Genomes of Herbaceous Land Plants

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