Strategies For Sequence Assembly Of Plant Genomes

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The Potato Genome

Author : Swarup Kumar Chakrabarti
Publisher : Springer
ISBN 13 : 3319661353
Total Pages : 332 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis The Potato Genome by : Swarup Kumar Chakrabarti

Download or read book The Potato Genome written by Swarup Kumar Chakrabarti and published by Springer. This book was released on 2017-12-26 with total page 332 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the historical importance of potato (Solanum tuberosum L.),potato genetic resources and stocks (including S. tuberosum group Phureja DM1-3 516 R44, a unique doubled monoploid homozygous line) used for potato genome sequencing. It also discusses strategies and tools for high-throughput sequencing, sequence assembly, annotation, analysis, repetitive sequences and genotyping-by-sequencing approaches. Potato (Solanum tuberosum L.; 2n = 4x = 48) is the fourth most important food crop of the world after rice, wheat and maize and holds great potential to ensure both food and nutritional security. It is an autotetraploid crop with complex genetics, acute inbreeding depression and a highly heterozygous nature. Further, the book examines the recent discovery of whole genome sequencing of a few wild potato species genomes, genomics in management and genetic enhancement of Solanum species, new strategies towards durable potato late blight resistance, structural analysis of resistance genes, genomics resources for abiotic stress management, as well as somatic cell genetics and modern approaches in true-potato-seed technology. The complete genome sequence provides a better understanding of potato biology, underpinning evolutionary process, genetics, breeding and molecular efforts to improve various important traits involved in potato growth and development.

The Barley Genome

Author : Nils Stein
Publisher : Springer
ISBN 13 : 3319925288
Total Pages : 400 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis The Barley Genome by : Nils Stein

Download or read book The Barley Genome written by Nils Stein and published by Springer. This book was released on 2018-08-18 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the state-of-the-art in barley genome analysis, covering all aspects of sequencing the genome and translating this important information into new knowledge in basic and applied crop plant biology and new tools for research and crop improvement. Unlimited access to a high-quality reference sequence is removing one of the major constraints in basic and applied research. This book summarizes the advanced knowledge of the composition of the barley genome, its genes and the much larger non-coding part of the genome, and how this information facilitates studying the specific characteristics of barley. One of the oldest domesticated crops, barley is the small grain cereal species that is best adapted to the highest altitudes and latitudes, and it exhibits the greatest tolerance to most abiotic stresses. With comprehensive access to the genome sequence, barley’s importance as a genetic model in comparative studies on crop species like wheat, rye, oats and even rice is likely to increase.

Plant Genomics

Author : Ibrokhim Y. Abdurakhmonov
Publisher : BoD – Books on Demand
ISBN 13 : 9535124552
Total Pages : 312 pages
Book Rating : 4.5/5 (351 download)

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Book Synopsis Plant Genomics by : Ibrokhim Y. Abdurakhmonov

Download or read book Plant Genomics written by Ibrokhim Y. Abdurakhmonov and published by BoD – Books on Demand. This book was released on 2016-07-14 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: Plant genomics aims to sequence, characterize, and study the genetic compositions, structures, organizations, functions, and interactions/networks of an entire plant genome. Its development and advances are tightly interconnected with proteomics, metabolomics, metagenomics, transgenomics, genomic selection, bioinformatics, epigenomics, phenomics, system biology, modern instrumentation, and robotics sciences. Plant genomics has significantly advanced over the past three decades in the land of inexpensive, high-throughput sequencing technologies and fully sequenced over 100 plant genomes. These advances have broad implications in every aspect of plant biology and breeding, powered with novel genomic selection and manipulation tools while generating many grand challenges and tasks ahead. This Plant genomics provides some updated discussions on current advances, challenges, and future perspectives of plant genome studies and applications.

Plant Genomes

Author : Jean-Nicolas Volff
Publisher : Karger Medical and Scientific Publishers
ISBN 13 : 3805584911
Total Pages : 155 pages
Book Rating : 4.8/5 (55 download)

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Book Synopsis Plant Genomes by : Jean-Nicolas Volff

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.

Mapping and Sequencing the Human Genome

Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309038405
Total Pages : 128 pages
Book Rating : 4.3/5 (9 download)

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Book Synopsis Mapping and Sequencing the Human Genome by : National Research Council

Download or read book Mapping and Sequencing the Human Genome written by National Research Council and published by National Academies Press. This book was released on 1988-01-01 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: There is growing enthusiasm in the scientific community about the prospect of mapping and sequencing the human genome, a monumental project that will have far-reaching consequences for medicine, biology, technology, and other fields. But how will such an effort be organized and funded? How will we develop the new technologies that are needed? What new legal, social, and ethical questions will be raised? Mapping and Sequencing the Human Genome is a blueprint for this proposed project. The authors offer a highly readable explanation of the technical aspects of genetic mapping and sequencing, and they recommend specific interim and long-range research goals, organizational strategies, and funding levels. They also outline some of the legal and social questions that might arise and urge their early consideration by policymakers.

