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Plant Small RNA
Author : Praveen Guleria,Vineet Kumar
Publisher : Academic Press
Release Date : 2020-02-19
ISBN 10 : 012817336X
Pages : 635 pages
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Plant Small RNA: Biogenesis, Regulation and Application describes the biosynthesis of small RNA in plant systems. With an emphasis on the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival, this books presents the basics and most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. In addition, it emphasizes the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival. Final sections cover the most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. Presents foundational information about small RNA biology and regulation in plants Includes small RNA pathway advances Describes the application and scope of small RNA technology for agricultural stability

Plant Small RNA
Author : Praveen Guleria,Vineet Kumar
Publisher : Academic Press
Release Date : 2020-02
ISBN 10 : 9780128171127
Pages : 660 pages
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Plant Small RNA: Biogenesis, Regulation and Application describes the biosynthesis of small RNA in plant systems. With an emphasis on the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival, this books presents the basics and most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. In addition, it emphasizes the various molecular mechanisms affected by small RNA and their applications in supporting plant growth and survival. Final sections cover the most recent advancements in small RNA mediated plant genomics, metabolomics, proteomics and physiology. Presents foundational information about small RNA biology and regulation in plants Includes small RNA pathway advances Describes the application and scope of small RNA technology for agricultural stability

Abiotic and Biotic Stress in Plants
Author : Arun Shanker,Chitra Shanker
Publisher : BoD – Books on Demand
Release Date : 2016-02-17
ISBN 10 : 9535122509
Pages : 768 pages
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The impact of global climate change on crop production has emerged as a major research priority during the past decade. Understanding abiotic stress factors such as temperature and drought tolerance and biotic stress tolerance traits such as insect pest and pathogen resistance in combination with high yield in plants is of paramount importance to counter climate change related adverse effects on the productivity of crops. In this multi-authored book, we present synthesis of information for developing strategies to combat plant stress. Our effort here is to present a judicious mixture of basic as well as applied research outlooks so as to interest workers in all areas of plant science. We trust that the information covered in this book would bridge the much-researched area of stress in plants with the much-needed information for evolving climate-ready crop cultivars to ensure food security in the future.

Plant MicroRNAs
Author : Blake C. Meyers,Pamela J. Green
Publisher : Humana Press
Release Date : 2012-08-09
ISBN 10 : 9781617796531
Pages : 261 pages
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MicroRNAs constitute a particularly important class of small RNAs given their abundance, broad phylogenetic conservation and strong regulatory effects, with plant miRNAs uniquely divulging their ancient evolutionary origins and their strong post-transcriptional regulatory effects. In Plant MicroRNAs: Methods and Protocols, experts in the field present chapters that focus on the identification, validation, and characterization of the miRNA class of RNAs, and address important aspects about heterochromatic small interfering RNAs. In addition, the methods contained in this volume emphasize miRNA analyses, but also include ways to distinguish one class of small RNAs from another. As a volume in the highly successful Methods in Molecular BiologyTM series, chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and easy to use, Plant MicroRNAs: Methods and Protocols provides the research community with a set of protocols that will help advance vital miRNA research for all plant species, both in typical model species and non-model species alike.

Plant RNA Biology
Author : Dóra Szakonyi,Ana Confraria,Concetta Valerio,Paula Duque,Dorothee Staiger
Publisher : Frontiers Media SA
Release Date : 2019-11-18
ISBN 10 : 2889630250
Pages : 329 pages
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Discoveries from the past decades revealed that RNA molecules are much more than inert intermediates between the coding DNA sequences and their functional products, proteins. Today, RNAs are recognized as active regulatory molecules influencing gene expression, chromatin organization and genome stability, thus impacting all aspects of plant life including development, growth, reproduction and stress tolerance. Innovations in methodologies, the expanding application of next-generation sequencing technologies, and the creation of public datasets and databases have exposed a new universe of RNA-based mechanisms and led to the discovery of new families of non-coding RNAs, uncovered the large extent of alternative splicing events, and highlighted the potential roles of RNA modifications and RNA secondary structures. Furthermore, considerable advances have been made in identifying RNA-binding and processing factors involved in the synthesis and maturation of different forms of RNA molecules as well as in RNA processing, biochemical modifications or degradation. This Research Topic showcases the broad biological significance of RNAs in plant systems and contains eight original research articles, one review and four mini-reviews, covering various RNA-based mechanisms in higher plants. Emerging new technologies and novel multidisciplinary approaches are empowering the scientific community and will expectedly bring novel insights into our understanding of the mechanisms through which RNA is regulated and regulates biological processes in plant cells.

