Download or read book Population and Comparative Genomics of Plant Pathogenic Bacteria written by Jeffrey Jones and published by Frontiers Media SA. This book was released on 2022-09-02 with total page 220 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Genomics of Plant Associated Bacteria written by Dennis C. Gross and published by Springer. This book was released on 2014-06-16 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes how genomics has revolutionized our scientific understanding of agriculturally important plant-associated bacteria. Each chapter focuses on the genomics of particular bacteria: the first described plant pathogen, Erwinia amylovora; phytoplasmas lacking cell walls; fastidious, phloem-restricted liberibacters; Pseudomonas syringae, which is a genetically tractable model system; Xanthomonas citri, which causes a disease that can devastate citrus crops and Pseudomonas fluorescens, which can protect plants from diseases. Topics considered in this volume include the importance of horizontal gene transfer in originating new bacterial strains and species and advances in transcriptomics that allow us to describe the complex regulatory networks critical to plant-microbe interactions. The availability of the Xanthomonas oryzae genome has led to new technologies in genome editing, which will revolutionize approaches to genetic engineering, even in eukaryotes. The contributions show how genomics has greatly accelerated progress toward understanding the biology of these bacteria and how that understanding can be translated into novel crop protection methods.

Download or read book Population Genomics Microorganisms written by Martin F. Polz and published by Springer. This book was released on 2019-01-07 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genomics is a rapidly emerging field that has the potential to transform our understanding of how evolutionary forces shape genomic diversity among microbes. There have already been considerable advances in understanding gene flow and spread of adaptive traits, and in linking epidemiology with evolutionary biology. The current challenge is to find unifying evolutionary principles for organisms that display a wide range of reproductive biology – from highly clonal to promiscuous – and for which the vast majority have eluded cultivation. This requires interdisciplinary approaches that incorporate novel computational tools, testing of existing and novel population genetic models, and creative new ways of linking genetic diversity to ecological factors. This pioneering book will discuss the advances made and promises of population genomics in microorganisms, outlining some of the key theoretical and practical challenges for microbial population genomics, including defining and identifying populations, genomics-based reverse ecology and building appropriate tools to understand microbes in a variety of complex environments.

Download or read book Comparative Genomics of a Plant Pathogenic Fungus Pyrenophora Tritici repentis Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence written by and published by . This book was released on 2012 with total page 23 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.

Download or read book Plant Pathogenic Bacteria written by Robert W. Jackson and published by . This book was released on 2009 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, internationally acclaimed experts review the most important developments providing an invaluable, up-to-date summary of the molecular biology and genomics of plant pathogenic bacteria. The book opens with two chapters on bacterial evolution, diversity and taxonomy, topics that have been transformed by molecular biology and genomics analyses. The third chapter delves into the crucially understudied area of pathogen adaptation to the plant apoplast environment. The following seven chapters focus on specific plant pathogens: Agrobacterium, Leifsonia, Pectobacterium, Pseudomonas, Ral.

Download or read book Population Biology of Plant Pathogens written by and published by . This book was released on 2015 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Population Genetics of Plant Pathogens written by Bruce A. McDonald and published by Amer Phytopathological Society. This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Population genetic analysis has provided fresh insights leading to revisions in disease cycles and control methods for many important pathogens. In this course clear explanations are provided for the five evolutionary forces (mutation, genetic drift, gene flow, reproduction system, and selection) and many examples are presented illustrating how these forces operate alone and in combination to determine the genetic structure of populations of plant pathogens. In addition, the final section of the course shows how to apply knowledge of pathogen population genetics to improve management of plant diseases.Population Genetics of Plant Pathogens CD-Rom is an excellent educational aid for training the next generation of plant pathologists as well as better informing the current generation of plant health practitioners. Plant Pathology students, teachers, and professionals; instructors and practitioners of Plant Breeding; and departments of Plant Pathology and Agronomy will all benefit from the expert knowledge provided in this new teaching tool.