The Pear Genome

Author : Schuyler S. Korban
Publisher : Springer
ISBN 13 : 3030110486
Total Pages : 322 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis The Pear Genome by : Schuyler S. Korban

Download or read book The Pear Genome written by Schuyler S. Korban and published by Springer. This book was released on 2019-07-03 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: Addressing the pear genome, this book covers the current state of knowledge regarding genetic and genomic resources, breeding approaches and strategies, as well as cutting-edge content on how these tools and resources are being / soon will be utilized to pursue genetic improvement efforts that will combine fruit quality, high productivity, precocious fruit bearing, and long postharvest storage life, along with elevated levels of resistance to various major diseases and insect pests. Throughout, the book also explores potential opportunities and challenges in genomic analysis, sequence assembly, structural features, as well as functional studies that will assist in future genetic improvement efforts for pears. The pear (Pyrus), an important tree fruit crop, is grown worldwide, and has several economically relevant cultivars. In recent years, modern genetic and genomic tools have resulted in the development of a wide variety of valuable resources for the pear. In the past few years, completion of whole genome assemblies of ‘Dangshansuli’, an Asian pear, and ‘Bartlett’, a European pear, have paved the way for new discoveries regarding for example, the pear’s genomic structure, chromosome evolution, and patterns of genetic variation. This wealth of new resources will have a major impact on our knowledge of the pear genome; in turn, these resources and knowledge will have significant impacts on future genetic improvement efforts.

The Amaranth Genome

Author : Dinesh Adhikary
Publisher : Springer Nature
ISBN 13 : 3030723658
Total Pages : 181 pages
Book Rating : 4.0/5 (37 download)

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Book Synopsis The Amaranth Genome by : Dinesh Adhikary

Download or read book The Amaranth Genome written by Dinesh Adhikary and published by Springer Nature. This book was released on 2021-06-01 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the development of genetic resources in amaranths, with a major focus on genomics, reverse, and forward genetics tools and strategies that have been developed for crop improvement. Amaranth is an ancient crop native to the New World. Interest in amaranths is being renewed, due to their adaptability, stress tolerance, and nutritional value. There are about 65 species in the genus, including Amaranthus caudatus L., A. cruentus L., and A. hypochondriacus L., which are primarily grown as protein-rich grains or pseudocereals. The genus also includes major noxious weeds (e.g., A. palmeri). The amaranths are within the Caryophyllales order and thus many species (e.g., A. tricolor) produce red (betacyanin) or yellow (betaxanthin) betalain pigments, which are chemically distinct from the anthocyanins responsible for red pigmentation in other plants. A. hypochondriacus, which shows disomic inheritance (2n = 32; n= 466 Mb), has been sequenced and annotated with 23,059 protein-coding genes. Additional members of the genus are now also been sequenced including weedy amaranths, other grain amaranths, and their putative progenitors.

The Capsicum Genome

Author : Nirala Ramchiary
Publisher : Springer
ISBN 13 : 3319972170
Total Pages : 244 pages
Book Rating : 4.3/5 (199 download)

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Book Synopsis The Capsicum Genome by : Nirala Ramchiary

Download or read book The Capsicum Genome written by Nirala Ramchiary and published by Springer. This book was released on 2019-02-18 with total page 244 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book contains complete information on Capsicum genetic resources, diversity, evolution, history and advances in capsicum improvement from classical breeding to whole genome sequencing, genomics, databases and its impact on next generation pepper breeding. Capsicum is one of the most important Solanaceae crops grown worldwide as vegetables and spices. Due to its high economic value and to meet the demands of enormous population growth amid biotic and abiotic stresses, there has been an ongoing breeding program utilizing available genetic resources with desired traits to increase the sustainable productivity of this crop for several decades. However, the precision breeding of this crop for desired traits only started with the advent of molecular markers. The recent advances in high-throughput genome sequencing technologies helped in the quick decoding of transcriptome, epigenome, nuclear and organeller genomes, thereby enhancing our understanding of the structure and function of the Capsicum genome, and helping in genomics assisted breeding. These advanced technologies coupled with conventional mapping have greatly contributed towards dissection and manipulation of economically important traits more precisely and made less time consuming.

