Alexandra J Weisberg, Niklaus J Grünwald, Elizabeth A Savory, Melodie L Putnam, Jeff H Chang
{"title":"Genomic Approaches to Plant-Pathogen Epidemiology and Diagnostics.","authors":"Alexandra J Weisberg, Niklaus J Grünwald, Elizabeth A Savory, Melodie L Putnam, Jeff H Chang","doi":"10.1146/annurev-phyto-020620-121736","DOIUrl":"https://doi.org/10.1146/annurev-phyto-020620-121736","url":null,"abstract":"<p><p>Diseases have a significant cost to agriculture. Findings from analyses of whole-genome sequences show great promise for informing strategies to mitigate risks from diseases caused by phytopathogens. Genomic approaches can be used to dramatically shorten response times to outbreaks and inform disease management in novel ways. However, the use of these approaches requires expertise in working with big, complex data sets and an understanding of their pitfalls and limitations to infer well-supported conclusions. We suggest using an evolutionary framework to guide the use of genomic approaches in epidemiology and diagnostics of plant pathogens. We also describe steps that are necessary for realizing these as standard approaches in disease surveillance.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"311-332"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38944309","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":"Harnessing Eco-Evolutionary Dynamics of Xanthomonads on Tomato and Pepper to Tackle New Problems of an Old Disease.","authors":"Neha Potnis","doi":"10.1146/annurev-phyto-020620-101612","DOIUrl":"https://doi.org/10.1146/annurev-phyto-020620-101612","url":null,"abstract":"<p><p>Bacterial spot is an endemic seedborne disease responsible for recurring outbreaks on tomato and pepper around the world. The disease is caused by four diverse species, <i>Xanthomonas gardneri</i>, <i>Xanthomonas euvesicatoria</i>, <i>Xanthomonas perforans</i>, and <i>Xanthomonas vesicatoria.</i> There are no commercially available disease-resistant tomato varieties, and the disease is managed by chemical/biological control options, although these have not reduced the incidence of outbreaks. The disease on peppers is managed by disease-resistant cultivars that are effective against <i>X. euvesicatoria</i> but not <i>X. gardneri</i>. A significant shift in composition and prevalence of different species and races of the pathogen has occurred over the past century. Here, I attempt to review ecological and evolutionary processes associated with the population dynamics leading to disease emergence and spread. The goal of this review is to integrate the knowledge on population genomics and molecular plant-microbe interactions for this pathosystem to tailor disease management strategies.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"289-310"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38944310","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":"Regulation of Cell Death and Signaling by Pore-Forming Resistosomes.","authors":"Guozhi Bi, Jian-Min Zhou","doi":"10.1146/annurev-phyto-020620-095952","DOIUrl":"https://doi.org/10.1146/annurev-phyto-020620-095952","url":null,"abstract":"<p><p>Nucleotide-binding leucine-rich repeat receptors (NLRs) are the largest class of immune receptors in plants. They play a key role in the plant surveillance system by monitoring pathogen effectors that are delivered into the plant cell. Recent structural biology and biochemical analyses have uncovered how NLRs are activated to form oligomeric resistosomes upon the recognition of pathogen effectors. In the resistosome, the signaling domain of the NLR is brought to the center of a ringed structure to initiate immune signaling and regulated cell death (RCD). The N terminus of the coiled-coil (CC) domain of the NLR protein HOPZ-ACTIVATED RESISTANCE 1 likely forms a pore in the plasma membrane to trigger RCD in a way analogous to animal pore-forming proteins that trigger necroptosis or pyroptosis. NLRs that carry TOLL-INTERLEUKIN1-RECEPTOR as a signaling domain may also employ pore-forming resistosomes for RCD execution. In addition, increasing evidence supports intimate connections between NLRs and surface receptors in immune signaling. These new findings are rapidly advancing our understanding of the plant immune system.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"239-263"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38956211","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":"Emerging Roles of Posttranslational Modifications in Plant-Pathogenic Fungi and Bacteria.","authors":"Wende Liu, Lindsay Triplett, Xiao-Lin Chen","doi":"10.1146/annurev-phyto-021320-010948","DOIUrl":"https://doi.org/10.1146/annurev-phyto-021320-010948","url":null,"abstract":"<p><p>Posttranslational modifications (PTMs) play crucial roles in regulating protein function and thereby control many cellular processes and biological phenotypes in both eukaryotes and prokaryotes. Several recent studies illustrate how plant fungal and bacterial pathogens use these PTMs to facilitate development, stress response, and host infection. In this review, we discuss PTMs that have key roles in the biological and infection processes of plant-pathogenic fungi and bacteria. The emerging roles of PTMs during pathogen-plant interactions are highlighted. We also summarize traditional tools and emerging proteomics approaches for PTM research. These discoveries open new avenues for investigating the fundamental infection mechanisms of plant pathogens and the discovery of novel strategies for plant disease control.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"99-124"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38915597","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}
