ADVANCES IN BOTANICAL RESEARCH

Transcription

1 o >VOLUME SIXTY NINE ADVANCES IN BOTANICAL RESEARCH Genomes of Herbaceous Land Plants Volume Editor ANDREW H. PATERSON Plant Genome Mapping Laboratory Department of Crop and Soil Sciences, Department of Plant Biology, and Department of Genetics University of Georgia USA ELSEVIER AMSTERDAM BOS TON HEIDELBERG LONDON NEW YORK OXFORD PARIS SAN DIEGO SAN FRANCISCO SINGAPORE SYDNEY TOKYO Academn Press is an imprint of Elsevier

2 CONTENTS Contributors xi 1. A Backdrop: Principles of Plant Genome Organization 1 Andrew H. Paterson 1. Background for this Volume 2 2. Recurring Features of Plant Genomes 4 References 9 2. Evolution of Plant Genome Analysis 13 Daniel G. Peterson 1. Introduction Evolution of the Term Genome Cytology and Cytogenetics Genome Size Determination Renaturation Kinetics Genetic Mapping Physical Mapping 38 Acknowledgements 41 References The Evolution of Plant Gene and Genome Sequencing 47 Stephen A. Goff, James C. Schnable, and Kenneth A. Feldmann 1. The Early Period of Plant Gene Sequencing Random Sequencing of Expressed Genes for Discovery Evolution of DNA Sequencing Beyond Sanger Methodology The First Whole Plant Genome Sequences The Second Round of Whole Plant Genome Sequences Examples of the Many Recently Published Plant Genome Projects A Summary of the Trends 77 Acknowledgement 79 References 79

3 vi Contents 4. The First Plant Genome Sequence Arabidopsis thaliana 91 Kenneth A. Feldmann and Stephen A. Goff 1. Introduction Sequencing Strategy and Outcome Evolutionary History Conclusions 111 References The First Monocot Genome Sequence: Oryza sativa (Rice) 119 Hiroaki Sakai, Tsuyoshi Tanaka, Baltazar A. Antonio, Takeshi Itoh, and Takuji Sasaki 1. Sequencing Strategies and Outcome The Rice Gene Set and Its Comparison to Dicots (Arabidopsis) Evolutionary History (Especially Genome Duplication) 127 References Insights into the Common Ancestor of Eudicots 137 Jingping Li, Haibao Tang, John E. Bowers, Ray Ming, and Andrew H. Paterson ( 1. Introduction Phylogeny and Evolution of Eudicot Plants Sequencing of Eudicot Genomes The Gamma Paleohexaploidy in Ancestral Eudicot Lineages Structural Comparison of Eudicot Genomes and Widespread Ancient Genome Duplications Progress in Reconstructing the Eudicot Ancestral Genome Further Inferences on Genome Structure Evolution Perspective 162 Acknowledgements 164 References Insights into the Common Ancestor of Cereals 175 Xiyin Wang, Hui Guo, and Jingpeng Wang 1. The Economic and Agricultural Importance of Cereals Genome Sequencing Opens a New Era of Grass Research Gene Colinearity Contributes to Decipher Genome Structure An Ancestral Polyploidization Presides the Divergence of Major Cereals Large-Scale Genomic Repatterning Followed Whole-Genome Duplication Recombination Between Homoeologous Chromosomes 185

4 Contents vii 7. Alignment of Multiple Genomes Inference of the Gene Composition of Ancestral Genomes Summary 191 Acknowledgements 191 References Early History of the Angiosperms 195 Haibao Tang, Eric Lyons, and James C. Schnable 1. Introduction Plant Genome Comparisons and Paleopolyploidy Events Analytic Tools and Workflow for Genome Comparisons Dating and Naming of Paleopolyploidy Events Circumscribing the Paneudicot Paleohexaploidy Circumscribing Ancient Polyploidy Events in Monocots Effective Comparisons Between Eudicot and Monocot Genomes Through PARs Panangiosperm Comparisons Through Ancestral Genome Reconstruction Deeply Conserved Noncoding Sequences in Flowering Plants Future Prospects 217 References Prehistory of the Angiosperms: Characterization of the Ancient Genomes 223 Yuannian Jiao and Hui Guo 1. Brief Evolutionary History from Algae to Flowering Plants Chloroplast Genome Evolution in Land Plants An Ancient Green Algae Model Organism: C. reinhardtii The First Model Moss Genome Sequence: P. patens The First Lycophyte Genome Sequence: Selaginella moellendorffii Current Knowledge of Ferns Based on Limited Genomic Resources Overview of Genomic Analyses in Gymnosperms Ancestral Polyploidy Events Before the Origin of Angiosperms Conclusion and Future Studies 239 References Decoding the Epigenomes of Herbaceous Plants 247 Robert J. Schmitz and Xiaoyu Zhang 1. Introduction DNA Methylation Nucleosome Positioning and Occupancy 255

5 viii Contents 4. Histone Variants Histone Modifications Concluding Remarks and Future Directions 266 References The Plant Microbiome 279 Mamie E. Rout 1. Background Currency of the Microbiome: Exudates Ecology of the Microbiome Importance of the Microbiome to Plant Genomics Conclusions 301 References Population Genomics, of Plant Species 311 Khaled M. Hazzouri, Michael D. Purugganan, and Jonathan M. Flowers 1. Introduction Genetic Diversity in Plant Populations Mutation Rate Variation Mating-System Effects on Genetic Diversity 315 ^ 5. Adaptation in Plant Populations Deleterious Variation in Plant Populations The Effects of Linked Selection Mapping of Quantitative Trait Loci Advances Through Whole Genome Resequencing Conclusion 327 References A Short Course on the Impact of Gene Duplications on the Evolution of Novelty 335 Michael Freeling 1. First Day of Class Lesson 1: Duplication of Genes and the Relaxation of Selection Lesson 2: Measuring Genetic Divergence and Its Meaning Lesson 3: Visualizing DNA Sequence Divergence Using GEvo in CoGe Running on iplant Servers (Use Firefox) Lesson 4: Visualizing Whole-Genome Duplications and Whole-Genome Divergence: SynMap (Use Firefox) Lesson 5: Polyploids 344

6 Contents ix 7. Lesson 6: Fractionation Lesson 7: Subfunctionalization, Nonfunctionalization (and Neofunctionalization) Lesson 8: The Gene Balance Hypothesis Lesson 9: Different Sorts of Gene Duplication Change the Gene Content of the Genome in Different Ways, and How the Subfunctionalization Idea Became Downgraded Lesson 10: Drive Lesson 11: Balanced Gene Drive Lesson 12: Genome Dominance Lesson 13: Chimps, Man and a Goodbye Present 358 Acknowledgement 360 References Synthetic Haplotypes, Species, Karyotypes, and Protoorganisms? 363 Andrew H. Paterson 1. Synthetic Haplotypes Novel Polyploids: Synthetic Plant Species Synthetic Karyotypes: Introducing Artificial Chromosomes into a Genome Protoorganisms: Mitigating the Constraints of a Sporophytic Stage of Development Synthesis 372 References 374 Author Index Subject Index