A Case Study for the de Novo Genome Assembly of Plant Genomes from Illumina Short Reads PDF Download
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Author: Godwin Mafireyi
Publisher:
ISBN:
Category :
Languages : en
Pages :
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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: Godwin Mafireyi
Publisher:
ISBN:
Category :
Languages : en
Pages :
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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: 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: Applied Research Press
Publisher: Createspace Independent Publishing Platform
ISBN: 9781515216209
Category :
Languages : en
Pages : 42
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Book Description
Next generation sequencing (NGS) technology has revolutionized genomic and genetic research. The pace of change in this area is rapid with three major new sequencing platforms having been released in 2011: Ion Torrent's PGM, Pacific Biosciences' RS and the Illumina MiSeq. Here we compare the results obtained with those platforms to the performance of the Illumina HiSeq, the current market leader. In order to compare these platforms, and get sufficient coverage depth to allow meaningful analysis, we have sequenced a set of 4 microbial genomes with mean GC content ranging from 19.3 to 67.7%. Together, these represent a comprehensive range of genome content. Here we report our analysis of that sequence data in terms of coverage distribution, bias, GC distribution, variant detection and accuracy. All three fast turnaround sequencers evaluated here were able to generate usable sequence. However there are key differences between the quality of that data and the applications it will support. Proceeds from the sale of this book go to the support of an elderly disabled person.
Author: Manuel Talon
Publisher: Woodhead Publishing
ISBN: 012812217X
Category : Technology & Engineering
Languages : en
Pages : 540
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Book Description
The Genus Citrus presents the enormous amount of new knowledge that has been generated in recent years on nearly all topics related to citrus. Beginning with an overview of the fundamental principles and understanding of citrus biology and behavior, the book provides a comprehensive view from Citrus evolution to current market importance. Reporting on new insights supported by the elucidation of the citrus genome sequence, it presents groundbreaking theories and fills in previous knowledge gaps. Because citrus is among the most difficult plants to improve through traditional breeding, citrus researchers, institutions and industries must quickly learn to adapt to new developments, knowledge and technologies to address the biological constraints of a unique fruit-tree such as citrus. Despite the challenges of working with citrus, tremendous progress has been made, mostly through advances in molecular biology and genomics. This book is valuable for all those involved with researching and advancing, producing, processing, and delivering citrus products. Includes the most current research on citrus genomic information Provides the first detailed description of citrus origin, a new proposal for citrus taxonomy, and a redefinition of the genus Citrus Details citrus challenges including climate change, global disease impacts, and plant improvement strategies
Author: David Edwards
Publisher: Springer
ISBN: 9780387929781
Category : Science
Languages : en
Pages : 451
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Book Description
Bioinformatics is a relatively new field of research. It evolved from the requirement to process, characterize, and apply the information being produced by DNA sequencing technology. The production of DNA sequence data continues to grow exponentially. At the same time, improved bioinformatics such as faster DNA sequence search methods have been combined with increasingly powerful computer systems to process this information. Methods are being developed for the ever more detailed quantification of gene expression, providing an insight into the function of the newly discovered genes, while molecular genetic tools provide a link between these genes and heritable traits. Genetic tests are now available to determine the likelihood of suffering specific ailments and can predict how plant cultivars may respond to the environment. The steps in the translation of the genetic blueprint to the observed phenotype is being increasingly understood through proteome, metabolome and phenome analysis, all underpinned by advances in bioinformatics. Bioinformatics is becoming increasingly central to the study of biology, and a day at a computer can often save a year or more in the laboratory. The volume is intended for graduate-level biology students as well as researchers who wish to gain a better understanding of applied bioinformatics and who wish to use bioinformatics technologies to assist in their research. The volume would also be of value to bioinformatics developers, particularly those from a computing background, who would like to understand the application of computational tools for biological research. Each chapter would include a comprehensive introduction giving an overview of the fundamentals, aimed at introducing graduate students and researchers from diverse backgrounds to the field and bring them up-to-date on the current state of knowledge. To accommodate the broad range of topics in applied bioinformatics, chapters have been grouped into themes: gene and genome analysis, molecular genetic analysis, gene expression analysis, protein and proteome analysis, metabolome analysis, phenome data analysis, literature mining and bioinformatics tool development. Each chapter and theme provides an introduction to the biology behind the data describes the requirements for data processing and details some of the methods applied to the data to enhance biological understanding.
Author: Rajeev K. Varshney
Publisher: Springer
ISBN: 3319637975
Category : Science
Languages : en
Pages : 113
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Book Description
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.
Author: Gianni Barcaccia
Publisher: Frontiers Media SA
ISBN: 2889638871
Category :
Languages : en
Pages : 377
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Book Description
Author: Dinesh Adhikary
Publisher: Springer Nature
ISBN: 3030723658
Category : Science
Languages : en
Pages : 181
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Book Description
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.