Plant Genomes
Author : Jean-Nicolas Volff
Publisher : Karger Medical and Scientific Publishers
Release Date : 2008-01-01
ISBN 10 : 3805584911
Pages : 145 pages
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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.

Non Coding RNAs in Plants
Author : Volker A. Erdmann,Jan Barciszewski
Publisher : Springer Science & Business Media
Release Date : 2011-07-20
ISBN 10 : 9783642194542
Pages : 510 pages
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In the most recent years, each of the RNA silencing pathways of plants have appeared to generate ncRNAs with dedicated functions, specialized biological activities and specific functional scopes. RNA silencing plays a crucial role in coordinating the expression, stability, protection and inheritance of eukaryotic genomes. It compromises several mechanisms, that invariably depend on core small non coding RNAs and that achieve dedicated sequence-specific functions. RNA silencing has been recognized to carry critical developmental, stress-response and bodyguard functions be coordinating the expression, protection, stability and inheritance of virtually all eukaryotic genomes. Thus, the ncRNAs encompass a wide set of mechanisms that achieve specialized functions.

Regulation of Gene Expression by Small RNAs
Author : Rajesh K. Gaur,John J. Rossi
Publisher : CRC Press
Release Date : 2009-04-27
ISBN 10 : 1420008706
Pages : 440 pages
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New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p

Function and Maintenance of Trans-species Small RNAs in the Cuscuta Genus of Parasitic Plants
Author : Nathan Johnson
Publisher : N.A
Release Date : 2019
ISBN 10 :
Pages : 329 pages
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Regulatory small RNAs are important components involved in the regulation of many cellular processes in eukaryotes. Typically 20-24 nucleotides in length, small RNAs can repress gene expression through directed degradation of messenger RNA or through the recruitment/maintenance of repressive chromatin marks in the genome. In plants, large-scale annotations of small RNAs have languished despite the definition of several common classes (microRNAs, secondary siRNAs, heterochromatic siRNAs). ShortStack, a tool developed for the alignment and annotation of small RNAs from high-throughput sequencing reads has made large advancements in this process. The alignment step in small RNA analysis represents a particular challenge. In this step, reads are aligned to the genome based on sequence identity, however large proportions of small RNA sequencing reads (>50%) are known to map ambiguously to multiple places in the genome. This motivated the improvement of algorithms for the placement of these reads. Utilizing the density of unambiguously aligned reads in vicinity as a guiding principle, ShortStack chooses a place for ambiguously mapping reads in the genome. With both simulated and real datasets, this method greatly increases alignment precision for a modest reduction in sensitivity, compared to widely-used alternatives. It also improves the approximation of small RNA locus expression miRNAs. This tool was tested with small-RNA-sequencing libraries from three different plants, showing its superior performance with varied input. Through this improved algorithm, alignments and resulting annotations have minimized false positive rates, improving their quality and enhancing the results obtained from small-RNA-sequencing experiments. Species-species interactions are of a particular interest for small RNA research. Work on fungal and oomycete pathogens of plants show that small RNAs are able to regulate gene expression in trans-species manner. Recently, the parasitic plant genus Cuscuta has been a focus in this context, as it has been shown that bi-directional movement of biomolecules readily occurs in its interaction with hosts. Small-RNA-sequencing of Cuscuta campestris parasitizing the host Arabidopsis thaliana showed that numerous small RNAs are highly expressed in the host-parasite interface. Many of these were shown to be microRNAs and indeed target messenger RNAs originating from the host. These trans-species microRNAs were expressed similarly when parasitizing different hosts, but lack of expression on non-living hosts, hinting that a host-based trigger might be required. Secondary siRNAs resulting from targeting by these microRNAs are produced using protein machinery from the host, shown through their loss on mutant host plants. This implies processing takes place inside the host tissue. However, loss of secondary siRNAs did not measurably affect the growth of the parasite. Growing the parasite on hosts with loss of function mutations in targets of trans-species microRNAs showed enhanced growth for several targets, indicating their importance in host defense. These data broaden the picture of how small RNAs can be used in species interactions, making the case that this process may be used to enhance parasitic success. It is not clear how trans-species microRNAs from C. campestris are able to maintain targeting of host messenger RNAs in the light of adaptive pressures. To investigate this, small RNAs from host-parasite interactions in three more Cuscuta species were sequenced, including several different isolates within species. Many small RNAs were found to be highly expressed in the host-parasite interface. Targeting of host messenger RNAs was confirmed for several small RNAs in all species and isolates, indicating that the mechanism of trans-species small RNAs may be present throughout Cuscuta. Grouping distantly similar small RNAs based on sequence shows superfamilies that are retained between species groups. This analysis shows that several similar small RNAs are produced in a single species or isolate, accounting for variation in the target sites among possible hosts. This may also be used as a way to target numerous homologous messenger RNAs in a single host, regulating entire gene families. This provides a mechanism by which Cuscuta can ensure targeting despite any selection in the host to invalidate targeting. This discovery is a major expansion of the scope of trans-species small RNAs in plants and hints that this process may be widespread in nature.

