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
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 13 2. Evolution of the Term Genome 14 3. Cytology and Cytogenetics 17 4. Genome Size Determination 25 5. Renaturation Kinetics 31 6. Genetic Mapping 35 7. Physical Mapping 38 Acknowledgements 41 References 41 3. 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 47 2. Random Sequencing of Expressed Genes for Discovery 49 3. Evolution of DNA Sequencing Beyond Sanger Methodology 50 4. The First Whole Plant Genome Sequences 53 5. The Second Round of Whole Plant Genome Sequences 58 6. Examples of the Many Recently Published Plant Genome Projects 60 7. A Summary of the Trends 77 Acknowledgement 79 References 79
vi Contents 4. The First Plant Genome Sequence Arabidopsis thaliana 91 Kenneth A. Feldmann and Stephen A. Goff 1. Introduction 92 2. Sequencing Strategy and Outcome 94 3. Evolutionary History 108 4. Conclusions 111 References 112 5. 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 120 2. The Rice Gene Set and Its Comparison to Dicots (Arabidopsis) 124 3. Evolutionary History (Especially Genome Duplication) 127 References 131 6. Insights into the Common Ancestor of Eudicots 137 Jingping Li, Haibao Tang, John E. Bowers, Ray Ming, and Andrew H. Paterson ( 1. Introduction 138 2. Phylogeny and Evolution of Eudicot Plants 139 3. Sequencing of Eudicot Genomes 141 4. The Gamma Paleohexaploidy in Ancestral Eudicot Lineages 146 5. Structural Comparison of Eudicot Genomes and Widespread Ancient Genome Duplications 150 6. Progress in Reconstructing the Eudicot Ancestral Genome 155 7. Further Inferences on Genome Structure Evolution 160 8. Perspective 162 Acknowledgements 164 References 164 7. Insights into the Common Ancestor of Cereals 175 Xiyin Wang, Hui Guo, and Jingpeng Wang 1. The Economic and Agricultural Importance of Cereals 176 2. Genome Sequencing Opens a New Era of Grass Research 176 3. Gene Colinearity Contributes to Decipher Genome Structure 179 4. An Ancestral Polyploidization Presides the Divergence of Major Cereals 182 5. Large-Scale Genomic Repatterning Followed Whole-Genome Duplication 184 6. Recombination Between Homoeologous Chromosomes 185
Contents vii 7. Alignment of Multiple Genomes. 186 8. Inference of the Gene Composition of Ancestral Genomes 188 9. Summary 191 Acknowledgements 191 References 191 8. Early History of the Angiosperms 195 Haibao Tang, Eric Lyons, and James C. Schnable 1. Introduction 196 2. Plant Genome Comparisons and Paleopolyploidy Events 198 3. Analytic Tools and Workflow for Genome Comparisons 200 4. Dating and Naming of Paleopolyploidy Events 202 5. Circumscribing the Paneudicot Paleohexaploidy 205 6. Circumscribing Ancient Polyploidy Events in Monocots 208 7. Effective Comparisons Between Eudicot and Monocot Genomes Through PARs 211 8. Panangiosperm Comparisons Through Ancestral Genome Reconstruction 212 9. Deeply Conserved Noncoding Sequences in Flowering Plants 216 10. Future Prospects 217 References 218 9. Prehistory of the Angiosperms: Characterization of the Ancient Genomes 223 Yuannian Jiao and Hui Guo 1. Brief Evolutionary History from Algae to Flowering Plants 224 2. Chloroplast Genome Evolution in Land Plants 225 3. An Ancient Green Algae Model Organism: C. reinhardtii 228 4. The First Model Moss Genome Sequence: P. patens 229 5. The First Lycophyte Genome Sequence: Selaginella moellendorffii 231 6. Current Knowledge of Ferns Based on Limited Genomic Resources 232 7. Overview of Genomic Analyses in Gymnosperms 233 8. Ancestral Polyploidy Events Before the Origin of Angiosperms 235 9. Conclusion and Future Studies 239 References 240 10. Decoding the Epigenomes of Herbaceous Plants 247 Robert J. Schmitz and Xiaoyu Zhang 1. Introduction 248 2. DNA Methylation 248 3. Nucleosome Positioning and Occupancy 255
viii Contents 4. Histone Variants 257 5. Histone Modifications 260 6. Concluding Remarks and Future Directions 266 References 268 11. The Plant Microbiome 279 Mamie E. Rout 1. Background 280 2. Currency of the Microbiome: Exudates 284 3. Ecology of the Microbiome 292 4. Importance of the Microbiome to Plant Genomics 297 5. Conclusions 301 References 302 12. Population Genomics, of Plant Species 311 Khaled M. Hazzouri, Michael D. Purugganan, and Jonathan M. Flowers 1. Introduction 312 2. Genetic Diversity in Plant Populations 313 3. Mutation Rate Variation 314 4. Mating-System Effects on Genetic Diversity 315 ^ 5. Adaptation in Plant Populations 316 6. Deleterious Variation in Plant Populations 319 7. The Effects of Linked Selection 321 8. Mapping of Quantitative Trait Loci 324 9. Advances Through Whole Genome Resequencing 325 10. Conclusion 327 References 327 13. A Short Course on the Impact of Gene Duplications on the Evolution of Novelty 335 Michael Freeling 1. First Day of Class 336 2. Lesson 1: Duplication of Genes and the Relaxation of Selection 337 3. Lesson 2: Measuring Genetic Divergence and Its Meaning 339 4. Lesson 3: Visualizing DNA Sequence Divergence Using GEvo in CoGe Running on iplant Servers (Use Firefox) 339 5. Lesson 4: Visualizing Whole-Genome Duplications and Whole-Genome Divergence: SynMap (Use Firefox) 341 6. Lesson 5: Polyploids 344
Contents ix 7. Lesson 6: Fractionation 345 8. Lesson 7: Subfunctionalization, Nonfunctionalization (and Neofunctionalization) 348 9. Lesson 8: The Gene Balance Hypothesis 350 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 351 11. Lesson 10: Drive 352 12. Lesson 11: Balanced Gene Drive 355 13. Lesson 12: Genome Dominance 357 14. Lesson 13: Chimps, Man and a Goodbye Present 358 Acknowledgement 360 References 360 14. Synthetic Haplotypes, Species, Karyotypes, and Protoorganisms? 363 Andrew H. Paterson 1. Synthetic Haplotypes 363 2. Novel Polyploids: Synthetic Plant Species 367 3. Synthetic Karyotypes: Introducing Artificial Chromosomes into a Genome 370 4. Protoorganisms: Mitigating the Constraints of a Sporophytic Stage of Development 371 5. Synthesis 372 References 374 Author Index Subject Index 377 407