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Advances in Botanical Research publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences. Currently in its 69th volume, the series features several… Read more
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Contributors
Chapter One. A Backdrop: Principles of Plant Genome Organization
Abstract
1 Background for this Volume
2 Recurring Features of Plant Genomes
References
Chapter Two. Evolution of Plant Genome Analysis
Abstract
1 Introduction
2 Evolution of the Term Genome
3 Cytology and Cytogenetics
4 Genome Size Determination
5 Renaturation Kinetics
6 Genetic Mapping
7 Physical Mapping
Acknowledgements
References
Chapter Three. The Evolution of Plant Gene and Genome Sequencing
Abstract
1 The Early Period of Plant Gene Sequencing
2 Random Sequencing of Expressed Genes for Discovery
3 Evolution of DNA Sequencing Beyond Sanger Methodology
4 The First Whole Plant Genome Sequences
5 The Second Round of Whole Plant Genome Sequences
6 Examples of the Many Recently Published Plant Genome Projects
7 A Summary of the Trends
Acknowledgement
References
Chapter Four. The First Plant Genome Sequence—Arabidopsis thaliana
Abstract
1 Introduction
2 Sequencing Strategy and Outcome
3 Evolutionary History
4 Conclusions
References
Chapter Five. The First Monocot Genome Sequence: Oryza sativa (Rice)
Abstract
1 Sequencing Strategies and Outcome
2 The Rice Gene Set and its Comparison to Dicots (Arabidopsis)
3 Evolutionary History (Especially Genome Duplication)
References
Chapter Six. Insights into the Common Ancestor of Eudicots
Abstract
1 Introduction
2 Phylogeny and Evolution of Eudicot Plants
3 Sequencing of Eudicot Genomes
4 The Gamma Paleohexaploidy in Ancestral Eudicot Lineages
5 Structural Comparison of Eudicot Genomes and Widespread Ancient Genome Duplications
6 Progress in Reconstructing the Eudicot Ancestral Genome
7 Further Inferences on Genome Structure Evolution
8 Perspective
Acknowledgements
References
Chapter Seven. Insights into the Common Ancestor of Cereals
Abstract
1 The Economic and Agricultural Importance of Cereals
2 Genome Sequencing Opens a New Era of Grass Research
3 Gene Colinearity Contributes to Decipher Genome Structure
4 An Ancestral Polyploidization Presides the Divergence of Major Cereals
5 Large-Scale Genomic Repatterning Followed Whole-Genome Duplication
6 Recombination Between Homoeologous Chromosomes
7 Alignment of Multiple Genomes
8 Inference of the Gene Composition of Ancestral Genomes
9 Summary
Acknowledgements
References
Chapter Eight. Early History of the Angiosperms
Abstract
1 Introduction
2 Plant Genome Comparisons and Paleopolyploidy Events
3 Analytic Tools and Workflow for Genome Comparisons
4 Dating and Naming of Paleopolyploidy Events
5 Circumscribing the Paneudicot Paleohexaploidy
6 Circumscribing Ancient Polyploidy Events in Monocots
7 Effective Comparisons Between Eudicot and Monocot Genomes Through PARs
8 Panangiosperm Comparisons Through Ancestral Genome Reconstruction
9 Deeply Conserved Noncoding Sequences in Flowering Plants
10 Future Prospects
References
Chapter Nine. Prehistory of the Angiosperms: Characterization of the Ancient Genomes
Abstract
1 Brief Evolutionary History from Algae to Flowering Plants
2 Chloroplast Genome Evolution in Land Plants
3 An Ancient Green Algae Model Organism: C. reinhardtii
4 The First Model Moss Genome Sequence: P. patens
5 The First Lycophyte Genome Sequence: Selaginella moellendorffii
6 Current Knowledge of Ferns Based on Limited Genomic Resources
7 Overview of Genomic Analyses in Gymnosperms
8 Ancestral Polyploidy Events Before the Origin of Angiosperms
9 Conclusion and Future Studies
References
Chapter Ten. Decoding the Epigenomes of Herbaceous Plants
Abstract
1 Introduction
2 DNA Methylation
3 Nucleosome Positioning and Occupancy
4 Histone Variants
5 Histone Modifications
6 Concluding Remarks and Future Directions
References
Chapter Eleven. The Plant Microbiome
Abstract
1 Background
2 Currency of the Microbiome: Exudates
3 Ecology of the Microbiome
4 Importance of the Microbiome to Plant Genomics
5 Conclusions
References
Chapter Twelve. Population Genomics of Plant Species
Abstract
1 Introduction
2 Genetic Diversity in Plant Populations
3 Mutation Rate Variation
4 Mating-System Effects on Genetic Diversity
5 Adaptation in Plant Populations
6 Deleterious Variation in Plant Populations
7 The Effects of Linked Selection
8 Mapping of Quantitative Trait Loci
9 Advances Through Whole Genome Resequencing
10 Conclusion
References
Chapter Thirteen. A Short Course on the Impact of Gene Duplications on the Evolution of Novelty
Abstract
1 First Day of Class
2 Lesson 1: Duplication of Genes and the Relaxation of Selection
3 Lesson 2: Measuring Genetic Divergence and Its Meaning
4 Lesson 3: Visualizing DNA Sequence Divergence Using GEvo in CoGe Running on IPlant Servers (Use Firefox)
5 Lesson 4: Visualizing Whole-Genome Duplications and Whole-Genome Divergence: SynMap (Use Firefox)
6 Lesson 5: Polyploids
7 Lesson 6: Fractionation
8 Lesson 7: Subfunctionalization, Nonfunctionalization (and Neofunctionalization)
9 Lesson 8: The Gene Balance Hypothesis
10 Lesson 9: Different Sorts of Gene Duplication Change the Gene Content of the Genome in Different Ways, and How the Subfunctionalization Idea Became Downgraded
11 Lesson 10: Drive
12 Lesson 11: Balanced Gene Drive
13 Lesson 12: Genome Dominance
14 Lesson 13: Chimps, Man and a Goodbye Present
Acknowledgement
References
Chapter Fourteen. Synthetic Haplotypes, Species, Karyotypes, and Protoorganisms?
Abstract
1 Synthetic Haplotypes
2 Novel Polyploids: Synthetic Plant Species
3 Synthetic Karyotypes: Introducing Artificial Chromosomes into a Genome
4 Protoorganisms: Mitigating the Constraints of a Sporophytic Stage of Development
5 Synthesis
References
Author Index
Subject Index
AP