1 Aspergillus

Genomics of Plants and Fungi edited by Rolf A. Prade Oklahoma State University Stillwater, Oklahoma, U.S.A. Hans J. Bohnert University of Illinois at Urbana-Champaign Urbana, Illinois, U.S.A. MARCEL DEKKER, INC. NEW YORK • BASEL Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress. ISBN: 0-8247-4125-0 This book is printed on acid-free paper. Headquarters Marcel Dekker, Inc. 270 Madison Avenue, New York, NY 10016 tel: 212-696-9000; fax: 212-685-4540 Eastern Hemisphere Distribution Marcel Dekker AG Hutgasse 4, Postfach 812, CH-4001 Basel, Switzerland tel: 41-61-260-6300; fax: 41-61-260-6333 World Wide Web http://www.dekker.com The publisher offers discounts on this book when ordered in bulk quantities. For more information, write to Special Sales/Professional Marketing at the headquarters address above. Copyright 2003 by Marcel Dekker, Inc. All Rights Reserved. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and recording, or by any information storage and retrieval system, without permission in writing from the publisher. Current printing (last digit): 10987654321 PRINTED IN THE UNITED STATES OF AMERICA MYCOLOGY SERIES Editor J. W. Bennett Professor Department of Cell and Molecular Biology Tulane University New Orleans, Louisiana Founding Editor Paul A. Lemke 1. Viruses and Plasmids in Fungi, edited by Paul A. Lemke 2 The Fungal Community: Its Organization and Role in the Ecosystem, edited by Donald T Wicklow and George C. Carroll 3 Fungi Pathogenic for Humans and Animals (in three parts), edited by Dexter H Howard 4. Fungal Differentiation: A Contemporary Synthesis, edited by John E. Smith 5 Secondary Metabolism and Differentiation in Fungi, edited by Joan W Bennett and Alex Ciegler 6 Fungal Protoplasts, edited by John F Peberdy and Lajos Ferenczy 1. Viruses of Fungi and Simple Eukaryotes, edited by Yigal Koltin and Michael J Leibowitz 8. Molecular Industrial Mycology: Systems and Applications for Fila mentous Fungi, edited by Sally A. Leong and Randy M Berka 9. The Fungal Community: Its Organization and Role in the Ecosystem, Second Edition, edited by George C. Carroll and Donald T. Wicklow 10. Stress Tolerance of Fungi, edited by D. H Jennings 11 Metal Ions in Fungi, edited by Gunther Winkelmann and Dennis R. Wmge 12. Anaerobic Fungi Biology, Ecology, and Function, edited by Douglas O. Mountfort and Colm G Orpin 13. Fungal Genetics Principles and Practice, edited by Gees J. Bos 14 Fungal Pathogenesis: Principles and Clinical Applications, edited by Richard A Calderone and Ronald L. Cihlar 15 Molecular Biology of Fungal Development, edited by Heinz D. Osie- wacz 16 Pathogenic Fungi in Humans and Animals: Second Edition, edited by Dexter H. Howard 17. Fungi in Ecosystem Processes, John Dighton 18. Genomics of Plants and Fungi, edited by Rolf A. Prade and Hans J. Bohnert Additional Volumes in Preparation Clavicipitalean Fungi: Evolutionary Biology, Chemistry, Biocontrol, and Cultural Impacts, edited by James F. White, Jr., Charles W. Bacon, Nigel L. Hywel-Jones, and Joseph W. Spatafora Preface GENOMICS: THE LINK BETWEEN GENETICS AND PHYSIOLOGY Access to the interpretation of entire-genome sequence information for numerous organisms representing Archaea, Eubacteria, Cyanobacteria, and a number of Eukaryote model organisms such as Saccharomyces cerevisiae (baker’s yeast), Caenorabiditis elegans (worm), Drosophila melanogaster (fruit fly), and Arabi- dopsis thaliana (mustard cress) have brought fundamental changes to biology— the comprehension of life as a whole instead of its smallest model unit. Additional genomes are currently in large-scale sequencing pipelines, and projections are that in the next few years, a wealth of whole-genome sequences spanning most taxonomic boundaries of living organisms will become publicly available. Thus, what not long ago appeared to be fiction or wishful thinking is quickly moving into the realm of reality, making it possible to study entire genomes. Scientists will be able to determine structural organization, monitor expression of the genetic code, and distinguish biochemical function, cellular components, and structural components defining the ‘‘wholesome’’ phenotype—the functioning not only of a living cell but also of the integration of all cells in an organism. Often, the reconstruction of entire metabolic pathways becomes possible through dynamic retrieval of biochemical functions, stored in the form of the universal genetic information code, comparative overviews of diverse biological systems, life histories, morphogenetic processes, and inference with respect to natural interactions with the environment. This scenario is not typical, however, because even in prokaryotes and other comparatively