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The Genetics and Genomics of the Brassicaceae provides a review of this important family (commonly termed the mustard family, or Cruciferae). The family contains several cultivated species, including radish, rocket, watercress, wasabi and horseradish, in addition to the vegetable and oil crops of the Brassica genus. There are numerous further species with great potential for exploitation in 21st century agriculture, particularly as sources of bioactive chemicals. These opportunities are reviewed, in the context of the Brassicaceae in agriculture. More detailed descriptions are provided of the genetics of the cultivated Brassica crops, including both the species producing most of the brassica vegetable crops (B. rapa and B. oleracea) and the principal species producing oilseed crops (B. napus and B. juncea). The Brassicaceae also include important “model” plant species. Most prominent is Arabidopsis thaliana, the first plant species to have its genome sequenced. Natural genetic variation is reviewed for A. thaliana, as are the genetics of the closely related A. lyrata and of the genus Capsella. Self incompatibility is widespread in the Brassicaceae, and this subject is reviewed. Interest arising from both the commercial value of crop species of the Brassicaceae and the importance of Arabidopsis thaliana as a model species, has led to the development of numerous resources to support research. These are reviewed, including germplasm and genomic library resources, and resources for reverse genetics, metabolomics, bioinformatics and transformation. Molecular studies of the genomes of species of the Brassicaceae revealed extensive genome duplication, indicative of multiple polyploidy events during evolution. In some species, such as Brassica napus, there is evidence of multiple rounds of polyploidy during its relatively recent evolution, thus the Brassicaceae represent an excellent model system for the study of the impacts of polyploidy and the subsequent process of diploidisation, whereby the genome stabilises. Sequence-level characterization of the genomes of Arabidopsis thaliana and Brassica rapa are presented, along with summaries of comparative studies conducted at both linkage map and sequence level, and analysis of the structural and functional evolution of resynthesised polyploids, along with a description of the phylogeny and karyotype evolution of the Brassicaceae. Finally, some perspectives of the editors are presented. These focus upon the Brassicaceae species as models for studying genome evolution following polyploidy, the impact of advances in genome sequencing technology, prospects for future transcriptome analysis and upcoming model systems.
Through comparative analysis, the genomes of a number of species are providing a deeper understanding of the human genome. This is highly useful in drug research, especially in the treatment of otherwise intractable conditions. Compiling first-hand descriptions of the pioneering achievements of prominent researchers, this text focuses on revolutionary advances in DNA-sequencing technology, new approaches to the organization and analysis of large phylogenetic data sets, new perspectives on evolution, and the development of novel antimicrobial drugs. This seminal volume demonstrates both the means and the fruits of cooperation across a number of fields, and in doing so lays the groundwork for continued progress.
A comprehensive account of genomic rearrangement, focusing on the mechanisms of inversion, translocation, gene and genome duplication and gene transfer and on the patterns that result from them in comparative maps. Includes analyses of genomic sequences in organelles, prokaryotes and eukaryotes as well as comparative maps of the nuclear genomes in higher plants and animals. The book showcases a variety of algorithmic and statistical approaches to rearrangement and map data.
This book presents comprehensive information on genetics, genomics and breeding in Brassica oleracea, an agriculturally important species that includes popular vegetable crops such as cabbage, cauliflower, broccoli, Brussels sprouts, kale, collard greens, savoy, kohlrabi, and gai lan. The content spans whole genome sequencing, assembly and gene annotation for this global vegetable species, along with molecular mapping and cloning of genes, physical genome mapping and analyses of the structure and composition of centromeres in the B. oleracea genome. The book also elaborates on asymmetrical genome evolution and transposable elements in the B. oleracea describes gene family differentiation in comparison to other Brassica species and structural and functional genomic resources and data bases developed for B. oleracea. Useful discussions on the impact of genome sequencing on genetic improvement in the species are also included.
This detailed book presents recent methodologies for the task of inspecting the genomic world of plants, extracting valuable information, and presenting it in a readable way. With a focus on bioinformatics tools, the volume explores phylogenetics and evolution, Omics analysis, as well as experimental procedures for trait characterization. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of vital expert implementation advice that will lead to successful results. Authoritative and practical, Plant Comparative Genomics serves as an ideal resource for researchers looking to implement comparative tools in order to explore their genomic data for their daily scientific work.
The genus Brassica is comprised of diploid and tetraploid species and includes many important crop plants. Several Brassica genomes have been sequenced are the subject of intensive investigation. The immediate impetus for a special Research Topic is the publication of genome sequence of B. rapa . B. rapa is of relatively recent paleopolyploid origin. Its triplicated genome is old enough such that the three genomes have diverged significantly, and young enough such that useful comparisons can be made using Arabidopsis thaliana as an out group, making the B. rapa genome an interesting model for comparative genomics and the analysis of genome evolution. Analysis of B. rapa is also informed by analyses of other Brassica genomes, and reciprocally, understanding of those genomes will be informed by comparisons with the B. rapa genome. We welcome all types of articles on subjects including comparative genomics, genome evolution, and functional genomics, as well as analyses of specific gene families or genes in specific pathways and utilization of genomic data in molecular breeding of Brassica species.
This volume introduces software used for gene prediction with focus on eukaryotic genomes. The chapters in this book describe software and web server usage as applied in common use-cases, and explain ways to simplify re-annotation of long available genome assemblies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary computational requirements, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and thorough, Gene Prediction: Methods and Protocols is a valuable resource for researchers and research groups working on the assembly and annotation of single species or small groups of species. Chapter 3 is available open access under a CC BY 4.0 license via link.springer.com.
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.
Advances in plant cell molecular biology have considerably increased our understanding of pollen-pistil barriers, particularly those operated by incompatibility mechanisms, and, at the same time, demonstrated the complexity and diversity of rejection systems once considered to be relatively simple. This book reviews the impressive knowledge acquired in the last century on the biology, particularly the inheritance and population genetics of self-incompatibility, and presents the new approaches to the study of the structure, function and evolution of incompatibility alleles and the analysis of cell-cell recognition and pollen rejection. The different methods now available for transforming the breeding behaviour of higher plants are also discussed.