Author: Ka-Kit Lam
Publisher:
ISBN:
Category :
Languages : en
Pages : 153
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Book Description
We study data-efficient and also practical de-novo genome assembly algorithm. Due to the advancement in high-throughput sequencing, the cost of read data has gone down rapidly in recent years. Thus, there is a growing need to do genome assembly in a cost effective manner on a large scale. However, the state-of-the-art assemblers are not designed to be data-efficient. This leads to wastage of read data, which translates to a significant monetary loss for large scale sequencing projects. Moreover, as technology advances, the nature of the read data also evolves. This makes the old assemblers insufficient for discovering all the information behind the data. Therefore, there is a need to re-invent genome assemblers to suit the growing demand. In this dissertation, we address the data efficiency aspect of genome assembly as follows. First, we show that even when there is noise in the reads, one can successfully reconstruct the genomes with information requirements close to the noiseless fundamental limit. We develop a new assembly algorithm, X-phased Multibridging, is designed based on a probabilistic model of the genome. We show, through analysis that it performs well on the model, and through simulation that it performs well on real genomes. Second, we introduce FinisherSC, a repeat-aware and scalable tool for upgrading de-novo haploid genome assembly using long and noisy reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance. Thus, FinisherSC achieves higher data efficiency than state-of-the-art haploid genome assembly pipelines. Third, we study whether post-processing metagenomic assemblies with the original input long reads can result in quality improvement. Previous approaches have focused on pre-processing reads and optimizing assemblers. We introduce BIGMAC, which takes an alternative perspective to focus on the post-processing step. Using both the assembled contigs and original long reads as input, BIGMAC first breaks the contigs at potentially mis-assembled locations and subsequently scaffolds contigs. Our experiments on metagenomes assembled from long reads show that BIGMAC can improve assembly quality by reducing the number of mis-assemblies while maintaining/increasing N50 and N75. Thus, BIGMAC achieves higher data efficiency than state-of-the-art metagenomic assembly pipelines. Moreover, we also discuss some theoretical work regarding genome assembly in terms of data, time and space efficiency; and a promising post-processing tool POSTME in improving metagenomic assembly using both short and long reads.
Author:
Publisher: Elsevier
ISBN: 0128163968
Category : Science
Languages : en
Pages : 2444
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Book Description
Comprehensive Foodomics, Three Volume Set offers a definitive collection of over 150 articles that provide researchers with innovative answers to crucial questions relating to food quality, safety and its vital and complex links to our health. Topics covered include transcriptomics, proteomics, metabolomics, genomics, green foodomics, epigenetics and noncoding RNA, food safety, food bioactivity and health, food quality and traceability, data treatment and systems biology. Logically structured into 10 focused sections, each article is authored by world leading scientists who cover the whole breadth of Omics and related technologies, including the latest advances and applications. By bringing all this information together in an easily navigable reference, food scientists and nutritionists in both academia and industry will find it the perfect, modern day compendium for frequent reference. List of sections and Section Editors: Genomics - Olivia McAuliffe, Dept of Food Biosciences, Moorepark, Fermoy, Co. Cork, Ireland Epigenetics & Noncoding RNA - Juan Cui, Department of Computer Science & Engineering, University of Nebraska-Lincoln, Lincoln, NE Transcriptomics - Robert Henry, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia Proteomics - Jens Brockmeyer, Institute of Biochemistry and Technical Biochemistry, University Stuttgart, Germany Metabolomics - Philippe Schmitt-Kopplin, Research Unit Analytical BioGeoChemistry, Neuherberg, Germany Omics data treatment, System Biology and Foodomics - Carlos Leon Canseco, Visiting Professor, Biomedical Engineering, Universidad Carlos III de Madrid Green Foodomics - Elena Ibanez, Foodomics Lab, CIAL, CSIC, Madrid, Spain Food safety and Foodomics - Djuro Josic, Professor Medicine (Research) Warren Alpert Medical School, Brown University, Providence, RI, USA & Sandra Kraljevic Pavelic, University of Rijeka, Department of Biotechnology, Rijeka, Croatia Food Quality, Traceability and Foodomics - Daniel Cozzolino, Centre for Nutrition and Food Sciences, The University of Queensland, Queensland, Australia Food Bioactivity, Health and Foodomics - Miguel Herrero, Department of Bioactivity and Food Analysis, Foodomics Lab, CIAL, CSIC, Madrid, Spain Brings all relevant foodomics information together in one place, offering readers a ‘one-stop,’ comprehensive resource for access to a wealth of information Includes articles written by academics and practitioners from various fields and regions Provides an ideal resource for students, researchers and professionals who need to find relevant information quickly and easily Includes content from high quality authors from across the globe