Plant MicroRNAs
Author : Stefan de Folter
Publisher : Humana Press
Release Date : 2019-01-31
ISBN 10 : 9781493990412
Pages : 363 pages
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This detailed volume provides a collection of protocols for the study of miRNA functions in plants. Beginning with coverage of miRNA function, biogenesis, activity, and evolution in plants, the book continues by guiding readers through methods on the identification and detection of plant miRNAs, bioinformatic analyses, and strategies for functional analyses of miRNAs. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Plant MicroRNAs: Method and Protocols aims to ensure successful results in the further study of this vital area of plant science.

Plant Genome Diversity Volume 1
Author : Jonathan Wendel,Johann Greilhuber,Jaroslav Dolezel,Ilia J. Leitch
Publisher : Springer Science & Business Media
Release Date : 2012-03-23
ISBN 10 : 3709111307
Pages : 282 pages
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In this timely new 2-volume treatise, experts from around the world have banded together to produce a first-of-its-kind synopsis of the exciting and fast moving field of plant evolutionary genomics. In Volume I of Plant Genome Diversity, an update is provided on what we have learned from plant genome sequencing projects. This is followed by more focused chapters on the various genomic “residents” of plant genomes, including transposable elements, centromeres, small RNAs, and the evolutionary dynamics of genes and non-coding sequences. Attention is drawn to advances in our understanding of plant mitochondrial and plastid genomes, as well as the significance of duplication in genic evolution and the non-independent evolution among sequences in plant genomes. Finally, Volume I provides an introduction to the vibrant new frontier of plant epigenomics, describing the current state of our knowledge and the evolutionary implications of the epigenomic landscape.

Plant Gene Silencing
Author : Tamas Dalmay
Publisher : CABI
Release Date : 2017-05-29
ISBN 10 : 1780647670
Pages : 223 pages
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Plant gene silencing is a crucially important phenomenon in gene expression and epigenetics. This book describes the way small RNA is produced and acts to silence genes, its likely origins in defence against viruses, and also its potential to improve plants. Plant gene silencing can be used to improve industrial traits, make plants more nutritious or more valuable to consumers, to remove allergens, and to improve resistance to weeds and pathogens.

Plant Systems Biology
Author : Sacha Baginsky,Alisdair R. Fernie
Publisher : Springer Science & Business Media
Release Date : 2007-06-25
ISBN 10 : 376437439X
Pages : 358 pages
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This volume aims to provide a timely view of the state-of-the-art in systems biology. The editors take the opportunity to define systems biology as they and the contributing authors see it, and this will lay the groundwork for future studies. The volume is well-suited to both students and researchers interested in the methods of systems biology. Although the focus is on plant systems biology, the proposed material could be suitably applied to any organism.