Bioinformatics in the Era of Post Genomics and Big Data

Author : Ibrokhim Y. Abdurakhmonov
Publisher : BoD – Books on Demand
ISBN 13 : 1789232686
Total Pages : 190 pages
Book Rating : 4.7/5 (892 download)

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Book Synopsis Bioinformatics in the Era of Post Genomics and Big Data by : Ibrokhim Y. Abdurakhmonov

Download or read book Bioinformatics in the Era of Post Genomics and Big Data written by Ibrokhim Y. Abdurakhmonov and published by BoD – Books on Demand. This book was released on 2018-06-20 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bioinformatics has evolved significantly in the era of post genomics and big data. Huge advancements were made toward storing, handling, mining, comparing, extracting, clustering and analysis as well as visualization of big macromolecular data using novel computational approaches, machine and deep learning methods, and web-based server tools. There are extensively ongoing world-wide efforts to build the resources for regional hosting, organized and structured access and improving the pre-existing bioinformatics tools to efficiently and meaningfully analyze day-to-day increasing big data. This book intends to provide the reader with updates and progress on genomic data analysis, data modeling and network-based system tools.

The Pangenome

Author : Hervé Tettelin
Publisher : Springer Nature
ISBN 13 : 3030382818
Total Pages : 311 pages
Book Rating : 4.0/5 (33 download)

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Book Synopsis The Pangenome by : Hervé Tettelin

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.

The Grape Genome

Author : Dario Cantu
Publisher : Springer Nature
ISBN 13 : 3030186016
Total Pages : 385 pages
Book Rating : 4.0/5 (31 download)

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Book Synopsis The Grape Genome by : Dario Cantu

Download or read book The Grape Genome written by Dario Cantu and published by Springer Nature. This book was released on 2019-11-13 with total page 385 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the current state of international grape genomics, with a focus on the latest findings, tools and strategies employed in genome sequencing and analysis, and genetic mapping of important agronomic traits. It also discusses how these are having a direct impact on outcomes for grape breeders and the international grape research community. While V. vinifera is a model species, it is not always appreciated that its cultivation usually requires the use of other Vitis species as rootstocks. The book discusses genetic diversity within the Vitis genus, the available genetic resources for breeding, and the available genomic resources for other Vitis species. Grapes (Vitis vinifera spp. vinifera) have been a source of food and wine since their domestication from their wild progenitor (Vitis vinifera ssp. sylvestris) around 8,000 years ago, and they are now the world’s most valuable horticultural crop. In addition to being economically important, V. vinifera is also a model organism for the study of perennial fruit crops for two reasons: Firstly, its ability to be transformed and micropropagated via somatic embryogenesis, and secondly its relatively small genome size of 500 Mb. The economic importance of grapes made V. vinifera an obvious early candidate for genomic sequencing, and accordingly, two draft genomes were reported in 2007. Remarkably, these were the first genomes of any fruiting crop to be sequenced and only the fourth for flowering plants. Although riddled with gaps and potentially omitting large regions of repetitive sequences, the two genomes have provided valuable insights into grape genomes. Cited in over 2,000 articles, the genome has served as a reference in more than 3,000 genome-wide transcriptional analyses. Further, recent advances in DNA sequencing and bioinformatics are enabling the assembly of reference-grade genome references for more grape genotypes revealing the exceptional extent of structural variation in the species.

The Moringa Genome

Author : N. Manikanda Boopathi
Publisher : Springer Nature
ISBN 13 : 3030809560
Total Pages : 195 pages
Book Rating : 4.0/5 (38 download)

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Book Synopsis The Moringa Genome by : N. Manikanda Boopathi

Download or read book The Moringa Genome written by N. Manikanda Boopathi and published by Springer Nature. This book was released on 2021-09-14 with total page 195 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides updated and all-inclusive data and evidences for Moringa botany, cytogenetical analysis, genetic resources and diversity, classical genetics, traditional breeding, tissue culture, genetic transformation, whole-genome sequencing, comparative genomics and elucidation on applications of functional genomics, nanotechnology, bioinformatics, processing and value addition besides providing perspectives of medicinal and therapeutic properties of Moringa. Moringa gained global attention in the recent past owing to its unique blend of affordable nutraceutical and pharmaceutical compounds in all parts of the plants. Scientific literatures supporting its health benefits besides the studies on its utility in various fields are scattered on several reports. This book is written by renowned global subject experts by compiling and narrating it in a sober style.