Download or read book Plant Disease Management in the Post Genomic Era from Functional Genomics to Genome Editing written by Sabrina Sarrocco and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Crop plants are continuously under attack by pathogens, both during pre and post-harvest stages, often causing economically important food losses. Chemical treatments can pose a serious treat to human health and the environment. Furthermore, there is an increasing market, especially in OECD countries for organic produce, for which most pesticides and inorganic fertilisers are unacceptable. There is therefore a pressing need to develop more effective, sustainable and environmentally friendly tools for disease control. The use of beneficial microorganisms for the control of plant pathogens is very attractive, and the availability of novel molecular techniques and a plethora of genomic information open unexplored avenues for plant protection approaches. Genome-enabled integration of research became a major strategy in the era of the 2000's (the post-genomic era) and set the basis for a different way to understand interactions in plant-pathogen-beneficial microorganisms systems. In recent decades we have moved from the sequencing of single genomes, to the comparison of different genomes, their expression (from single organism to communities) and, more recently, we can apply novel techniques to edit a genome in a precise manner. Together with the complete sequencing of plant genomes, the genome sequences of plant pathogens as well as that of some beneficial organisms (bacteria, fungi, viruses), and the furnished information on their virulence, gave support to relatively new strategies such as transcriptome, proteome, metabolome and secretome analysis. Analyses of avirulence and resistance genes, their products and the cross-talking mechanisms, as well as proteins and metabolites - at an "omics" level - in highly performing beneficial microorganisms/pathogens interactions, represents a major contribution to plant protection, providing information at an unprecedented level of resolution. While single genomes are explored to infer the range of biological activities accomplished by a single organism or species, and comparative genomics allows evaluating the diversity and evolution of biochemical pathways adopted by individual species to perform a common function, information is being obtained about processes carried out by a diverse set of organisms interacting with each other. Environmental genomics, popularized by the metagenome concept, can generate billions of DNA sequences from a given environment furnishing a comparative assessment of a community in situ. Metagenomics (sequence-based approaches applied across genomes in an environment) provides information about functional capabilities and responses of organism (plant, pathogen and beneficial agent) assemblages in different niches, giving a different perspective in the management of plant diseases at a multitrophic level. Advances in functional genomics and genome editing approaches have recently provided new tools to manage the plant-pathogen-beneficial microorganism system, for preventing or controlling disease. The use of RNA-based technologies is extremely appealing, and these include artificial micro-RNA and transacting small interfering RNA, which are currently being used for generating plant virus-resistant plants, thus fostering plant virus control researches. Finally, targeted genome editing strategies - exemplified by, but not limited to, the CRISPR-Cas technique - are among the most modern ways for inducing targeted deletions, insertions and precise changes in the genome of host plants or pathogens, as well as in the genomes of beneficial microorganisms. The aim of the present Research Topic is to give an exhaustive and up to date overview of examples of genomic techniques (genome sequencing, genome comparison, transcriptomics, metagenomics, RNA based technologies and genome editing strategies) applied to plants, pathogens or beneficial microorganisms to promote the exploitation of these modern tools as a new frontier in plant disease management.

Download or read book Comparative and Evolutionary Genomics of Pseudomonas Syringae written by Shalabh Thakur and published by . This book was released on 2017 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The Pseudomonas syringae species complex comprises many genetically diverse strains ubiquitously found in both agricultural and non-agricultural environments. More popularly known as a plant pathogenic bacteria, P. syringae has a very broad host range. However, distinct strains show strong host specificity and are able to cause disease on limited crops. Multi-locus sequence typing studies have sub-divided the P. syringae complex into at least 13 different subgroups referred as phylogroups. Given such extensive genetic and ecological diversity within the species complex, there is an ongoing debate over the species definition of P. syringae strains. My research work investigated strains within the P. syringae species complex to determine if they belong to a single species population or if distinct phylogroups are in fact different species by performing whole-genome analysis of approximately 400 P. syringae strains using various comparative and evolutionary approaches. To overcome the computational challenges of large-scale comparative genome analysis, we designed a novel comparative genomic pipeline named DeNoGAP. The DeNoGAP pipeline provides a robust computational pipeline for performing various comparative genomics tasks, such as gene prediction, ortholog prediction, functional annotation, and analysis of a pan-genome. The comparative genome analysis of more than 400 strains shed insight into the P. syringae pan-genome. We found P. syringae pan-genome to be big and diverse, comprising of more than 77,000 gene families. Evolutionary analyses of gene families showed evidence of homologous recombination and positive selection across entire genomes of P. syringae strains. Although our analysis showed that phylogroups rarely exchange genes via homologous recombination, we found that inter-phylogroup homologous recombination occurs disproportinately among virulence-associated and positively-selected genes that are essential for ecological adaptation and evolution of P. syringae strains. Based on these findings, we hypothesized that P. syringae maintains genetic cohesion between its divergent strains due to an exchange of ecological and evolutionarily relevant genes. Together, my work provides a robust computational pipeline for large-scale comparative genomics projects and sheds insight into species definition of the P. syringae species complex based on strong evolutionary species concepts rather than molecular methods.

