Dunlap Fungal Genomics

1. Auflage 2011
ISBN: 978-0-08-047495-3
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band Volume 57, 320 Seiten, Web PDF

Reihe: Advances in Genetics

The sequencing of several fungi genomes has spurred major advances in the field. Fungal genomics has been having a pivotal impact on applied research in agriculture, food sciences, natural resource management, pharmaceuticals, and biotechnology, as well as to basic studies in the life sciences. Fungal Genomics covers exciting new developments in this growth field, from genomic analysis to human fungal pathogen genomics, comparative genomics of fungi, and the genomics of fungal development. - Includes information on aspergillus genomes - Discusses sex and its role in virulence of human fungal pathogens - Covers the genomic analysis of neurospora

Autoren/Hrsg.

Dunlap, Jay C.

Inhaltsverzeichnis

1;Fungal Genomics;4
2;Copyright Page;5
3;Contents;6
4;Contributors;10
5;Preface;14
6;Chapter 1: Genetics of Morphogenesis and Pathogenic Development of Ustilago maydis;15
6.1;I. Introduction;17
6.2;II. Mating;18
6.2.1;A. The mating loci;18
6.2.2;B. The a locus: Self/nonself-recognition;18
6.2.3;C. The b locus: Self/nonself-recognition;20
6.2.4;D. Targets of bE/bW regulation;21
6.2.5;E. The response to mating: Activation of cAMP and MAPK pathways;22
6.2.6;F. Interplay between the cAMP and MAPK pathways;24
6.3;III. Dimorphism;26
6.3.1;A. Low nitrogen;27
6.3.2;B. pH;28
6.3.3;C. Additional stimuli: Air and polyamines;29
6.3.4;D. Lipids as signals;29
6.3.5;E. Chitin synthases;30
6.4;IV. Cell Cycle and Cytoskeletal Regulation;31
6.4.1;A. Cell cycle;31
6.4.2;B. Microtubules and actin;32
6.4.3;C. Molecular motors and transport;33
6.4.4;D. Differences with other fungi;34
6.4.5;E. Connecting the signaling nodes;34
6.5;V. Pathogenesis;35
6.5.1;A. Penetration and colonization;35
6.5.2;B. Gall formation and in planta teliospore production;37
6.6;VI. Genome-Wide Approaches for the Study of U. maydis;41
6.6.1;A. Genome structure;41
6.6.2;B. An expanding toolbox for the study of U. maydis;44
6.6.3;C. Differential screens;45
6.6.4;D. Adapted for pathogenicity;48
6.7;VII. The Plant Side of the Disease Equation;50
6.8;VIII. Conclusion;52
6.9;References;52
7;Chapter 2: Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project;63
7.1;I. Introduction;65
7.1.1;A. Why study fungi?;66
7.1.2;B. Why Neurospora?;66
7.1.3;C. Overview of the functional genomics effort;69
7.2;II. Project 1: Systematic Gene Knockouts;70
7.2.1;A. Creation of gene knockouts in Neurospora;72
7.2.2;B. Basic phenotypic characterization of mutants;82
7.2.3;C. Deposition of the strains in the Fungal Genetics Stock Center (FGSC) and their distribution to the scientific community at large;83
7.2.4;D. Summary of gene knockouts;84
7.3;III. Project 2: Genome Informatics and Functional Annotation Studies;85
7.3.1;A. Introduction;85
7.3.2;B. Improving automated genome annotation;85
7.3.3;C. Community annotation;87
7.3.4;D. Annotation of allele-specific phenotypes;89
7.4;IV. Project 3: Profiling Transcription in Neurospora;92
7.4.1;A. Oligonucleotide design and synthesis;92
7.4.2;B. Experimental design for microarray experiments;93
7.4.3;C. Technical aspects to transcriptional profiling: RNA extraction, cDNA labeling, image acquisition, and normalization procedures;94
7.4.4;D. Neurospora functional genomics microarray database;95
7.4.5;E. Proof-of-principle: Transcriptional profiling of conidial germination;95
7.4.6;F. Future prospects;97
7.5;V. Project 4: cDNA Libraries and the Generation of a High-Density SNP Map;99
7.5.1;A. Introduction and rationale for the design of the project;99
7.5.2;B. Construction of the map;100
7.5.3;C. Validation of the SNP map;103
7.5.4;D. Implementation of the SNP map;106
7.6;VI. Conclusions;107
7.7;Acknowledgments;107
7.8;References;107
8;Chapter 3: Genomics of the Plant Pathogenic Oomycete Phytophthora: Insights into Biology and Evolution;111
8.1;I. Introduction;112
8.2;II. Advances in Structural Genomics;114
8.2.1;A. Current datasets;114
8.2.2;B. Expressed sequence tags;115
8.2.3;C. Genome sequencing;117
8.3;III. Organization of Phytophthora Genomes;118
8.3.1;A. Genetic maps;118
8.3.2;B. Gene distribution and structure;120
8.3.3;C. Overview of gene content;122
8.3.4;D. Noncoding and repetitive DNA;125
8.3.5;E. Transposable elements;126
