Essential Fungal Genetics

Preface......Page 6
Contents......Page 8
Revision Concepts......Page 14
1.1 Origins......Page 15
1.2 Diversity in the Kingdom Fungi: Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota......Page 21
1.3 Fungi in Nature......Page 27
1.4 Fungi in Technology......Page 30
1.5 Fungi as Models......Page 32
1.6 Genes to Genomics......Page 34
Publications and Websites Worth a Visit......Page 37
Historical Publications Worth Knowing About......Page 38
Revision Concepts......Page 39
2.1 Fungal Lifestyles: Hyphal Fusions Are the Key to Advanced Hyphal Systems......Page 41
2.2 Population Biology Aspects of Compatibility Systems......Page 47
2.3 Compatibility and the Individualistic Mycelium......Page 52
2.4 Nuclear Migration......Page 57
2.5 Other Incompatibility Reactions......Page 61
2.6 Structure and Function of Mating-Type Factors: Mating-Type Factors in Saccharomyces cerevisiae......Page 64
2.7 Structure and Function of Mating-Type Factors: Mating-Type Factors of Neurospora......Page 68
2.8 Structure and Function of Mating-Type Factors: Mating-Type Factors in Ustilago maydis......Page 72
2.9 Structure and Function of Mating-Type Factors: Mating-Type Factors in Coprinus cinereus and Schizophyllum commune......Page 75
2.10 Overview: Biology of Incompatibility Factors......Page 80
Publications and Websites Worth a Visit......Page 82
Historical Publications Worth Knowing About......Page 83
Revision Concepts......Page 84
3.1 Phenotypes and Genotypes: Variations and Mutations......Page 85
3.2 Molecular Nature of Mutation......Page 87
3.3 Natural Variation and Spontaneous Mutation......Page 89
3.4 Generating Mutants: Mutagenesis......Page 90
3.5 Generating Mutants: Irradiation......Page 92
3.6 Generating Mutants: Chemical Mutagens......Page 94
3.7 Types of Functional Mutant......Page 96
3.8 Isolating Auxotrophic Mutants......Page 97
3.9 Resistance Mutations......Page 102
3.10 Reverse Mutation: From Auxotroph to Prototroph......Page 103
3.11 Molecular Variants......Page 104
Publications and Websites Worth a Visit......Page 106
Historical Publications Worth Knowing About......Page 107
Revision Concepts......Page 109
4.1 Complementing Mutants......Page 110
4.2 Adenine Auxotrophs of Coprinus......Page 111
4.3 Functional Allelism......Page 117
4.4 Gene Segregation Depends on the Behavior of Chromosomes During Nuclear Division......Page 119
4.5 Meiosis......Page 120
4.6 Analyzing Gene Segregations from Random Spores......Page 122
4.7 Use of χ[sup(2)] Tables......Page 124
4.8 Testing for Homogeneity......Page 126
4.9 Detecting Linkage......Page 131
Publications and Websites Worth a Visit......Page 133
Historical Publications Worth Knowing About......Page 134
Revision Concepts......Page 135
5.1 Linkage Studies Make Maps......Page 137
5.2 Multipoint Crosses......Page 139
5.3 Rules of the Three-Point Crosses Game......Page 142
5.4 A Three-Point Cross in Coprinus......Page 143
5.5 Mapping Centromeres Using Gene Segregations in Tetrads and Eight-Spored Asci (Octads): Single Gene Segregations......Page 145
5.6 Mapping Using Multiple Gene Segregations in Tetrads and Octads......Page 148
5.7 Unordered Tetrads......Page 153
5.8 Linkage Analysis to Linkage Map......Page 158
5.9 Tetrad Segregations Leading to Secondary Homothallism......Page 159
5.10 Gene Segregation During the Mitotic Division Cycle......Page 160
5.11 Cytoplasmic Segregations: Mitochondria, Plasmids, Viruses, and Prions......Page 167
Publications and Websites Worth a Visit......Page 172
Historical Publications Worth Knowing About......Page 173
Revision Concepts......Page 174
6.1 Gene Conversion......Page 175
6.2 Hybrid- or Heteroduplex-DNA......Page 177
6.3 A Basic Mechanism for Recombination......Page 179