Download or read book Population Biology of Plant Pathogens written by and published by . This book was released on 2015 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book From Metagenome to Gene written by and published by . This book was released on 2019 with total page 290 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant pathogens can have great social and economic impact, and are a continuous threat to food security. This is clearly the case for Synchytrium endobioticum, the species causing potato wart disease. S. endobioticum is an obligate biotrophic fungus of the phylum Chytridiomycota (chytrids), which is a basal lineage in the fungal kingdom. The lack of chemical control agents, the impact of the pathogen (complete loss of tuber yields from infected field have been reported), and the production of resting spores that remain viable and infectious in infested soils for decades, led to a quarantine status for S. endobioticum in most countries world-wide. Potato wart disease has been reported from all continents where potato is cultivated, and strict phytosanitary control measures are enforced to prevent the introduction and spread of the pathogen. The use of resistant potato varieties has proven successful in achieving these goals. In chapter 1, over a century of potato wart research is reviewed to place our current knowledge in historic perspective. Observations from light microscopy and electron microscopy studies of S. endobioticum performed in the twentieth century are combined with recent molecular studies. Based on our current knowledge on molecular plant-pathogen interactions, a model is presented to describe the interaction between S. endobioticum and its host in particular with respect to plant resistance. Chapter 2 describes the independent sequencing, assembly and functionally annotation of two S. endobioticum genomes. A comparative genomics approach, in which knowledge acquired from other fungal taxa is exploited, is used to gain insights into genomic features underlying the obligate biotrophic and pathogenic lifestyle of the pathogen. Our study underlines the high diversity in chytrids compared to the well-studied Ascomycota and Basidiomycota, and reflects biological differences between the phyla. Moreover, it highlights the surprising commonalities between plant pathogenic fungi that are so evolutionary distinct. In chapter 3, the within-species diversity is determined using mitochondrial genomes, and four major mitochondrial lineages are identified. Furthermore, mitochondrial genomic variation shows that S. endobioticum has likely been introduced into Europe multiple times, and that several pathotypes emerged multiple times. We also demonstrate that isolates represent communities of different genotypes, and that the use of semi-resistant potato cultivars triggers a rapid shift in the mitochondrial haplotype. This shift is associated with 266 increased virulence and is likely the result of disruptive selection in the community. Our analysis reveals diversity of S. endobioticum isolates, which is undetected with the currently used bioassays. In chapter 4, by means of an alternative “aboveground” bioassay, it is demonstrated that potato resistance genes are expressed in green aboveground plant organs similar to etiolated “belowground” sprouts. As potato wart resistance is active in both belowground and aboveground organs, the alternative bioassay can potentially speed up screening for S. endobioticum resistance in potato breeding programs as it omits the requirement for tuber formation. In addition, possibilities arise to express S. endobioticum effectors in potato leaves through agroinfiltration, thereby providing additional phenotyping tools for research and breeding. Chapter 5 describes the identification of the S. endobioticum effector AvrSen1, which represents the first effector gene identified in Chytridiomycota. A single dominant gene (Sen1) governs pathotype 1(D1) resistance and we hypothesized that the underlying molecular model would involve a pathogen effector (AvrSen1) that is recognized by the host. Expression of AvrSen1 in Sen1 plants showed a hypersensitive response which co-segregated with Sen1 in potato populations. In non-pathotypes 1(D1) isolates, five different variants resulting in the loss of recognition by the plant were observed suggesting that AvrSen1 is under strong selective pressure. Chapter 6 is a summarizing discussion in which the chapters are integrated, and several aspects linked to pathogenicity and pathotype diversity are further discussed. The impact of the research described in chapters 2 to 5 is specified. Finally, opportunities and challenges for future research on S. endobioticum are presented with a central role for an improved Avr-R gene based pathotyping system, which will contribute to the improvement of durable potato wart resistance breeding and phytosanitary control.