Loup Rimbaud, Frédéric Fabre, Julien Papaïx, Benoît Moury, Christian Lannou, Luke G Barrett, Peter H Thrall
{"title":"Models of Plant Resistance Deployment.","authors":"Loup Rimbaud, Frédéric Fabre, Julien Papaïx, Benoît Moury, Christian Lannou, Luke G Barrett, Peter H Thrall","doi":"10.1146/annurev-phyto-020620-122134","DOIUrl":"https://doi.org/10.1146/annurev-phyto-020620-122134","url":null,"abstract":"<p><p>Owing to their evolutionary potential, plant pathogens are able to rapidly adapt to genetically controlled plant resistance, often resulting in resistance breakdown and major epidemics in agricultural crops. Various deployment strategies have been proposed to improve resistance management. Globally, these rely on careful selection of resistance sources and their combination at various spatiotemporal scales (e.g., via gene pyramiding, crop rotations and mixtures, landscape mosaics). However, testing and optimizing these strategies using controlled experiments at large spatiotemporal scales are logistically challenging. Mathematical models provide an alternative investigative tool, and many have been developed to explore resistance deployment strategies under various contexts. This review analyzes 69 modeling studies in light of specific model structures (e.g., demographic or demogenetic, spatial or not), underlying assumptions (e.g., whether preadapted pathogens are present before resistance deployment), and evaluation criteria (e.g., resistance durability, disease control, cost-effectiveness). It highlights major research findings and discusses challenges for future modeling efforts.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"125-152"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38933826","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}
Gary P Munkvold, Robert H Proctor, Antonio Moretti
{"title":"Mycotoxin Production in <i>Fusarium</i> According to Contemporary Species Concepts.","authors":"Gary P Munkvold, Robert H Proctor, Antonio Moretti","doi":"10.1146/annurev-phyto-020620-102825","DOIUrl":"https://doi.org/10.1146/annurev-phyto-020620-102825","url":null,"abstract":"<p><p><i>Fusarium</i> is one of the most important genera of plant-pathogenic fungi in the world and arguably the world's most important mycotoxin-producing genus. <i>Fusarium</i> species produce a staggering array of toxic metabolites that contribute to plant disease and mycotoxicoses in humans and other animals. A thorough understanding of the mycotoxin potential of individual species is crucial for assessing the toxicological risks associated with <i>Fusarium</i> diseases. There are thousands of reports of mycotoxin production by various species, and there have been numerous attempts to summarize them. These efforts have been complicated by competing classification systems based on morphology, sexual compatibility, and phylogenetic relationships. The current depth of knowledge of <i>Fusarium</i> genomes and mycotoxin biosynthetic pathways provides insights into how mycotoxin production is distributedamong species and multispecies lineages (species complexes) in the genus as well as opportunities to clarify and predict mycotoxin risks connected with known and newly described species. Here, we summarize mycotoxin production in the genus <i>Fusarium</i> and how mycotoxin risk aligns with current phylogenetic species concepts.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"373-402"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39053776","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}
Yongli Qiao, Rui Xia, Jixian Zhai, Yingnan Hou, Li Feng, Yi Zhai, Wenbo Ma
{"title":"Small RNAs in Plant Immunity and Virulence of Filamentous Pathogens.","authors":"Yongli Qiao, Rui Xia, Jixian Zhai, Yingnan Hou, Li Feng, Yi Zhai, Wenbo Ma","doi":"10.1146/annurev-phyto-121520-023514","DOIUrl":"https://doi.org/10.1146/annurev-phyto-121520-023514","url":null,"abstract":"<p><p>Gene silencing guided by small RNAs governs a broad range of cellular processes in eukaryotes. Small RNAs are important components of plant immunity because they contribute to pathogen-triggered transcription reprogramming and directly target pathogen RNAs. Recent research suggests that silencing of pathogen genes by plant small RNAs occurs not only during viral infection but also in nonviral pathogens through a process termed host-induced gene silencing, which involves <i>trans</i>-species small RNA trafficking. Similarly, small RNAs are also produced by eukaryotic pathogens and regulate virulence. This review summarizes the small RNA pathways in both plants and filamentous pathogens, including fungi and oomycetes, and discusses their role in host-pathogen interactions. We highlight secondarysmall interfering RNAs of plants as regulators of immune receptor gene expression and executors of host-induced gene silencing in invading pathogens. The current status and prospects of <i>trans</i>-species gene silencing at the host-pathogen interface are discussed.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"265-288"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39053777","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}