8.4;IV. Other Genetic Elements;128
8.5;V. Tools for Functional Genomics;129
8.5.1;A. Transformation systems for Phytophthora;129
8.5.2;B. Heterologous systems for functional genomics;131
8.6;VI. Selected Areas of Phytophthora Research;132
8.6.1;A. Plant-Phytophthora interactions;132
8.6.2;B. Developmental biology;138
8.6.3;C. Transcription mechanisms;141
8.6.4;D. Evolution;144
8.7;VII. Conclusions and Prospects;145
8.8;Acknowledgments;146
8.9;References;146
9;Chapter 4: Sex and Virulence of Human Pathogenic Fungi;157
9.1;I. The Predominant Human Pathogenic Fungi;158
9.2;II. Sex in Fungal Pathogens: Cost Versus Benefit;160
9.3;III. Mating-Type Loci Are the Sex-Determining Regions in Fungi;162
9.4;IV. Sex in Cryptococcus;163
9.5;V. The Unusual Cryptococcus Mating-Type Locus;167
9.6;VI. Genome Sequencing Identified Mating-Type Locus in the "Asexual" C. albicans and Led to the Discovery of Mating;167
9.7;VII. Mating-Type Locus in A. fumigatus;171
9.8;VIII. Mating-Type Loci in Other Human Pathogenic Fungi;171
9.9;IX. Population Genetic Studies in "Asexual" Fungi Reveal Evidence of Sex;173
9.10;X. The Role of Sex in Pathogenesis;176
9.11;XI. Concluding Remarks;179
9.12;References;180
10;Chapter 5: From Genes to Genomes: A New Paradigm for Studying Fungal Pathogenesis in Magnaporthe oryzae;189
10.1;I. Introduction;190
10.2;II. Attachment and Appressorium Morphogenesis;191
10.2.1;A. Attachment and germination;191
10.2.2;B. Surface recognition and cAMP signaling;192
10.2.3;C. Appressorium formation and maturation;196
10.2.4;D. The Pmk1 MAP kinase pathway;198
10.2.5;E. Genes expressed during appressorium formation;201
10.3;III. Mechanisms of Penetration;201
10.3.1;A. Penetration peg formation and penetration forces;201
10.3.2;B. Appressorium turgor generation;202
10.3.3;C. Appressorial penetration involves many coordinated processes;203
10.4;IV. Invasive Growth and Host-Pathogen Interactions;204
10.4.1;A. Infectious hyphal growth;204
10.4.2;B. Genes involved in race-specific interactions;205
10.4.3;C. Physiological activities of infectious hyphae;206
10.4.4;D. Genes involved in infectious growth;208
10.5;V. Genes and Genome Features;209
10.5.1;A. Genome sequence and annotation;209
10.5.2;B. Gene families and secreted proteins;210
10.5.3;C. Chromosome organization;211
10.5.4;D. Colinearity;212
10.5.5;E. Repetitive sequences;213
10.5.6;F. Receptors;214
10.5.7;G. Secondary metabolism and phytotoxic compounds;214
10.5.8;H. Repeat-induced mutation and silencing;216
10.6;VI. Functional Genomics;218
10.6.1;A. Large-scale mutagenesis;218
10.6.2;B. Genome-wide transcriptional profiling;220
10.7;VII. Concluding Remarks;222
10.8;Acknowledgments;223
10.9;References;223
11;Chapter 6: Genetic and Genomic Dissection of the Cochliobolus heterostrophus Tox1 Locus Controlling Biosynthesis of the Polyketide Virulence factor T-toxin;233
11.1;I. Introduction;234
11.1.1;A. C. heterostrophus biology;235
11.1.2;B. Cochliobolus and disease;237
11.2;II. Tools for Genetic Analysis;242
11.2.1;A. Classical genetics;242
11.2.2;B. Molecular genetics;242
11.2.3;C. Electrophoretic karyotype analysis;246
11.2.4;D. Restriction fragment length polymorphism mapping;246
11.3;III. C. heterostrophus and SCLB;247
11.3.1;A. T-toxin;247
11.3.2;B. T-cytoplasm corn and URF13 protein;247
11.3.3;C. Microbial bioassay for T-toxin production;249
11.4;IV. The Genetics of T-Toxin Production;249
11.4.1;A. The Tox1 locus;249
11.4.2;B. Identification of genes at Tox1;254
11.5;V. Genomic Analysis of the Tox1 Locus;256
11.5.1;A. cDNA profiling;256
11.5.2;B. Tox1-associated genome scaffolds;257
11.6;VI. The PM-Toxin Gene Cluster;261
11.7;VII. Are Additional Tox Loci Involved in T-Toxin Production?;263
11.8;VIII. Model for Biosynthesis of T-Toxin;264
11.9;IX. The Evolution of Polyketide-Mediated Fungal Specificity for T-Cytoplasm Corn;266
11.10;X. Conclusions;268
11.11;Acknowledgments;269
11.12;References;269
12;Chapter 7: Fungal Genomics: A Tool to Explore Central Metabolism of Aspergillus fumigatus and Its Role in Virulence;277
12.1;I. Introduction;278
12.2;II. Nutritional Auxotrophy and Fungal Genetics;279
12.3;III. Regulation of Amino Acid Biosynthesis;282
12.4;IV. Regulation of Ambient pH Response;286
12.5;V. Regulation of Nitrogen Response Pathways;289
12.6;VI. Regulation of Carbon Response Pathways;291
12.7;VII. Concluding Remarks;295
12.8;References;295
13;Index;299