The Brassica rapa genome /

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Bibliographic Details
Imprint:Heidelberg : Springer, 2015.
Description:1 online resource (viii, 169 pages) : color illustrations.
Language:English
Series:Compendium of plant genomes, 2199-4781
Compendium of plant genomes.
Subject:Brassica -- Genetics.
Vegetables, Chinese.
GARDENING -- Essays.
GARDENING -- Reference.
GARDENING -- Vegetables.
SCIENCE -- Life Sciences -- Horticulture.
Brassica -- Genetics.
Vegetables, Chinese.
Electronic books.
Format: E-Resource Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/11096099
Hidden Bibliographic Details
Other authors / contributors:Wang, Xiaowu, editor.
Kole, Chittaranjan, editor.
ISBN:9783662479018
366247901X
3662479001
9783662479001
9783662479001
Digital file characteristics:text file PDF
Notes:References2 Background History of the National and International Brassica rapa Genome Sequencing Initiatives; Abstract; References; 3 Genomic Resources and Physical Mapping of the B. rapa Genome; Abstract; 3.1 Introduction; 3.2 Genome Structure; 3.2.1 Karyotype; 3.2.2 Heterochromatin; 3.3 Genomic Resources; 3.3.1 BAC Libraries and BAC-end Sequences; 3.3.2 cDNA Libraries and Expressed Sequence Tags; 3.3.3 BAC Sequences; 3.4 Physical Mapping; 3.4.1 High-Information Content Fingerprinting; 3.4.2 Physical Map Based on the HICF Method; 3.5 Conclusion; Acknowledgments; References.
References6 Miniature Transposable Elements (mTEs) : Impacts and Uses in the Brassica Genome; Abstract; 6.1 Introduction; 6.2 Characteristics and Distribution of mTEs; 6.2.1 TRIMs; 6.2.2 SINEs; 6.2.3 MITEs; 6.3 Identification of mTEs; 6.4 Influence of mTEs on Evolution of the Triplicated Brassica Genome; 6.5 Copy Number Variation of mTE Members Between Accessions and Species; 6.6 Utility of mTEs as Molecular Markers; 6.6.1 Insertion Polymorphism of mTEs; 6.6.2 Transposon Display (TD) for mTEs; 6.7 Conclusion; Acknowledgments; References.
Online resource; title from PDF title page (EBSCO, viewed September 11, 2015).
Summary:This book provides insights into the latest achievements in genomics research on Brassica rapa. It describes the findings on this Brassica species, the first of the U's triangle that has been sequenced and a close relative to the model plant Arabidopsis, which provide a basis for investigations of major Brassica crop species. Further, the book focuses on the development of tools to facilitate the transfer of our rich knowledge on Arabidopsis to a cultivated Brassica crop. Key topics covered include genomic resources, assembly tools, annotation of the genome, transposable elements, comparative genomics, evolution of Brassica genomes, and advances in the application of genomics in the breeding of Brassica rapa crops.
Other form:Print version: Wang, Xiaowu. Brassica rapa Genome. Berlin, Heidelberg : Springer Berlin Heidelberg, ©2015 9783662479001
Standard no.:10.1007/978-3-662-47901-8
Table of Contents:
  • Preface; Contents; 1 Economic/Academic Importance of Brassica rapa; Abstract; 1.1 Introduction; 1.2 Origins of Brassica rapa; 1.3 Biosystematic Relationship Among the Brassica Species; 1.4 Crops of Brassica rapa; 1.5 Production of Doubled Haploids in Brassica rapa; 1.6 Reproduction Biology; 1.6.1 Self-incompatibility; 1.6.2 Male Sterility; 1.6.2.1 Genic Male Sterility; 1.6.2.2 Cytoplasmic Male Sterility; 1.6.2.3 Polima CMS; 1.7 Resistance to Disease; 1.7.1 Resistance to Turnip Mosaic Virus; 1.7.2 Resistance to Clubroot; 1.8 Glucosinolates; 1.9 Transfer of Genes Between B. rapa and B. napus.
  • 4 De Novo Genome Assembly of Next-Generation Sequencing DataAbstract; 4.1 Introduction; 4.2 The Challenge of Genome Assembly; 4.3 De Novo Assembly Algorithm; 4.3.1 Classification of De Novo Assembly Algorithm; 4.3.2 The Overlap Layout Consensus Approach; 4.3.3 De Bruijn Graph Approach; 4.3.4 Extension-Based Approach; 4.4 Comparison of Algorithms; 4.4.1 Datasets and Assemblers; 4.4.2 Performance Comparison Using Medium-Sized Genomes; 4.4.3 Performance Comparison Using Nine Bacterial Genomes; 4.5 Discussion; References; 5 Crop Genome Annotation: A Case Study for the Brassica rapa Genome.
  • Abstract5.1 Introduction; 5.2 The Processes of a Genome Annotation; 5.2.1 Filtering the Sequences and Masking Putative Repeats; 5.2.2 Prediction of Protein-Coding Genes; 5.2.3 Identification of Non-coding RNAs; 5.2.4 Functional Annotation of Proteins and Genome Visualization; 5.3 The Annotation Results of the Reference Sequence; 5.3.1 Repetitive Elements in the Reference Genome; 5.3.2 Protein-Coding Genes and NcRNAs; 5.3.3 Summary of the Previous Annotation of Brassica Rapa; 5.3.4 Comparison of the Results of This Study with Those of the Previous Annotation; 5.4 Conclusion; Acknowledgments.