Genome Dynamics. Vol. 4. Series Editor Jean-Nicolas Volff. Executive Editor Michael Schmid

Transcription

1 Plant Genomes

2 Genome Dynamics Vol. 4 Series Editor Jean-Nicolas Volff Executive Editor Michael Schmid Lyon Würzburg Advisory Board John F.Y. Brookfield Nottingham Jürgen Brosius Münster Pierre Capy Gif-sur-Yvette Brian Charlesworth Edinburgh Bernard Decaris Vandoeuvre-lès-Nancy Evan Eichler Seattle, WA John McDonald Atlanta, GA Axel Meyer Konstanz Manfred Schartl Würzburg

3 Plant Genomes Volume Editor Jean-Nicolas Volff Lyon 12 figures, 2 in color, and 2 tables, 2008 Basel Freiburg Paris London New York Bangalore Bangkok Shanghai Singapore Tokyo Sydney

4 Prof. Jean-Nicolas Volff Institut de Génomique Fonctionnelle de Lyon Ecole Normale Supérieure de Lyon 46 allée d'italie F Lyon Cedex 07 (France) Library of Congress Cataloging-in-Publication Data Plant genomes / volume editor, Jean-Nicolas Volff. p. ; cm. (Genome dynamics, ISSN ; v. 4) Includes bibliographical references and indexes. ISBN (hard cover : alk. paper) 1. Plant genomes. I. Volff, Jean-Nicolas. II. Series. [DNLM: 1. Genome, Plant. 2. Evolution, Molecular. 3. Variation (Genetics) QK 981 P ] QK981.P dc Bibliographic Indices. This publication is listed in bibliographic services, including Current Contents and Index Medicus. Disclaimer. The statements, options and data contained in this publication are solely those of the individual authors and contributors and not of the publisher and the editor(s). The appearance of advertisements in the book is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements. Drug Dosage. The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any change in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug. All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher. Copyright 2008 by S. Karger AG, P.O. Box, CH 4009 Basel (Switzerland) Printed in Switzerland on acid-free and non-aging paper (ISO 9706) by Reinhardt Druck, Basel ISSN ISBN

5 Contents VII Preface Volff, J.-N. (Lyon) 1 Paleopolyploidy and its Impact on the Structure and Function of Modern Plant Genomes Paterson, A.H. (Athens, Ga.) 13 Genomic History and Gene Family Evolution in Angiosperms: Challenges and Opportunities Sampedro, J.; Cosgrove, D. (State College, Pa.) 25 The Evolutionary Position of Subfunctionalization, Downgraded Freeling, M. (Berkeley, Calif.) 41 Grass Genome Structure and Evolution Messing, J. (Piscataway, N.J.); Bennetzen, J.L. (Athens, Ga.) 57 Phylogenetic Insights Into the Pace and Pattern of Plant Genome Size Evolution Grover, C.E.; Hawkins, J.S.; Wendel, J.F. (Ames, Iowa) 69 Plant Transposable Elements Deragon, J.M. (Aubière/Perpignan); Casacuberta, J.M. (Barcelona); Panaud, O. (Perpignan) 83 Plant Sex Chromosomes Charlesworth, D. (Edinburgh) V

6 95 Plant Centromeres Lamb, J.C.; Yu, W.; Han, F.; Birchler, J.A. (Columbia, Mo.) 108 mirnas in the Plant Genome: All Things Great and Small Meyers, B.C.; Green, P.J.; Lu, C. (Newark, Del.) 119 Recent Insights Into the Evolution of Genetic Diversity of Maize Rafalski, A.; Tingey, S. (Wilmington, Del.) 131 The Rice Genome Structure as a Trail from the Past to Beyond Sasaki, T. (Tsukuba) 143 Author Index 144 Subject Index Contents VI

7 Preface The fourth volume of Genome Dynamics is dedicated to Plant Genomes. In 2000, the sequencing of the genome of the thale cress Arabidopsis thaliana has opened a new era of plant genomics. In the mean time, genome sequences have been completed for additional plants including rice and grapevine, and an important amount of data is already available for many other species. As a consequence, comparative genomics has completely modified our vision of the structure and evolution of plant genomes, with important implications for plant physiology, developmental biology, genetics and evolution as well as obvious applications in the field of agriculture. This volume of Genome Dynamics aims to reflect the astonishing plasticity of plant genomes and to present the molecular and evolutionary processes involved in genome and biological diversity. Particular emphasis is given on the evolutionary impact of genome duplications and transposable elements. Recent progress in the understanding of the evolution of protein-coding gene families and micrornas are reviewed, with specific focus on the evolutionary consequences of gene duplication. Mechanisms involved in size variations are also discussed, as well as new insights into the structure and evolution of sex chromosomes and centromeres. Analyses included in this book range from wide comparisons between very divergent plant species to deep studies of specific models such as rice and maize. All papers published in Genome Dynamics are reviewed according to classical standards. I would like to thank all contributors and referees involved in this book, Michael Schmid and his team, as well as Karger Publishers for their invaluable help during the preparation of this volume. Jean-Nicolas Volff Lyon, December 2007 VII

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