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Author: Stéphane Deschamps
Publisher:
ISBN:
Category : Science
Languages : en
Pages :
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Book Description
The field of plant genome assembly has greatly benefited from the development and widespread adoption of next-generation DNA sequencing platforms. Very high sequencing throughputs and low costs per nucleotide have considerably reduced the technical and budgetary constraints associated with early assembly projects done primarily with a traditional Sanger-based approach. Those improvements led to a sharp increase in the number of plant genomes being sequenced, including large and complex genomes of economically important crops. Although next-generation DNA sequencing has considerably improved our understanding of the overall structure and dynamics of many plant genomes, severe limitations still remain because next-generation DNA sequencing reads typically are shorter than Sanger reads. In addition, the software tools used to de novo assemble sequences are not necessarily designed to optimize the use of short reads. These cause challenges, common to many plant species with large genome sizes, high repeat contents, polyploidy and genome-wide duplications. This chapter provides an overview of historical and current methods used to sequence and assemble plant genomes, along with new solutions offered by the emergence of technologies such as single molecule sequencing and optical mapping to address the limitations of current sequence assemblies.
Author: Stéphane Deschamps
Publisher:
ISBN:
Category : Science
Languages : en
Pages :
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Book Description
The field of plant genome assembly has greatly benefited from the development and widespread adoption of next-generation DNA sequencing platforms. Very high sequencing throughputs and low costs per nucleotide have considerably reduced the technical and budgetary constraints associated with early assembly projects done primarily with a traditional Sanger-based approach. Those improvements led to a sharp increase in the number of plant genomes being sequenced, including large and complex genomes of economically important crops. Although next-generation DNA sequencing has considerably improved our understanding of the overall structure and dynamics of many plant genomes, severe limitations still remain because next-generation DNA sequencing reads typically are shorter than Sanger reads. In addition, the software tools used to de novo assemble sequences are not necessarily designed to optimize the use of short reads. These cause challenges, common to many plant species with large genome sizes, high repeat contents, polyploidy and genome-wide duplications. This chapter provides an overview of historical and current methods used to sequence and assemble plant genomes, along with new solutions offered by the emergence of technologies such as single molecule sequencing and optical mapping to address the limitations of current sequence assemblies.
Author: Nils Stein
Publisher: Springer
ISBN: 3319925288
Category : Science
Languages : en
Pages : 400
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Book Description
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.
Author: Swarup Kumar Chakrabarti
Publisher: Springer
ISBN: 3319661353
Category : Science
Languages : en
Pages : 332
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Book Description
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.
Author: Ibrokhim Y. Abdurakhmonov
Publisher: BoD – Books on Demand
ISBN: 9535124552
Category : Science
Languages : en
Pages : 312
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Book Description
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.
Author: Jean-Nicolas Volff
Publisher: Karger Medical and Scientific Publishers
ISBN: 3805584911
Category : Medical
Languages : en
Pages : 155
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Book Description
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.
Author: Godwin Mafireyi
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Book Description
The aim of this study was to create a genomic resource for a typical plant genome from Illumina short reads, using Psidium guajava as a case study. Here we present a bioinformatics approach to produce a de novo plant genome assembly, perform annotation, and compare the newly assembled and annotated genome to that of a reference genome, in this case Eucalyptus grandis. The assembly pipeline was constructed using a combination of the best results from four different assemblers namely (ABySS, Allpaths-LG, SGA and MaSurCA) with a combination of Illumina paired end and mate pair reads. Each assembler used a different graph-based approach in their assembly strategy, and the output from these assemblers were merged by Metassembler to produce a best assembly. We manage to create comprehensive genomic resource for the guava fruit tree from Illumina short reads. The annotated genome of Psidium guajava will serve a major genomic resource in the investigation of the interaction between the plant and pathogens such as Nalanthamala psidii (N. psidii). Also,our comparative genomics work is a starting point to learn more about the genetic diversity in the Myrtaceae family. In Chapter 1 a comprehensive literature review of the current state of sequencing technologies, with a focus on third generation sequencing technologies is presented. This is followed by a discussion on different whole genome assembly approaches and techniques, with examples of each type of approach implemented as a software package. The relevance and importance of the non-model organism that we used as a case study, Psidium guajava, is also discussed in Chapter 1 In Chapter 2 the genome assembly and annotation pipelines and processes are discussed. Detailed materials and methods used in this study are provided. The main findings and results of the study is discussed in Chapter 3, with a concluding remarks chapter presented as the last chapter of this dissertation. The work presented here has been presented at the following conferences, and a manuscript on the genome resource is in preparation: 1. Poster Presentation "0́− SAGS/SASBI conference 2016 (Durban)
Author: Chittaranjan Kole
Publisher: CRC Press
ISBN: 1439845522
Category : Science
Languages : en
Pages : 628
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Book Description
This book presents the basic and applied aspects of sequencing of genes and genomes and their implication in the fine-scale elucidation of the plant genomes. The third volume presents an overview on the advances of plant genomics made in the past century; deliberations on the genomics resources; concepts, tools, strategies, and achievements of
Author: Kai-Hua Jia
Publisher: Frontiers Media SA
ISBN: 2832542077
Category : Science
Languages : en
Pages : 133
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Book Description
Highly contiguous reference genome sequences are a prerequisite for genomics research and for the optimal utilization of plant species. However, whole-genome duplication events and subsequent chromosomal rearrangements and losses shape the complex features and extensive diversity of plant genomes, and hinder their highly contiguous assembly. With the advent of single-molecule, long-read sequencing technologies, such as PacBio High-Fidelity (HiFi) and Oxford Nanopore Technologies (ONT), as well as Bionano genomics and high-throughput chromatin conformation capture (Hi-C), many highly complex chromosome-level genomes have been revealed, even with phased haplotypes. These advanced sequencing technologies, coupled with improvements in assembly methods, have greatly improved the quality of the assembled genomes. Transcriptomics and metabolomics are playing an increasingly important role in research into genetic variation and functional genes, and enable their combination with other omics studies. For example, in studies of plant stress resistance, the application of transcriptomics and metabolomics technologies allows comprehensive and dynamic detection of the spatial and temporal changes in plant genes/metabolite expression under stress, enabling functional genes to be “mined” and the regulatory mechanism underlying stress responses to be analyzed, providing a molecular genetic basis for the breeding of stress-resistant varieties.
Author: Schuyler S. Korban
Publisher: Springer
ISBN: 3030110486
Category : Science
Languages : en
Pages : 315
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Book Description
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.
Author: Weihua Pan
Publisher: Frontiers Media SA
ISBN: 283252012X
Category : Science
Languages : en
Pages : 185
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Book Description