Laura C Iles, Ana C Fulladolsa, Alicyn Smart, John Bonkowski, Tom Creswell, Carrie L Harmon, Ray Hammerschmidt, R Roz Hirch, Lina Rodriguez Salamanca
{"title":"Everything Is Faster: How Do Land-Grant University-Based Plant Diagnostic Laboratories Keep Up with a Rapidly Changing World?","authors":"Laura C Iles, Ana C Fulladolsa, Alicyn Smart, John Bonkowski, Tom Creswell, Carrie L Harmon, Ray Hammerschmidt, R Roz Hirch, Lina Rodriguez Salamanca","doi":"10.1146/annurev-phyto-020620-102557","DOIUrl":"https://doi.org/10.1146/annurev-phyto-020620-102557","url":null,"abstract":"<p><p>Plant diagnostic laboratories (PDLs) are at the heart of land-grant universities (LGUs) and their extension mission to connect citizens with research-based information. Although research and technological advances have led to many modern methods and technologies in plant pathology diagnostics, the pace of adopting those methods into services at PDLs has many complexities we aim to explore in this review. We seek to identify current challenges in plant disease diagnostics, as well as diagnosticians' and administrators'perceptions of PDLs' many roles. Surveys of diagnosticians and administrators were conducted to understand the current climate on these topics. We hope this article reaches researchers developing diagnostic methods with modern and new technologies to foster a better understanding of PDL diagnosticians' perspective on method implementation. Ultimately, increasing researchers' awareness of the factors influencing method adoption by PDLs encourages support, collaboration, and partnerships to advance plant diagnostics.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"333-349"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39357272","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":"Damage-Associated Molecular Patterns (DAMPs) in Plant Innate Immunity: Applying the Danger Model and Evolutionary Perspectives.","authors":"Kiwamu Tanaka, Martin Heil","doi":"10.1146/annurev-phyto-082718-100146","DOIUrl":"https://doi.org/10.1146/annurev-phyto-082718-100146","url":null,"abstract":"<p><p>Danger signals trigger immune responses upon perception by a complex surveillance system. Such signals can originate from the infectious nonself or the damaged self, the latter termed damage-associated molecular patterns (DAMPs). Here, we apply Matzinger's danger model to plant innate immunity to discuss the adaptive advantages of DAMPs and their integration into preexisting signaling pathways. Constitutive DAMPs (cDAMPs), e.g., extracellular ATP, histones, and self-DNA, fulfill primary, conserved functions and adopt a signaling role only when cellular damage causes their fragmentation or localization to aberrant compartments. By contrast, immunomodulatory peptides (also known as phytocytokines) exclusively function as signals and, upon damage, are activated as inducible DAMPs (iDAMPs). Dynamic coevolutionary processes between the signals and their emerging receptors and shared co-receptors have likely linked danger recognition to preexisting, conserved downstream pathways.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"53-75"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38908603","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":"Interkingdom Signaling Interference: The Effect of Plant-Derived Small Molecules on Quorum Sensing in Plant-Pathogenic Bacteria.","authors":"Janak Raj Joshi, Netaly Khazanov, Amy Charkowski, Adi Faigenboim, Hanoch Senderowitz, Iris Yedidia","doi":"10.1146/annurev-phyto-020620-095740","DOIUrl":"https://doi.org/10.1146/annurev-phyto-020620-095740","url":null,"abstract":"<p><p>In the battle between bacteria and plants, bacteria often use a population density-dependent regulatory system known as quorum sensing (QS) to coordinate virulence gene expression. In response, plants use innate and induced defense mechanisms that include low-molecular-weight compounds, some of which serve as antivirulence agents by interfering with the QS machinery. The best-characterized QS system is driven by the autoinducer <i>N</i>-acyl-homoserine lactone (AHL), which is produced by AHL synthases (LuxI homologs) and perceived by response regulators (LuxR homologs). Several plant compounds have been shown to directly inhibit LuxI or LuxR. Gaining atomic-level insight into their mode of action and how they interfere with QS enzymes supports the identification and design of novel QS inhibitors.Such information can be gained by combining experimental work with molecular modeling and docking simulations. The summary of these findings shows that plant-derived compounds act as interkingdom cues and that these allomones specifically target bacterial communication systems.</p>","PeriodicalId":8251,"journal":{"name":"Annual review of phytopathology","volume":"59 ","pages":"153-190"},"PeriodicalIF":10.2,"publicationDate":"2021-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38962020","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}