Plant Epigenetics
Author : Nikolaus Rajewsky,Stefan Jurga,Jan Barciszewski
Publisher : Springer
Release Date : 2017-04-27
ISBN 10 : 3319555200
Pages : 536 pages
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This book presents, in 26 chapters, the status quo in epigenomic profiling. It discusses how functional information can be indirectly inferred and describes the new approaches that promise functional answers, collectively referred to as epigenome editing. It highlights the latest important advances in our understanding of the functions of plant epigenomics and new technologies for the study of epigenomic marks and mechanisms in plants. Topics include the deposition or removal of chromatin modifications and histone variants, the role of epigenetics in development and response to environmental signals, natural variation and ecology, as well as applications for epigenetics in crop improvement. Discussing areas ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, it presents breakthroughs in our understanding of complex phenotypic phenomena.

Plant microRNAs
Author : Célia Miguel,Tamas Dalmay,Inês Chaves
Publisher : Springer Nature
Release Date : 2020-02-01
ISBN 10 : 3030357724
Pages : 238 pages
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This book summarizes the latest findings on the functions of microRNAs in the regulation of plant development and responses to the surrounding environment. MicroRNAs are an important class of molecules that can be found in diverse groups of organisms, including plants and animals, and the investigation of their roles is a highly dynamic and “hot” research topic. The respective chapters address four main aspects, namely: microRNA investigation and annotation, the regulatory roles of microRNAs in various developmental processes, in response to abiotic factors, and in the context of biotic stress response regulation. Systematically reviewing the most important findings in this field, the book offers an essential guide for undergraduate and graduate students, teachers, and plant science researchers. Due to the potential applications of microRNAs in crop breeding and plant protection, it also represents a valuable resource for scientists in academia and the private sector alike.

Molecular Techniques in Crop Improvement
Author : Shri Mohan Jain,D.S. Brar
Publisher : Springer Science & Business Media
Release Date : 2013-10-14
ISBN 10 : 9401723567
Pages : 616 pages
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This book provides comprehensive information on the latest tools and techniques of molecular genetics and their applications in crop improvement. It thoroughly discusses advanced techniques used in molecular markers, QTL mapping, marker-assisted breeding, and molecular cytogenetics.

Bioinformatics Tools to Classify and Characterize Plant Small RNAs
Author : Reza Hammond
Publisher : N.A
Release Date : 2019
ISBN 10 : 9781687974853
Pages : 140 pages
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Small RNAs (sRNAs) in plants are a highly abundant class of noncoding RNAs that regulate silencing processes, mostly on the basis of sequence complementarity. There are several classes of small RNA that differ in both their biogenesis and mode of silencing. With the advent of next generation sequencing technologies, sRNA presence can be quantified at a relatively low cost and in a short amount of time. Due to the large amount of data however, there are many challenges associated with the classification of individual sRNAs in these datasets. It is for this reason that I have developed several tools to assist in the classification of sRNAs. The first of these tools is miRador, a novel micro RNA (miRNA) prediction tool that I designed to predict miRNAs from a set of sRNA libraries. This tool utilizes a newly established set of criteria for annotating plant miRNAs which enable it to predict miRNAs with a high level of accuracy. sPARTA is a miRNA target prediction and validation tool which utilizes Parallel Analysis of RNA Ends (PARE) sequencing libraries to validate target cleavage facilitated by a miRNA. Utilizing sPARTA in conjunction with miRador allows for the prediction and validation of novel miRNAs for a variety of plant species. In this dissertation, I utilize this pipeline on maize sRNA data to predict four novel miRNAs. I also present a clustering script that makes use of the Meyers Lab database systems to quickly cluster a variety of sequencing data. Using this approach, I attempted to characterize 24-nt phasiRNA producing loci for two separate projects, presented as case studies. In the first case study, we identify that 24-nt phasiRNAs in maize may be required for robust fertility at higher growth temperatures. In the second case study, we identify that asparagus generates inverted repeat-derived phasiRNAs from mRNAs lacking a miR2275 target site. Taken together, these tools improve scientists ability to characterize various classes of small RNAs, and their effects on their encoding genomes.

