The Brassica rapa genome
Xiaowu Wang (Editor), Chittaranjan Kole (Editor)
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
1 online resource (viii, 169 pages) : color illustrations
9783662479018, 9783662479001, 366247901X, 3662479001
920519618
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