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APPLIED MYCOLOGY
AND BIOTECHNOLOGY
VOLUME 3
FUNGAL GENOMICS
APPLIED MYCOLOGY
AND BIOTECHNOLOGY
VOLUME 3
FUNGAL GENOMICS
This Page Intentionally Left Blank
APPLIED MYCOLOGY
AND BIOTECHNOLOGY
VOLUME 3
FUNGAL GENOMICS

Edited by

Dilip K. Arora
Department of Botany
Banaras Hindu University
India

George G. Khachatourians
Department of Applied Microbiology and Food Sciences
College of Agriculture
University of Saskatchewan
Saskatoon, SK, Canada

2003
ELSEVIER
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Paris - San Diego - San Francisco - Singapore - Sydney - Tokyo
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© 2003 Elsevier Science B.V. All rights reserved.

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First edition 2003

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Editors

Dilip K. Arora
Department of Botany
Banaras Hindu University
India
Fax: +91 542 2368141
Tel:+ 91 542 2369570
E-mail: [email protected]

George G. Khachatourians
Department of Applied Microbiology
and Food Sciences
College of Agriculture
University of Saskatchewan
Saskatoon, Canada
Tel:+1 306 966 5032
E- mail: [email protected]

Editorial Board

Deepak Bhatnagar USDA/ARS, New Orleans, USA.

Thomas E. Cleveland USDA/ARS, New Orleans, USA.
Eric A. Johnson University of Wisconsin, Madison, USA.
Etta Kafer Simon Fraser University, Canada.
Christian P. Kubicek Technical University of Vienna, Austria.
B. Franz Lang Universite de Montreal, Canada.
M. Hyakumachi Gifu University, Japan.
Mary Anne Nelson University of New Mexico, USA.
Helena Nevalainen Macquarie University, Australia.
Nicholas J. Talbot University of Exeter, U.K.
P. Tudzynski Institut fiir Botanik, Miinster, Germany.
This Page Intentionally Left Blank
Contents
Editorial Board for Volume 3 v
Contents vii
Contributors ix
Preface xiii

Fungal Genomics: An Overview 1

Anne E. Desjardins and Deepak Bhatnagar

Meiotic Recombination in Fungi: Mechanisms and Controls of

Crossing-Over and Gene Conversion 15
Bernard Lamb

Molecular Genetics of Circadian Rhythms in Neurospora crassa 43

Alejandro Correa, Andrew V. Greene, Zachary A. Lewis
and Deborah Bell-Pedersen

Genome Sequencing, Assembly and Gene Prediction in Fungi 65

Brendan Loftus

Fungal Transposable Elements: Inducers of Mutations

and Molecular Tools 83
Frank Kempken

Fungal Mitochondrial Genomes, Plasmids and Introns 101

Georg Hausner

Evolution of the Fungi and Mitochondrial Genomes 133

Charles E. Bullerwell, Jessica Leigh, Elias Seif, Joyce E. Longcore
and B. Franz Lang

Ribosome Biogenesis in Yeast: rRNA Processing and Quality Control 161

Ross N. Nazar

Fungal Pathogenicity Genes 187

Paul Tudzynski and Amir Sharon
Genetic Improvement of Baker's Yeasts 213
Paul V. Attfield and Philip J.L. Bell

Enzyme Production in Industrial Fungi: Molecular Genetic Strategies

for Integrated Strain Improvement 241
K.M. Helena Nevalainen and Valentino S. Jnr. Te 'o

Global Expression Profiling of the Lignin Degrading Fungus

Ceriporiopsis subvermispora for the Discovery of Novel Enzymes 261
Debbie Sue Yaver, Barbara Weber and JeffMurrell

Microarrays: Technologies and Applications 271

Leming Shi, Weiming Hu, Zhenqiang Su, Xianping Lu and Weida Tong

Fungal Germplasm and Databases 295

Kevin McCluskey

Keyword Index 311

Contributors

Paul V. Attfield Microbiogen Pty Ltd, c/- Department of Biological Sciences,

Macquarie University, Sydney, NSW 2109, Australia
([email protected])

Philip J. L. Bell Microbiogen Pty Ltd, c/- Department of Biological Sciences,

Macquarie University, Sydney, NSW 2109, Australia
([email protected])

Deborah Bell-Pedersen Program in Biological Clocks, Department of Biology,

Texas A&M University, College Station, TX 77845, USA
([email protected])

Deepak Bhatnagar U.S. Department of Agriculture, Agricultural Research Service,

Southern Regional Research Center, New Orleans,
LA 70124, USA
([email protected])

Charles E. BuUerwell Department of Biochemistry and Molecular Biology,

Dalhousie University, Halifax (Nova Scotia),
B3H 4R2 Canada

Alejandro Correa Program in Biological Clocks, Department of Biology,

Texas A&M University, College Station, TX 77845, USA
([email protected])

Anne E. Desjardins U.S. Department of Agriculture, Agricultural Research Service,

National Center for Agriculture Utilization Research, Peoria,
IL 61604, USA
([email protected])

Andrew V. Greene Program in Biological Clocks, Department of Biology,

Texas A&M University, College Station, TX 77845, USA

Georg Hausner Department of Microbiology, University of Manitoba,

Winnipeg, MB, R3T 2N2, Canada
([email protected])
Weiming Hu Chipscreen Biosciences, Ltd., Research Institute of Tsinghua
University, Suite C301, Shenzhen, Guangdong 518057, China
([email protected])