The Model Legume Medicago truncatula, 2 Volume Set
Author : Frans J. de Bruijn
Publisher : John Wiley & Sons
Release Date : 2020-01-29
ISBN 10 : 1119409160
Pages : 1264 pages
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Fully covers the biology, biochemistry, genetics, and genomics of Medicago truncatula Model plant species are valuable not only because they lead to discoveries in basic biology, but also because they provide resources that facilitate translational biology to improve crops of economic importance. Plant scientists are drawn to models because of their ease of manipulation, simple genome organization, rapid life cycles, and the availability of multiple genetic and genomic tools. This reference provides comprehensive coverage of the Model Legume Medicago truncatula. It features review chapters as well as research chapters describing experiments carried out by the authors with clear materials and methods. Most of the chapters utilize advanced molecular techniques and biochemical analyses to approach a variety of aspects of the Model. The Model Legume Medicago truncatula starts with an examination of M. truncatula plant development; biosynthesis of natural products; stress and M. truncatula; and the M. truncatula-Sinorhizobium meliloti symbiosis. Symbiosis of Medicago truncatula with arbuscular mycorrhiza comes next, followed by chapters on the common symbiotic signaling pathway (CSSP or SYM) and infection events in the Rhizobium-legume symbiosis. Other sections look at hormones and the rhizobial and mycorrhizal symbioses; autoregulation of nodule numbers (AON) in M. truncatula; Medicago truncatula databases and computer programs; and more. Contains reviews, original research chapters, and methods Covers most aspects of the M. truncatula Model System, including basic biology, biochemistry, genetics, and genomics of this system Offers molecular techniques and advanced biochemical analyses for approaching a variety of aspects of the Model Legume Medicago truncatula Includes introductions by the editor to each section, presenting the summary of selected chapters in the section Features an extensive index, to facilitate the search for key terms The Model Legume Medicago truncatula is an excellent book for researchers and upper level graduate students in microbial ecology, environmental microbiology, plant genetics and biochemistry. It will also benefit legume biologists, plant molecular biologists, agrobiologists, plant breeders, bioinformaticians, and evolutionary biologists.

Computational Non-coding RNA Biology
Author : Yun Zheng
Publisher : Academic Press
Release Date : 2018-09-14
ISBN 10 : 0128143665
Pages : 320 pages
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Computational Non-coding RNA Biology is a resource for the computation of non-coding RNAs. The book covers computational methods for the identification and quantification of non-coding RNAs, including miRNAs, tasiRNAs, phasiRNAs, lariat originated circRNAs and back-spliced circRNAs, the identification of miRNA/siRNA targets, and the identification of mutations and editing sites in miRNAs. The book introduces basic ideas of computational methods, along with their detailed computational steps, a critical component in the development of high throughput sequencing technologies for identifying different classes of non-coding RNAs and predicting the possible functions of these molecules. Finding, quantifying, and visualizing non-coding RNAs from high throughput sequencing datasets at high volume is complex. Therefore, it is usually possible for biologists to complete all of the necessary steps for analysis. Presents a comprehensive resource of computational methods for the identification and quantification of non-coding RNAs Introduces 23 practical computational pipelines for various topics of non-coding RNAs Provides a guide to assist biologists and other researchers dealing with complex datasets Introduces basic computational methods and provides guidelines for their replication by researchers Offers a solution to researchers approaching large and complex sequencing datasets

MicroRNAs in Plant Development and Stress Responses
Author : Ramanjulu Sunkar
Publisher : Springer Science & Business Media
Release Date : 2012-02-21
ISBN 10 : 364227384X
Pages : 296 pages
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Precise regulation of gene expression in both time and space is vital to plant growth, development and adaptation to biotic and abiotic stress conditions. This is achieved by multiple mechanisms, with perhaps the most important control being exerted at the level of transcription. However, with the recent discovery of microRNAs another ubiquitous mode of gene regulation that occurs at the post-transcriptional level has been identified. MicroRNAs can silence gene expression by targeting complementary or partially complementary mRNAs for degradation or translational inhibition. Recent studies have revealed that microRNAs play fundamental roles in plant growth and development, as well as in adaptation to biotic and abiotic stresses. This book highlights the roles of individual miRNAs that control and regulate diverse aspects of plant processes.