6.4 Correction of Base Mismatches in Heteroduplex-DNA Generates Aberrant Segregation Ratios......Page 183
6.5 Modifying the Basic Recombination Model......Page 185
6.6 Models and the Real World......Page 190
Publications and Websites Worth a Visit......Page 195
Historical Publications Worth Knowing About......Page 196
Revision Concepts......Page 197
7.1 Molecular Markers......Page 199
7.2 DNA Polymorphisms......Page 200
7.3 Restriction Fragment Length Polymorphisms......Page 201
7.4 Polymerase Chain Reaction......Page 205
7.5 PCR Primers: AP-PCR and RAPD......Page 206
7.6 Single-Strand Conformation Polymorphisms......Page 208
7.7 DNA Fingerprinting......Page 209
7.8 Microsatellites......Page 212
7.9 Minisatellites......Page 213
7.10 Transposable Elements......Page 214
7.11 Genes and Spacers......Page 217
7.12 Electrophoretic Karyotypes......Page 218
Publications and Websites Worth a Visit......Page 220
Historical Publications Worth Knowing About......Page 222
Revision Concepts......Page 224
8.1 Genes and Maps: The Story So Far......Page 225
8.2 Physical Maps......Page 228
8.3 Restriction Mapping: A Real-Life Example......Page 229
8.4 Optical Mapping......Page 236
8.5 DNA Cloning: Plasmids, Cosmids, BACs, and YACs......Page 238
8.6 Chain Termination Sequencing......Page 240
8.7 The First Complete Eukaryotic Genome Sequence: Saccharomyces cerevisiae......Page 246
8.8 Comparisons Between Genomes......Page 249
Publications and Websites Worth a Visit......Page 253
Historical Publications Worth Knowing About......Page 256
Revision Concepts......Page 258
9.1 Phylogenetics: Inferring Evolutionary Development......Page 259
9.2 The Molecule Is the Message......Page 261
9.3 Inferring Relationships......Page 264
9.4 Making Trees Make Sense......Page 269
9.5 Horizontal Transfer of Genetic Information......Page 274
9.6 Genes in Populations......Page 275
9.7 Genes in Fungal Populations......Page 279
9.8 Genetic Variation in Hosts and Pathogens......Page 283
9.9 Evolution in Captivity: Natural and Artificial Selection......Page 286
9.10 Mycotechnology......Page 288
Publications and Websites Worth a Visit......Page 292
Historical Publications Worth Knowing About......Page 294
Revision Concepts......Page 295
10.1 Differentiation and Morphogenesis......Page 297
10.2 Genetic Approaches for Analyzing Gene Regulation......Page 299
10.3 Regulating Gene Expression: DNA-Binding Proteins......Page 301
10.4 Regulating Gene Expression: Chromatin Remodeling......Page 303
10.5 Regulating Gene Expression: Transcription......Page 305
10.6 Galactose Utilization in Yeast: The Epitome of Eukaryote Regulation......Page 308
10.7 Regulating Gene Expression: Repression and Silencing......Page 311
10.8 Regulating Gene Expression: High-Level Control Mechanisms, DNA Modification, and Epigenetics......Page 313
10.9 Posttranscriptional Regulation: Spliceosomes, Proteasomes, and Protein Networks......Page 318
10.10 Shape, Form, and Differential Gene Expression......Page 323
10.11 Yeast–Mycelial Dimorphism......Page 324
10.12 Conidiation: Translational Triggering and Feedback Fixation......Page 328
10.13 Sexual Reproductive Structures in Ascomycetes and Basidiomycetes......Page 334
10.14 Genetic Control of Morphogenesis of Fungal Fruit Bodies......Page 345
Publications and Websites Worth a Visit......Page 352
Historical Publications Worth Knowing About......Page 354
A......Page 356
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D......Page 359
F......Page 360
H......Page 361
I......Page 362
M......Page 363
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P......Page 365
R......Page 367
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T......Page 369
Z......Page 370