156","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100156","url":null,"abstract":"<p><p>Boxwood blight, caused by <i>Calonectria pseudonaviculata</i> and <i>Calonectria henricotiae</i>, has had devastating effects in gardens since its first appearance in the United Kingdom in 1994. The disease affects two other plants in the Buxaceae: sweet box (<i>Sarcococca</i> spp.) and pachysandra (<i>Pachysandra</i> spp.). <i>C. pseudonaviculata</i> was likely introduced to Europe by nursery trade from East Asia on an ornamental species and then to western Asia and North America. Thus far, <i>C. henricotiae</i> has been seen only in Europe. Boxwood, valued at $126 million wholesale per year in the United States alone, is now besieged by an aggressive foliar blight active over a broad temperature range when there are long periods of leaf wetness. Research on inoculum, means of dissemination, cultivar susceptibility, environmental influences, fungicides, sanitizers, and detection methods has vastly improved knowledge of this new invasive disease in a short time. Boxwood with genetic resistance to the disease is critically needed.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"189-209"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100156","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37126817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Louise-Marie Dandurand, Inga A Zasada, Xiaohong Wang, Benjamin Mimee, Walter De Jong, Richard Novy, Jonathan Whitworth, Joseph C Kuhl
{"title":"Current Status of Potato Cyst Nematodes in North America.","authors":"Louise-Marie Dandurand, Inga A Zasada, Xiaohong Wang, Benjamin Mimee, Walter De Jong, Richard Novy, Jonathan Whitworth, Joseph C Kuhl","doi":"10.1146/annurev-phyto-082718-100254","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100254","url":null,"abstract":"<p><p>The potato cyst nematodes (PCNs) <i>Globodera rostochiensis</i> and <i>Globodera pallida</i> are internationally recognized quarantine pests. Although not widely distributed in either the United States or Canada, both are present and are regulated by the national plant protection organizations (NPPOs) of each country. <i>G. rostochiensis</i> was first discovered in New York in the 1940s, and <i>G. pallida</i> was first detected in a limited area of Idaho in 2006. In Canada, <i>G. rostochiensis</i> and <i>G. pallida</i> were first detected in Newfoundland in 1962 and 1977, respectively, and further detections of <i>G. rostochiensis</i> occurred in British Columbia and Québec, most recently in 2006. Adherence to a stringent NPPO-agreed-upon phytosanitary program has prevented the spread of PCNs to other potato-growing areas in both countries. The successful research and regulatory PCN programs in both countries rely on a network of state, federal, university, and private industry cooperatorspursuing a common goal of containment, management/eradication, and regulation. The regulatory and research efforts of these collaborative groups spanning from the 1940s to the present are highlighted in this review.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"117-133"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100254","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37249949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Kevin V Pixley, Jose B Falck-Zepeda, Ken E Giller, Leland L Glenna, Fred Gould, Carol A Mallory-Smith, David M Stelly, C Neal Stewart
{"title":"Genome Editing, Gene Drives, and Synthetic Biology: Will They Contribute to Disease-Resistant Crops, and Who Will Benefit?","authors":"Kevin V Pixley, Jose B Falck-Zepeda, Ken E Giller, Leland L Glenna, Fred Gould, Carol A Mallory-Smith, David M Stelly, C Neal Stewart","doi":"10.1146/annurev-phyto-080417-045954","DOIUrl":"https://doi.org/10.1146/annurev-phyto-080417-045954","url":null,"abstract":"<p><p>Genetically engineered crops have been grown for more than 20 years, resulting in widespread albeit variable benefits for farmers and consumers. We review current, likely, and potential genetic engineering (GE) applications for the development of disease-resistant crop cultivars. Gene editing, gene drives, and synthetic biology offer novel opportunities to control viral, bacterial, and fungal pathogens, parasitic weeds, and insect vectors of plant pathogens. We conclude that there will be no shortage of GE applications totackle disease resistance and other farmer and consumer priorities for agricultural crops. Beyond reviewing scientific prospects for genetically engineered crops, we address the social institutional forces that are commonly overlooked by biological scientists. Intellectual property regimes, technology regulatory frameworks, the balance of funding between public- and private-sector research, and advocacy by concerned civil society groups interact to define who uses which GE technologies, on which crops, and for the benefit of whom. Ensuring equitable access to the benefits of genetically engineered crops requires affirmative policies, targeted investments, and excellent science.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"165-188"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-080417-045954","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37295546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Resolving <i>Fusarium</i>: Current Status of the Genus.","authors":"Brett A Summerell","doi":"10.1146/annurev-phyto-082718-100204","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100204","url":null,"abstract":"<p><p>The fungal genus <i>Fusarium</i> is one of the most important groups of plant-pathogenic fungi and affects a huge diversity of crops in all climatic zones across the globe. In addition, it is also a human pathogen and produces several extremely important mycotoxins in food products that have deleterious effects on livestock and humans. These fungi have been plagued over the past century by different perspectives of what constitutes the genus <i>Fusarium</i> and how many species occur within the genus. Currently, there are conflicting views on the generic boundaries and what defines a species that impact disease diagnosis, management, and biosecurity legislation. An approach to defining and identifying <i>Fusarium</i> that places the needs of the community of users (especially, in this case, phytopathologists) to the forefront is presented in this review.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"323-339"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100204","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37349782","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Niklaus J Grünwald, Jared M LeBoldus, Richard C Hamelin
{"title":"Ecology and Evolution of the Sudden Oak Death Pathogen <i>Phytophthora ramorum</i>.","authors":"Niklaus J Grünwald, Jared M LeBoldus, Richard C Hamelin","doi":"10.1146/annurev-phyto-082718-100117","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100117","url":null,"abstract":"<p><p>The sudden oak and sudden larch death pathogen <i>Phytophthora ramorum</i> emerged simultaneously in the United States on oak and in Europe on <i>Rhododendron</i> in the 1990s. This pathogen has had a devastating impact on larch plantations in the United Kingdom as well as mixed conifer and oak forests in the Western United States. Since the discovery of this pathogen, a large body of research has provided novel insights into the emergence, epidemiology, and genetics of this pandemic. Genetic and genomic resources developed for <i>P. ramorum</i> have been instrumental in improving our understanding of the epidemiology, evolution, and ecology of this disease. The recent reemergence of EU1 in the United States and EU2 in Europe and the discovery of <i>P. ramorum</i> in Asia provide renewed impetus for research on the sudden oak death pathogen.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"57 ","pages":"301-321"},"PeriodicalIF":10.2,"publicationDate":"2019-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-phyto-082718-100117","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37349781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}