Download or read book The Pangenome written by Hervé Tettelin and published by Springer Nature. This book was released on 2020-04-30 with total page 311 pages. Available in PDF, EPUB and Kindle. Book excerpt: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

Download or read book Sustainable Approaches to Controlling Plant Pathogenic Bacteria written by V. Rajesh Kannan and published by CRC Press. This book was released on 2015-09-08 with total page 517 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant diseases and changes in existing pathogens remain a constant threat to our forests, food, and fiber crops as well as landscape plants. However, many economically important pathosystems are largely unexplored and biologically relevant life stages of familiar systems remain poorly understood. In a multifaceted approach to plant pathogenic behav

Download or read book Handbook of Statistical Genomics written by David J. Balding and published by John Wiley & Sons. This book was released on 2019-07-09 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt: A timely update of a highly popular handbook on statistical genomics This new, two-volume edition of a classic text provides a thorough introduction to statistical genomics, a vital resource for advanced graduate students, early-career researchers and new entrants to the field. It introduces new and updated information on developments that have occurred since the 3rd edition. Widely regarded as the reference work in the field, it features new chapters focusing on statistical aspects of data generated by new sequencing technologies, including sequence-based functional assays. It expands on previous coverage of the many processes between genotype and phenotype, including gene expression and epigenetics, as well as metabolomics. It also examines population genetics and evolutionary models and inference, with new chapters on the multi-species coalescent, admixture and ancient DNA, as well as genetic association studies including causal analyses and variant interpretation. The Handbook of Statistical Genomics focuses on explaining the main ideas, analysis methods and algorithms, citing key recent and historic literature for further details and references. It also includes a glossary of terms, acronyms and abbreviations, and features extensive cross-referencing between chapters, tying the different areas together. With heavy use of up-to-date examples and references to web-based resources, this continues to be a must-have reference in a vital area of research. Provides much-needed, timely coverage of new developments in this expanding area of study Numerous, brand new chapters, for example covering bacterial genomics, microbiome and metagenomics Detailed coverage of application areas, with chapters on plant breeding, conservation and forensic genetics Extensive coverage of human genetic epidemiology, including ethical aspects Edited by one of the leading experts in the field along with rising stars as his co-editors Chapter authors are world-renowned experts in the field, and newly emerging leaders. The Handbook of Statistical Genomics is an excellent introductory text for advanced graduate students and early-career researchers involved in statistical genetics.

Download or read book Plant Pathogenic Bacteria written by Robert W. Jackson and published by Caister Academic Press Limited. This book was released on 2009 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The third chapter delves into the crucially understudied area of pathogen adaptation to the plant apoplast environment.

Download or read book Plant Genomes written by Jean-Nicolas Volff and published by Karger Medical and Scientific Publishers. This book was released on 2008-01-01 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent major advances in the field of comparative genomics and cytogenomics of plants, particularly associated with the completion of ambitious genome projects, have uncovered astonishing facets of the architecture and evolutionary history of plant genomes. The aim of this book was to review these recent developments as well as their implications in our understanding of the mechanisms which drive plant diversity. New insights into the evolution of gene functions, gene families and genome size are presented, with particular emphasis on the evolutionary impact of polyploidization and transposable elements. Knowledge on the structure and evolution of plant sex chromosomes, centromeres and microRNAs is reviewed and updated. Taken together, the contributions by internationally recognized experts present a panoramic overview of the structural features and evolutionary dynamics of plant genomes.This volume of Genome Dynamics will provide researchers, teachers and students in the fields of biology and agronomy with a valuable source of current knowledge on plant genomes.

Download or read book Evolutionary Dynamics of Plant Pathogen Interactions written by Jeremy J. Burdon and published by Cambridge University Press. This book was released on 2019-01-31 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: A broad view of plant-pathogen interactions illustrating the fundamental reciprocal role pathogens and hosts play in shaping each other's ecology and evolution.