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


Chapter One. A Backdrop: Principles of Plant Genome Organization


1 Background for this Volume

2 Recurring Features of Plant Genomes


Chapter Two. 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



Chapter Three. 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



Chapter Four. The First Plant Genome Sequence—Arabidopsis thaliana


1 Introduction

2 Sequencing Strategy and Outcome

3 Evolutionary History

4 Conclusions


Chapter Five. 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)


Chapter Six. Insights into the Common Ancestor of Eudicots


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



Chapter Seven. 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



Chapter Eight. 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


Chapter Nine. 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


Chapter Ten. 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


Chapter Eleven. 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


Chapter Twelve. 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


Chapter Thirteen. 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



Chapter Fourteen. 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


Author Index

Subject Index


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


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


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Academic Press
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Ratings and Reviews

About the Series Volume Editors

Andrew Paterson Series Volume Editor

Affiliations and Expertise

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