Genomes of Herbaceous Land Plants - 1st Edition - ISBN: 9780124171633, 9780124171824

Genomes of Herbaceous Land Plants, Volume 69

1st Edition

Series Volume Editors: Andrew Paterson
eBook ISBN: 9780124171824
Hardcover ISBN: 9780124171633
Imprint: Academic Press
Published Date: 23rd April 2013
Page Count: 432
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Table of Contents

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


Description

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 reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology. This thematic volume features reviews on genomes of herbaceous land plants

Key Features

  • Publishes in-depth and up-to-date reviews on a wide range of topics in plant sciences
  • Features a wide range of reviews by recognized experts on all aspects of plant genetics, biochemistry, cell biology, molecular biology, physiology and ecology
  • Volume features reviews on genomes of herbaceous land plants

Readership

Postgraduates and researchers in plant sciences, including botany, plant biochemistry, plant physiology, plant pathology, virology, entomology, and molecular biology


Details

No. of pages:
432
Language:
English
Copyright:
© Academic Press 2014
Published:
Imprint:
Academic Press
eBook ISBN:
9780124171824
Hardcover ISBN:
9780124171633

About the Series Volume Editors

Andrew Paterson Series Volume Editor

Affiliations and Expertise

Plant Genome Mapping Laboratory, University of Georgia, Athens, USA