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 Microbial Megaplasmids written by Edward Schwartz and published by Springer Science & Business Media. This book was released on 2009-01-29 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside. Microbial Megaplasmids reviews our knowledge of the extensively studied representatives, such as the catabolic plasmids of the pseudomonads, the rhizobial Sym plasmids, the Ti plasmids of the genus Agrobacterium and the giant enterobacterial virulence plasmids. It also presents snapshots of more recently discovered megaplasmids. The contribution of megaplasmids to the biology of their hosts is described, highlighting the interactions between megaplasmid and chromosomal genes.
Download or read book Evolutionary Genomics of Pseudomonas Syringae Plasmids written by STAVRINIDES. and published by . This book was released on 2007 with total page 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 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 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 Comparison of the Complete Genome Sequences of Pseudomonassyringae Pv Syringae B728a and Pv Tomato DC3000 written by and published by . This book was released on 2005 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The complete genomic sequence of Pseudomonas syringaepathovar syringae B728a (Pss B728a), has been determined and is comparedwith that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). Thesetwo pathovars of this economically important species of plant pathogenicbacteria differ in host range and apparent patterns of interaction withplants, with Pss having a more pronounced epiphytic stage of growth andhigher abiotic stress tolerance and Pst DC3000 having a more pronouncedapoplastic growth habitat. The Pss B728a genome (6.1 megabases) containsa circular chromosome and no plasmid, whereas the Pst DC3000 genome is6.5 mbp in size, composed of a circular chromosome and two plasmids. While a high degree of similarity exists between the two sequencedPseudomonads, 976 protein-encoding genes are unique to Pss B728a whencompared to Pst DC3000, including large genomic islands likely tocontribute to virulence and host specificity. Over 375 repetitiveextragenic palindromic sequences (REPs) unique to Pss B728a when comparedto Pst DC3000 are widely distributed throughout the chromosome except in14 genomic islands, which generally had lower GC content than the genomeas a whole. Content of the genomic islands vary, with one containing aprophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the976 genes of Pss B728a with no counterpart in Pst DC3000 are thoseencoding for syringopeptin (SP), syringomycin (SR), indole acetic acidbiosynthesis, arginine degradation, and production of ice nuclei. Thegenomic comparison suggests that several unique genes for Pss B728a suchas ectoine synthase, DNA repair, and antibiotic production may contributeto epiphytic fitness and stress tolerance of this organism. Pseudomonassyringae, a member of the gamma subgroup of the Proteobacteria, is awidespread bacterial pathogen of many plant species. The species P.syringae is subdivided into approximately 50 pathovars based onpathogenicity and host range. P. syringae is capable of producing avariety of different symptoms depending on the host species and site ofinfection. For example, it causes leaf spot diseases that defoliateplants such as tomato, bean, soybean, trunk cankers, and so-called"blast" diseases on fruit, nut and ornamental species. Considerablevariation occurs both between and within different pathovars of P.syringae (1). Because of its importance as a plant pathogen, it has beenthe subject of much research, especially of its epidemiology andvirulence mechanisms (2). Pseudomonas syringae pv. syringae (Pss) strainB728a is typical of most strains of this pathovar in that it exhibits avery pronounced epiphytic phase on plants. Such strains achieve andmaintain large populations on healthy plants, where they are exposed tostressful conditions such as dryness and sunlight that are hostile tobacterial growth(2). Epiphytic Pss populations serve as inocula that cansubsequently invade plants and initiate disease. Pss strains are distinctfrom many P. syringae strains, such as P. syringae pv. tomato (Pst)strain DC3000, that poorly colonize the exterior of plants; these strainsmay be considered "endophytes" based on their ability to multiply mostlywithin the plant (3). True epiphytes such as Pss B728a often reachsurface populations of over 107 cells/g while strains such as Pst DC3000seldom exceed 105 cells/g (2, 3). Thus, these strains might be consideredto occupy different ends of the epiphytic/endophytic spectrum of plantcolonization as described by Beattie and Lindow (4). As a pathogen and anepiphyte, Pss B728a has evolved to exploit at least two distincthabitats: the leaf surface and apoplast. Because rapid changes intemperature, low water content, and incident solar radiation occur onleaf surfaces, it has been hypothesized that the epiphyte Pss B728aposseses more genes conferring environmental stress tolerance than theendophyte Pst DC3000 (4). Pss B728a also exhibits several traits such asice nucleation activity and SR production (2) that are lacking in manyother strains of P. syringae including Pst DC3000. As the most icenucleation active bacterial species, P. syringae is responsible forinciting frost injury to frost sensitive plants that can supercool andavoid damaging ice formation if not colonized by ice nucleation activebacteria (2,4). We present here a genomic comparison between strains PssB728a and Pst DC3000 of P. syringae pathovars as well as between thesestrains and P. aeruginosa and P. putida, two additional Pseudomonadsrecently sequenced. These genomic comparisons provide insights into theevolutionary history and diverse life styles of the pseudomonads, including their association with the environment, plant or mammalianhosts.
Download or read book The Evolution of Host Specificity and Virulence in the Plant Pathogen Pseudomonas Syringae written by Honour Claire McCann and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 The genus Actinidia a world monograph written by Hongwen [VNV] Huang and published by . This book was released on 2014 with total page 317 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Parasite Diversity and Diversification written by Serge Morand and published by Cambridge University Press. This book was released on 2015-02-26 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: By joining phylogenetics and evolutionary ecology, this book explores the patterns of parasite diversity while revealing diversification processes.
