Genomes of herbaceous land plants /
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| Imprint: | Amsterdam : Academic Press, 2014. |
|---|---|
| Description: | 1 online resource. |
| Language: | English |
| Series: | Advances in botanical research ; v. 69 Advances in botanical research ; v. 69. |
| Subject: | |
| Format: | E-Resource Book |
| URL for this record: | http://pi.lib.uchicago.edu/1001/cat/bib/11209508 |
Table of Contents:
- Contributors
- 1. A Backdrop: Principles of Plant Genome Organization
- 1. Background for this Volume
- 2. Recurring Features of Plant Genomes
- References
- 2. Evolution of Plant Genome Analysis
- 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
- 3. The Evolution of Plant Gene and Genome Sequencing
- 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
- 4. The First Plant Genome Sequence-Arabidopsis thaliana
- 1. Introduction
- 2. Sequencing Strategy and Outcome
- 3. Evolutionary History
- 4. Conclusions
- References
- 5. The First Monocot Genome Sequence: Oryza sativa (Rice)
- 1. Sequencing Strategies and Outcome
- 2. The Rice Gene Set and Its Comparison to Dicots (Arabidopsis)
- 3. Evolutionary History (Especially Genome Duplication)
- References
- 6. Insights into the Common Ancestor of Eudicots
- 1. Introduction
- 2. Phytogeny 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
- 7. Insights into the Common Ancestor of Cereals
- 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
- 8. Early History of the Angiosperms
- 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
- 9. Prehistory of the Angiosperms: Characterization of the Ancient Genomes
- 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
- 10. Decoding the Epigenomes of Herbaceous Plants
- 1. Introduction
- 2. DNA Methylation
- 3. Nucleosome Positioning and Occupancy
- 4. Histone Variants
- 5. Histone Modifications
- 6. Concluding Remarks and Future Directions
- References
- 11. The Plant Microbiome
- 1. Background
- 2. Currency of the Microbiome: Exudates
- 3. Ecology of the Microbiome
- 4. Importance of the Microbiome to Plant Genomics
- 5. Conclusions
- References
- 12. Population Genomics of Plant Species
- 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
- 13. A Short Course on the Impact of Gene Duplications on the Evolution of Novelty
- 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
- 14. Synthetic Haplotypes, Species, Karyotypes, and Protoorganisms?
- 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