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Plastid Genome Evolution ADVANCES in BOTANICAL RESEARCH VOLUME EIGHTY FIVE ADVANCES IN BOTANICAL RESEARCH Plastid Genome Evolution ADVANCES IN BOTANICAL RESEARCH Series Editors Jean-Pierre Jacquot Professor, Membre de L’Institut Universitaire de France, Unite´ Mixte de Recherche INRA, UHP 1136 “Interaction Arbres Microorganismes”, Universite de Lorraine, Faculte des Sciences, Vandoeuvre, France Pierre Gadal Honorary Professor, Universite Paris-Sud XI, Institut Biologie des Plantes, Orsay, France VOLUME EIGHTY FIVE ADVANCES IN BOTANICAL RESEARCH Plastid Genome Evolution Volume Editors SHU-MIAW CHAW Biodiversity Research Center, Academia Sinica; Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan ROBERT K. JANSEN Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States; Genomics and Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia Academic Press is an imprint of Elsevier 125 London Wall, London, EC2Y 5AS, United Kingdom The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, United Kingdom 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States 525 B Street, Suite 1800, San Diego, CA 92101-4495, United States First edition 2018 Copyright © 2018 Elsevier Ltd. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. ISBN: 978-0-12-813457-3 ISSN: 0065-2296 For information on all Academic Press publications visit our website at https://www.elsevier.com/books-and-journals Publisher: Zoe Kruze Acquisition Editor: Sam Mahfoudh Editorial Project Manager: Joanna Collett Production Project Manager: James Selvam Cover Designer: Greg Harris Typeset by SPi Global, India CONTENTS Contributors ix Preface xiii 1. Plastid Autonomy vs Nuclear Control Over Plastid Function 1 Jan de Vries and John M. Archibald 1. Introduction: Endosymbiosis and the Genomic Remnants of Cyanobacteria in Archaeplastida 2 2. Cyanobacterial Genes in Two Genetic Compartments 6 3. Plastid Genomes: Coding Capacity and Functional Diversity 7 4. Role of Genetic Autonomy in Endosymbiosis 11 5. Kleptoplasty and Genetic Semiautonomy of (Stolen) Plastids 13 6. Plastid Autonomy and the Evolution of Land Plants 16 7. Outlook 19 Acknowledgements 20 References 20 2. Lost in the Light: Plastid Genome Evolution in Nonphotosynthetic Algae 29 David R. Smith 1. Introduction 30 2. And Then There Was Light 33 3. Burning Out: The Evolutionary Loss of Photosynthesis 36 4. Genetic Ball and Chain: Plastomes in Colourless Algae 39 5. Adiós ptDNA: The Outright Loss of a Plastome 43 6. Nonphotosynthetic ptDNA: Not so Small After All 46 7. Concluding Thoughts 48 Acknowledgements 49 References 49 Further Reading 53 3. Plastid Genomes in the Myzozoa 55 Sergio A. Muñoz-Gómez and Claudio H. Slamovits 1. Introduction 56 2. The Myzozoa 56 3. The Origin of Myzozoan Plastids 60 v vi Contents 4. Diversity of Plastids in the Myzozoa 61 5. The Plastomes of Myzozoans 68 6. Gene Transfer in Myzozoans 81 7. Conclusions and Future Directions 86 Acknowledgements 87 References 87 4. Comparative Plastid Genomics of Glaucophytes 95 Adrian Reyes-Prieto, Sarah Russell, Francisco Figueroa-Martinez, and Christopher Jackson 1. Introduction 96 2. The Glaucophyta Plastids, Organelles With Ancestral Morphological Traits 98 3. The Genetic Repertoire of the Blue-Green Plastids 103 4. Interspecific Comparative Genomics 110 5. Phylogenomics, the Origin of the Primary Plastids and the Archaeplastida Hypothesis 115 6. The Known Glaucophyte Groups Represent Lineages of Putative Ancient Divergence 117 7. Conclusions 119 References 121 5. Evolution of the Plastid Genomes in Diatoms 129 Mengjie Yu, Matt P. Ashworth, Nahid H. Hajrah, Mohammad A. Khiyami, Mumdooh J. Sabir, Alawiah M. Alhebshi, Abdulrahman L. Al-Malki, Jamal S.M. Sabir, Edward C. Theriot, and Robert K. Jansen 1. Introduction 130 2. Materials and Methods 133 3. Results 