Frank Kempken Abteilung fiir Botanik mit Schwerpunkt Genetik und

Molekularbiologie, Botanisches Institut und Botanischer
Garten, Christian-Albrechts-Universitat zu Kiel,
Olshausenstrasse 40, D-24098 Kiel, Germany
([email protected])

Bernard Lamb Department of Biological Sciences, Imperial College of

Science, Technology and Medicine, London SW7 2 AZ, UK
([email protected])

B. Franz Lang Program in Evolutionary Biology, Canadian Institute for

Advanced Research; Departement de Biochimie, Universite de
Montreal, 2900 Boulevard Edouard-Montpetit, Montreal,
H3T 1J4 Canada
([email protected])

Jessica Leigh Program in Evolutionary Biology, Canadian Institute for

Advanced Research, Departement de Biochimie, Universite de
Montreal, 2900 Boulevard Edouard-Montpetit, Montreal,
H3T1J4, Canada
([email protected])

Zachary A. Lewis Program in Biological Clocks, Department of Biology,

Texas A&M University, College Station, TX 77845, USA
([email protected])

Brendan Loftus The Institute for Genomic Research (TIGR), 9712 Medical
Centre Drive, Rockville, MD 20850, USA
(bj [email protected])

Joyce E. Longcore Department of Biological Sciences, University of Maine, Orono,

ME 04469-5722, USA

Xianping Lu Chipscreen Biosciences, Ltd., Research Institute of Tsinghua

University, Suite C301, Shenzhen, Guangdong 518057, China
([email protected])

Kevin McCluskey Fungal Genetics Stock Center, Department of Microbiology,

University of Kansas Medical Center, Kansas City, KS, USA
(kmcclusk@kumc. edu)

Jeff Murrell Novozymes Biotech Inc., 1445 Drew Avenue, Davis,

CA 95616-4880, USA
Ross N. Nazar Department of Molecular Biology and Genetics,
University of Guelph, Guelph, Ontario, Canada NIG 2W1
(mnazar@uoguelph. ca)

K.M. Helena Nevalainen Department of Biological Sciences, Macquarie University,

Sydney, NSW 2109, Australia

Elias Self Departement de Biochimie, Universite de Montreal, 2900

Boulevard Edouard-Montpetit, Montreal, H3T 1J4 Canada
(Franz. Lang@Umontreal. ca)

Amir Sharon Department of Plant Sciences, Tel Aviv University, Tel Aviv
69978, Israel

Leming Shi Chipscreen Biosciences, Ltd., Research Institute of Tsinghua

University, Suite C 301, Shenzen, Guangdong 518057, China
(Imshi @ chipscreen.com)

Zhenqiang Su Chipscreen Biosciences, Ltd., Research Institute of Tsinghua

University, Suite C301, Shenzhen, Guangdong 518057, China

Valentino S. Jnr. Te'o Department of Biological Sciences, Macquarie University,

Sydney, NSW 2109, Austraha

Weida Tong National Center for Toxicological Research, Food and Drug
Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
(wtong@nctr. fda. gov)

Paul Tudzynski Institut flir Botanik, Schlossgarten 3, D-48149 Miinster,

Germany
([email protected])

Barbara Weber Novozymes Biotech Inc., 1445 Drew Avenue, Davis,

CA 95616-4880, USA

Debbie Sue Yaver Novozymes Biotech Inc., 1445 Drew Avenue, Davis,
CA 95616-4880, USA
This Page Intentionally Left Blank
Preface
Fungi have been pivotal to the development of societies. Presently they have contributed
much to the development of various industrial materials and processes, agri-food
commodities and human health products. Thus, mycology and its pursuit through modem
biotechnology have led to the practical application in broad sense to many spheres of
human enterprise.
Fungi represent the second largest species in the biological world after the insects.
They number over 1.5 milhon, of which fewer than 10% of species have been described
and only about 1% of known species have been deposited in various collections. With
these facts in mind fungi are significant contributors to the vitality of the biosphere. As
indicated in our previous volumes, fungi and their study have taught us their value in
contemporary production and post-production agriculture. It is unusual that utilization of
a small percentage of fungi could have such an enormous intellectual and practical drive
and value. We would like to inferentially suggest that knowledge of diversity of fungi
and their genome sequences could have a dramatic multiplier effect on their value in all
spheres of life and economy. While it is unlikely that in the next quarter century we will
characterize any more than a fraction of fungi, we believe it to be highly possible that we
will have the genomic sequences of many more fungi.
The field of genomics is developing at an unparalleled rate. Recent accomplishments
in the sequencing of the human genome, and that of other animals, several plants,
microorganisms and the elucidation of the relationship between biological and ecological
or environmental interactions have presented massive new information. Genomes of
fungi, as compiled in this volume of Applied Mycology and Biotechnology, contain
diverse genes and sequences. Each genome with its compliment of genes and sequences
encodes for products that determine the types and influence the quality of interactions to
bring about an organism's survival, communication and evolution. Further, the
establishment of differences in gene number, structure, conservation, homologue and
ortholog, regulatory type and network, and the huge differences in structure and function
relationships are the most significant scientific accomplishments in fungal biology.
The methodologies of genomic sequence determination have changed in strategies
available and the speed with which this is now accomplished. The commercial and
governmental incentives have generated an industry of sizable significance. The allied
fields of proteomics and computational analysis of sequences for intelligent use have had
a synergistic effect in genomics. Comprehensive genomic map development is no longer
the technological challenge of the decade earlier. Structural genomics is a field that
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CIVET scarce of

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