Contributors ................................................ ix
Preface ................................................... xiii
1 Genetics of Morphogenesis and Pathogenic Development of
Ustilago maydis .............................................. 1
Steven J. Klosterman, Michael H. Perlin, Maria
Garcia-Pedrajas, Sarah F. Covert, and Scott E. Gold
I Introduction ............................................ 3
II Mating .................................................. 4
III Dimorphism ............................................. 12
IV Cell Cycle and Cytoskeletal Regulation ................. 17
V Pathogenesis ........................................... 21
VI Genome-Wide Approaches for the Study of U. maydis ...... 27
VII The Plant Side of the Disease Equation ................. 36
VIII Conclusion ............................................. 38
References .................................................. 38
2 Enabling a Community to Dissect an Organism: Overview of
the Neurospora Functional Genomics Project .................. 49
Jay C. Dunlap, Katherine A. Borkovich, Matthew R. Henn,
Gloria E. Turner, Matthew S. Sachs, N. Louise Glass,
Kevin McCluskey, Michael Plamann, James E. Galagan,
Bruce W. Birren, Richard L. Weiss, Jeffrey P. Townsend,
Jennifer J. Loros, Mary Anne Nelson, Randy Lambreghts,
Hildur V. Colot, Gyungsoon Park, Patrick Collopy, Carol
Ringelberg, Christopher Crew, Liubov Litvinkova, Dave
DeCaprio, Heather M. Hood, Susan Curilla, Mi Shi, Matthew
Crawford, Michael Koerhsen, Phil Montgomery, Lisa Larson,
Matthew Pearson, Takao Kasuga, Chaoguang Tian, Meray
Bafturkmen, Lorena Altamirano, and Junhuan Xu
I Introduction ........................................... 51
II Project 1: Systematic Gene Knockouts ................... 56
III Project 2: Genome Informatics and Functional
Annotation Studies ..................................... 71
IV Project 3: Profiling Transcription in Neurospora ....... 78
V Project 4: cDNA Libraries and the Generation of a
High-Density SNP Map ................................... 85
VI Conclusions ............................................ 93
References .................................................. 93
3 Genomics of the Plant Pathogenic Oomycete Phytophthora:
Insights into Biology and Evolution ......................... 97
Howard S. Judelson
I Introduction ........................................... 98
II Advances in Structural Genomics ....................... 100
III Organization of Phytophthora Genomes .................. 104
IV Other Genetic Elements ................................ 114
V Tools for Functional Genomics ......................... 115
VI Selected Areas of Phytophthora Research ............... 118
VII Conclusions and Prospects ............................. 131
References ................................................. 132
4 Sex and Virulence of Human Pathogenic Fungi ................ 143
Kirsten Nielsen and Joseph Heitman
I The Predominant Human Pathogenic Fungi ................ 144
II Sex in Fungal Pathogens: Cost Versus Benefit .......... 146
III Mating-Type Loci Are the Sex-Determining Regions in
Fungi ................................................. 148
IV Sex in Cryptococcus ................................... 149
V The Unusual Cryptococcus Mating-Type Locus ............ 153
VI Genome Sequencing Identified Mating-Type Locus
in the "Asexual" C. albicans and Led to the
Discovery of Mating ................................... 153
VII Mating-Type Locus in A. fumigatus ..................... 157
VIII Mating-Type Loci in Other Human Pathogenic Fungi ...... 157
IX Population Genetic Studies in "Asexual" Fungi Reveal
Evidence of Sex ....................................... 159
X The Role of Sex in Pathogenesis ....................... 162
XI Concluding Remarks .................................... 165
References ................................................. 166
5 From Genes to Genomes: A New Paradigm for Studying Fungal
Pathogenesis in Magnaporthe oryzae ......................... 175
Jin-Rong Xu, Xinhua Zhao, and Ralph A. Dean
I Introduction .......................................... 176
II Attachment and Appressorium Morphogenesis ............. 177
III Mechanisms of Penetration ............................. 187
IV Invasive Growth and Host-Pathogen Interactions ........ 190
V Genes and Genome Features ............................. 195
VI Functional Genomics ................................... 204
VII Concluding Remarks .................................... 208
References ................................................. 209
6 Genetic and Genomic Dissection of the Cochliobolus
heterostrophus Tox1 Locus Controlling Biosynthesis of
the Polyketide Virulence Factor T-toxin .................... 219
B. Gillian Turgeon and Scott E. Baker
I Introduction .......................................... 220
II Tools for Genetic Analysis ............................ 228
III C. heterostrophus and SCLB ............................ 233
IV The Genetics of T-Toxin Production .................... 235
V Genomic Analysis of the Tox1 Locus .................... 242
VI The PM-Toxin Gene Cluster ............................. 247
VII Are Additional Tox Loci Involved in T-Toxin
Production? ........................................... 249
VIII Model for Biosynthesis of T-Toxin ..................... 250
IX The Evolution of Polyketide-Mediated Fungal
Specificity for T-Cytoplasm Corn ...................... 252
X Conclusions ........................................... 254
References ................................................. 255
7 Fungal Genomics: A Tool to Explore Central Metabolism of
Aspergillus fumigatus and Its Role in Virulence ............ 263
Taylor Schoberle and Gregory S. May
I Introduction .......................................... 264
II Nutritional Auxotrophy and Fungal Genetics ............ 265
III Regulation of Amino Acid Biosynthesis ................. 268
IV Regulation of Ambient pH Response ..................... 272
V Regulation of Nitrogen Response Pathways .............. 275
VI Regulation of Carbon Response Pathways ................ 277
VII Concluding Remarks .................................... 281
References ................................................. 281
Index ...................................................... 285
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