137 4. Discussion 146 Acknowledgements 151 Author Contributions 152 References 152 6. Evolution of the Plastid Genome in Green Algae 157 Monique Turmel and Claude Lemieux 1. Introduction 158 2. Classification and Phylogeny of Green Algae 159 3. Plastome Architecture of the Common Ancestor of All Green Algae 164 Contents vii 4. Plastome Evolution in the Chlorophyta 165 5. Plastome Evolution in Streptophyte Algae 182 6. Future Directions 186 References 188 7. Evolution of Gymnosperm Plastid Genomes 195 Shu-Miaw Chaw, Chung-Shien Wu, and Edi Sudianto 1. Introduction 196 2. Sequencing the Plastomes of Gymnosperms 198 3. Plastome Characteristics in Gymnosperms 201 4. Plastome Rearrangements 206 5. Evolution of Nucleotide Substitution Rates 209 6. Plastid Phylogenomics of Gymnosperms 212 7. Conclusions and Future Directions 216 Acknowledgments 216 References 216 8. Aberration or Analogy? The Atypical Plastomes of Geraniaceae 223 Tracey A. Ruhlman and Robert K. Jansen 1. Introduction 224 2. The Great and the Small 225 3. Change or Stay the Same 231 4. Keeping Up With the Rate Race: Acceleration and Coevolution 242 5. Staying in Sync: Hybrid Harmony or Dissonance 251 6. Aberration or Analogy? 254 Acknowledgements 255 References 255 9. Structural Diversity Among Plastid Genomes of Land Plants 263 Jeffrey P. Mower and Trisha L. Vickrey 1. Introduction 264 2. Typical Structure of a Land Plant Plastome 264 3. Conserved Plastomes and Inference of Ancestral Structures 266 4. Structural Diversity of the Plastome Among Plants 270 5. Functional Effect of Structural Change 277 6. What Is Left in Plastome Structural Research? 281 Acknowledgements 283 References 283 viii Contents 10. Plastome Phylogenetics: 30 Years of Inferences Into Plant Evolution 293 Matthew A. Gitzendanner, Pamela S. Soltis, Ting-Shuang Yi, De-Zhu Li, and Douglas E. Soltis 1. Introduction 294 2. The Plastid Genome and Plant Systematics 294 3. Plastome Phylogeny: State of the Tree 300 4. Plastome Phylogenetics: Ongoing Challenges 306 5. Conclusions 307 References 308 11. Molecular Evolution of Plastid Genomes in Parasitic Flowering Plants 315 Susann Wicke and Julia Naumann 1. Introduction 316 2. Plastome Size Diversity in Heterotrophic Land Plants 317 3. Reconstructing and Annotating Divergent Plastomes of Heterotrophs 321 4. Are We Always Dealing With (Pseudo)genes? 324 5. Evolution of Plastome Structure Under Relaxed Selective Constraints 326 6. Functional Reduction Along the Transition to a Nonphotosynthetic Lifestyle 329 7. Evolution of Substitution Rates 332 8. Models of Plastome Degradation 335 9. Conclusions and Future Directions 339 Acknowledgements 340 Glossary 341 References 341 Subject Index 349 Author Index 357 CONTRIBUTORS Abdulrahman L. Al-Malki Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia Alawiah M. Alhebshi Genomics and Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia John M. Archibald Dalhousie University, Halifax, NS; Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, ON, Canada Matt P. Ashworth Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States Shu-Miaw Chaw Biodiversity Research Center, Academia Sinica; Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan Jan de Vries Dalhousie University, Halifax, NS, Canada Francisco Figueroa-Martinez CONACyT-Universidad Auto´noma Metropolitana, Mexico City, Mexico Matthew A. Gitzendanner Department of Biology, University of Florida, Gainesville, FL, United States Nahid H. Hajrah Genomics and Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia Christopher Jackson School of Biosciences, University of Melbourne, Melbourne, VIC, Australia Robert K. Jansen Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States; Genomics and Biotechnology Research Group, Faculty of Science, King Abdulaziz University,
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