Download or read book Pseudomonas syringae Pathovars and Related Pathogens Identification Epidemiology and Genomics written by M’Barek Fatmi and published by Springer Science & Business Media. This book was released on 2008-06-03 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reports on recent advances on: (1) new methods and approaches for specific and sensitive detection and identification of Pseudomonas syringae and Ralstonia solanacearum; (2) ecology and epidemiology bases of Pseudomonas syringae that enable the development of management strategies; (3) pathogenesis and determinant of pathogenicity, and in particular, mechanisms involved in virulence and virulence gene expression; (4) evolution and diversity of the pseudomonads through multilocus sequence typing (MLST) analysis; (5) determination of pathogens associated with new and emerging diseases; (6) effect of global warming on increase and emergence of new bacterial diseases."
Download or read book The Kiwifruit Genome written by Raffaele Testolin and published by Springer. This book was released on 2016-05-02 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the basic botanical features of kiwifruit and its wild relatives, reports on the steps that led to its genome sequencing, and discusses the results obtained with the assembly and annotation. The core chapters provide essential insights into the main gene families that characterize this species as a crop, including the genes controlling sugar and starch metabolism, pigment biosynthesis and degradation, the ascorbic-acid pathway, fruit softening and postharvest metabolism, allergens, and resistance to pests and diseases. The book offers a valuable reference guide for taxonomists, geneticists and horticulturists. Further, since information gained from the genome sequence is extraordinarily useful in assessing the breeding value of individuals based on whole-genome scans, it will especially benefit plant breeders. Accordingly, chapters are included that focus on gene introgression from wild relatives and genome-based breeding.
Download or read book Effectors in Plant Microbe Interactions written by Francis Martin and published by John Wiley & Sons. This book was released on 2012-01-03 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plants and microbes interact in a complex relationship that can have both harmful and beneficial impacts on both plant and microbial communities. Effectors, secreted microbial molecules that alter plant processes and facilitate colonization, are central to understanding the complicated interplay between plants and microbes. Effectors in Plant-Microbe Interactions unlocks the molecular basis of this important class of microbial molecules and describes their diverse and complex interactions with host plants. Effectors in Plant Microbe Interactions is divided into five sections that take stock of the current knowledge on effectors of plant-associated organisms. Coverage ranges from the impact of bacterial, fungal and oomycete effectors on plant immunity and high-throughput genomic analysis of effectors to the function and trafficking of these microbial molecules. The final section looks at effectors secreted by other eukaryotic microbes that are the focus of current and future research efforts. Written by leading international experts in plant-microbe interactions, Effectors in Plant Microbe Interactions, will be an essential volume for plant biologists, microbiologists, pathologists, and geneticists.
Download or read book Electrotransformation of Bacteria written by Natalie Eynard and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 296 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this manual, protocols for the transformation of about 40 strains of bacteria are described, with the emphasis placed on the individual critical procedural steps, since the practical details mainly depend on the bacterial strain under investigation. This presentation together with the theoretical introductionary chapters, allows users to modify and adapt each protocol to their own experiments. Bacterial strains with relevance in the food industry, biotechnology, medical and veterinary fields, agroindustry and environmental sciences are covered.
Download or read book Evolutionary Trajectories in Plant Associated Pseudomonas and Xanthomonas Strains written by Marco Scortichini and published by Frontiers Media SA. This book was released on 2024-04-29 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The strict relationships between bacteria and plants represents one of the major facets of terrestrial ecology. Depending on the type of interaction and amount of metabolic advantage one organism can obtain from such relationships, these are classified as mutualistic, commensal or parasitic interactions. Within this context, Pseudomonas and Xanthomonas are bacterial genera with a worldwide spread, capable of establishing all of the above mentioned interactions with plants. Therefore, they represent good models for studying different lifestyles and, accordingly, deciphering distinct evolutionary trajectories followed by different lineages of a single genus to infect and/or to establish a mutualistic relationships with the plant. Some members of these two genera are regulated pests that are recognized as economically major threats for their host crop(s) both in temperate and tropical environments.
Download or read book Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria written by Frans J. de Bruijn and published by John Wiley & Sons. This book was released on 2016-07-13 with total page 1472 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA’s, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent response, efflux pumps, alarmones, and modulation of the cell envelope or membranes, to name a few. Many regulatory elements are conserved in different bacteria; however there are endless variations on the theme and novel elements of gene regulation in bacteria inhabiting particular environments are constantly being discovered. Especially in (pathogenic) bacteria colonizing the human body a plethora of bacterial responses to innate stresses such as pH, reactive nitrogen and oxygen species and antibiotic stress are being described. An attempt is made to not only cover model systems but give a broad overview of the stress-responsive regulatory systems in a variety of bacteria, including medically important bacteria, where elucidation of certain aspects of these systems could lead to treatment strategies of the pathogens. Many of the regulatory systems being uncovered are specific, but there is also considerable “cross-talk” between different circuits. Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria is a comprehensive two-volume work bringing together both review and original research articles on key topics in stress and environmental control of gene expression in bacteria. Volume One contains key overview chapters, as well as content on one/two/three component regulatory systems and stress responses, sigma factors and stress responses, small non-coding RNAs and stress responses, toxin-antitoxin systems and stress responses, stringent response to stress, responses to UV irradiation, SOS and double stranded systems repair systems and stress, adaptation to both oxidative and osmotic stress, and desiccation tolerance and drought stress. Volume Two covers heat shock responses, chaperonins and stress, cold shock responses, adaptation to acid stress, nitrosative stress, and envelope stress, as well as iron homeostasis, metal resistance, quorum sensing, chemotaxis and biofilm formation, and viable but not culturable (VBNC) cells. Covering the full breadth of current stress and environmental control of gene expression studies and expanding it towards future advances in the field, these two volumes are a one-stop reference for (non) medical molecular geneticists interested in gene regulation under stress.