lower complexity systems we are faced with a large number of open questions that often present themselves iii iv Preface through the detection of functionally unknown or novel coding regions. In addi- tion, examples of functional ambiguity—coding regions for more than one function, which had held a position of infrequent oddities—are becoming more numerous. As an immediate result of the fast-paced progress that occurred during the last decade, it became apparent that our knowledge of the complexity and number of genes was woefully incomplete. With new protein-coding regions ap- pearing in every organism whose genomic DNA sequence has been determined, realization came that the function(s) of more than half the genes, encoded by the Homo sapiens or A. thaliana genome, remain completely unknown. Moreover, assignments of gene function continue to be missed, although the accuracy of predictive algorithms continues to improve rapidly, even in cases where established biochemical data exist for well-defined coding regions. Some of the com- plications of annotating well-characterized functions to genes are associated with nonuniversal biological processes, such as the generation of multiple functionally diverse proteins through alternate mRNA splicing, single proteins with multiple functions depending on spatiotemporal expression, and a significant and growing number of RNAs that are neither protein coding nor ribosomal RNA nor transfer RNA, yet that seem to have important additional structural or regulatory roles. Direct interpretation of genome DNA sequence information alone has brought recognition of how much more complementary gene function analysis is still needed and simultaneously, has provided new avenues by which to do so. Genome sequences are catalysts for the generation of hypotheses. Figures 1 and F1 2 illustrate the concepts underlying the term “genomics.” Initially, these concepts F2 were geared toward high-throughput detection of which genes and which tran- scripts make up the complexity of an organism. In a comparative fashion, patterns of commonalities and uniqueness were established. In subdisciplines, labeled as proteomics and metabolomics, the complexity, cellular localization, dynamics of protein associations, and their interactions with substrates and products are being determined at the whole-cell level. Thus, all disciplines derived from the original concept of genomics—considering the genomic information as a whole—are based on finding commonalities and differences among organisms, spatiotemporal cell stages, physiological conditions, and interactions with the environment between or within organisms of a given species. In a way, the underlying idea is similar to the collection of the existing knowledge that was undertaken some 200 years ago by scholars, encyclopedists who reasoned that understanding would arise from the compilation and synthesis of all existing knowledge. Genomics is similar in its attempt to gather data points, but it is not at all similar to the encyclopedists’ reasoning because, so far, genomics is generating not only the data but also the new tools to understand them. In this book, we have assembled contributions from dedicated practitioners who have been responsible for shaping the field of fungal and plant genomics. The individual chapters are meant to provide technical insight and to highlight Preface v Figure 1 Schematic representation of cellular organization. Genes are the genetic infor- mational units encoding one or more proteins (polypeptide). Proteins are the products of gene translation. Metabolites are the products of protein function. Components are one or more proteins or protein products assembled into a subcellular component, a complex or functional unit that exerts a specific function. Processes are combinations of proteins, protein products, and cellular components into a network that exerts a new function. En- gines are biological processes that provide metabolites—carbon, nitrogen, phosphorus, and sulfur as well as chemical energy required to drive biological processes. Motors are cellular components that provide energy and motion to protein complexes, cellular components, or biological processes (e.g., vesicle movement, polar growth, or chromosome divi- sion). Machines are cellular components exerting constitutive functions such as transcription, translation, and secretion. Factories are cellular components exerting customized products used by other cellular components or biological processes. Transcriptomics, proteomics, and metabolomics are whole-genome analysis technologies that approach the transcription, function, and products of the genotype.

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