The Rubber Tree Genome

Author : Minami Matsui
Publisher : Springer
ISBN 13 : 9783030422608
Total Pages : 175 pages
Book Rating : 4.4/5 (226 download)

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Book Synopsis The Rubber Tree Genome by : Minami Matsui

Download or read book The Rubber Tree Genome written by Minami Matsui and published by Springer. This book was released on 2021-05-04 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the first comprehensive compilation of genome research on the Hevea brasiliensis rubber tree. The genomes of Hevea tree clones (cultivars) are described by three major international groups. Chapters on omics-driven investigations address a broad range of topics including genome annotation and utilisation, transcriptome and gene family analysis, genetic mapping, metabolic pathways in latex and molecular breeding. Additionally, an overview of fundamental rubber biology, especially on laticifers, provides a historical background that is relevant to rubber genome analysis. The book concludes with several perspectives on the future needs of rubber investigations and prospects of rubber genomics. Given the scope of topics, this book will appeal to researchers and university students working in genomics and biotechnology of the rubber tree, and to rubber breeders with an interest in non-conventional approaches to trait analysis, selection and breeding.

The Tomato Genome

Author : Mathilde Causse
Publisher : Springer
ISBN 13 : 3662533898
Total Pages : 260 pages
Book Rating : 4.6/5 (625 download)

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Book Synopsis The Tomato Genome by : Mathilde Causse

Download or read book The Tomato Genome written by Mathilde Causse and published by Springer. This book was released on 2016-11-21 with total page 260 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the strategy used for sequencing, assembling and annotating the tomato genome and presents the main characteristics of this sequence with a special focus on repeated sequences and the ancestral polyploidy events. It also includes the chloroplast and mitochondrial genomes. Tomato (Solanum lycopersicum) is a major crop plant as well as a model for fruit development, and the availability of the genome sequence has completely changed the paradigm of the species’ genetics and genomics. The book describes the numerous genetic and genomic resources available, the identified genes and quantitative trait locus (QTL) identified, as well as the strong synteny across Solanaceae species. Lastly, it discusses the consequences of the availability of a high-quality genome sequence of the cultivated species for the research community. It is a valuable resource for students and researchers interested in the genetics and genomics of tomato and Solanaceae.

Approaches and applications in plant genome assembly and sequence analysis

Author : Weihua Pan
Publisher : Frontiers Media SA
ISBN 13 : 283252012X
Total Pages : 185 pages
Book Rating : 4.8/5 (325 download)

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Book Synopsis Approaches and applications in plant genome assembly and sequence analysis by : Weihua Pan

Download or read book Approaches and applications in plant genome assembly and sequence analysis written by Weihua Pan and published by Frontiers Media SA. This book was released on 2023-04-06 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt:

The Pigeonpea Genome

Author : Rajeev K. Varshney
Publisher : Springer
ISBN 13 : 3319637975
Total Pages : 113 pages
Book Rating : 4.3/5 (196 download)

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Book Synopsis The Pigeonpea Genome by : Rajeev K. Varshney

Download or read book The Pigeonpea Genome written by Rajeev K. Varshney and published by Springer. This book was released on 2017-12-15 with total page 113 pages. Available in PDF, EPUB and Kindle. Book excerpt: Pigeonpea (Cajanus cajan) is a crop of small land holding farmers in arid and semi-arid regions of the world. It has a number of usages starting from protein rich food to vegetarian families; fuel wood; nitrogen supplier to soil; recycling minerals in soil to animal feed etc. Pigeonpea has been considered to be originated and domesticated in central India from where it travelled to different parts of the world such as Africa and Latin America. In ongoing scenario of climate change, biotic and especially abiotic stresses will make the conditions more challenging for entire agriculture. This volume focusing on the pigeonpea genome will collate the information on the genome sequencing and its utilization in genomics activities, with a focus on the current findings, advanced tools and strategies deployed in pigeonpea genome sequencing and analysis, and how this information is leading to direct outcomes for plant breeders and subsequently to farmers.

The New Science of Metagenomics

Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309106761
Total Pages : 170 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis The New Science of Metagenomics by : National Research Council

Download or read book The New Science of Metagenomics written by National Research Council and published by National Academies Press. This book was released on 2007-06-24 with total page 170 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although we can't usually see them, microbes are essential for every part of human life-indeed all life on Earth. The emerging field of metagenomics offers a new way of exploring the microbial world that will transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas. Metagenomics allows researchers to look at the genomes of all of the microbes in an environment at once, providing a "meta" view of the whole microbial community and the complex interactions within it. It's a quantum leap beyond traditional research techniques that rely on studying-one at a time-the few microbes that can be grown in the laboratory. At the request of the National Science Foundation, five Institutes of the National Institutes of Health, and the Department of Energy, the National Research Council organized a committee to address the current state of metagenomics and identify obstacles current researchers are facing in order to determine how to best support the field and encourage its success. The New Science of Metagenomics recommends the establishment of a "Global Metagenomics Initiative" comprising a small number of large-scale metagenomics projects as well as many medium- and small-scale projects to advance the technology and develop the standard practices needed to advance the field. The report also addresses database needs, methodological challenges, and the importance of interdisciplinary collaboration in supporting this new field.