Description
Having experienced unprecedented growth since the turn of the millennium, the dramatic expansion of resources and techniques in fungal genomics is poised to fundamentally redefine the study of fungal biology. In Fungal Genomics: Methods and Protocols, expert researchers explore the three most likely fronts upon which the field will advance: the sequencing of more and more fungal genomes, the mining of sequenced genomes for useful information, and most importantly, the use of genomics sequences to provide a foundation for powerful techniques to explain biological processes. Much of the book is dedicated to explaining established and emerging genomics-based technologies in filamentous fungi, including gene expression profiling techniques, techniques for fungal proteomics as well as various case studies that could be adapted to a wide range of fungi. Written in the highly successful Methods in Molecular Biology(TM) series format, protocol chapters include brief introductions to their respective topics, lists of the necessary materials and reagents, step-by-step laboratory protocols, and key unpublished tips, potential pitfalls, common mistakes, and special considerations based on the unique experiences of the contributors. Authoritative and cutting-edge, Fungal Genomics: Methods and Protocols provides fungal biologists at any stage of their careers a user-friendly resource for fungal genomics, especially as readers branch out into unfamiliar but exciting new areas of study. 1. Genome Sequencing and Assembly Manfred G. Grabherr, Evan Mauceli, and Li-Jun Ma 2. Targeted Cloning of Fungal Telomeres Mark L. Farman 3. Identification and Annotation of Repetitive Sequences in Fungal Genomes Braham Dhillon and Stephen B. Goodwin 4. Next-Generation Sequencing and Potential Applications in Fungal Genomics Phillip SanMiguel 5. Getting the Most Out of Your Fungal Microarray Data: Two Cost and Time-Effective Methods Sandra M. Mathioni, Andr Bel, Jeffrey P. Townsend, and Nicole M. Donofrio 6. Fusarium graminearum from Expression Analysis to Functional Assays Heather E. Hallen-Adams, Brad L. Cavinder, and Frances Trail 7. EST Analysis Pipeline: Use of Distributed Computing Resources Francisco Javier Gonzlez and Juan Antonio Vizcano 8. The Application of ChIP-chip Analysis in the Rice Blast Pathogen Soonok Kim and Thomas Mitchell 9. Proteome Studies of Filamentous Fungi Scott E. Baker and Ellen A. Panisko 10. A Bioinformatics Pipeline for Sequence-Based Analyses of Fungal Biodiversity D. Lee Taylor and Shawn Huston 11. Identifying Protein Complexes by Affinity Purification and Mass Spectrometry Analysis in the Rice Blast Fungus Wende Liu, Anton Iliuk, Andy Tao, and Shengli Ding 12. Large Scale Identification of Genes Involved in Plant-Fungal Interactions Using Illumina’s Sequencing-By-Synthesis Technology R. C. Venu, Yuan Zhang, Brian Weaver, Peter Carswell, Thomas K. Mitchell, Blake C. Meyers, Michael J. Boehm, and Guo-Liang Wang 13. High-Throughput Production of Gene Replacement Mutants in Neurospora crassa Gyungsoon Park, Hildur V. Colot, Patrick D. Collopy, Svetlana Krystofova, Christopher Crew, Carol Ringelberg, Liubov Litvinkova, Lorena Altamirano, Liande Li, Susan Curilla, Wei Wang, Norma Gorrochotegui-Escalante, Jay C. Dunlap, and Katherine A. Borkovich 14. Phenotypic Analysis of Neurospora crassa Gene Deletion Strains Gloria E. Turner 15. Efficient Approaches for Generating GFP Fusion and Epitope-Tagging Constructs in Filamentous Fungi Xiaoying Zhou, Guotian Li, and Jin-Rong Xu 16. Large Scale Insertional Mutagenesis in Magnaporthe oryzae by Agrobacterium tumefaciens-Mediated Transformation Xiao-Lin Chen, Jun Yang, and You-Liang Peng 17. Molecular Methods for Studying the Cryphonectria parasitica – Hypovirus Experimental System Angus L. Dawe, Rong Mu, Gloricelys Rivera, and Joanna A. Salamon 18. Metabolic Fingerprinting in Fusarium verticillioides to Determine Gene Function Jonathon E. Smith and Burton H. Bluhm 19. Tapping Genomics to Unravel Ectomycorrhizal Symbiosis Jonathan M. Plett, Barbara Montanini, Annegret Kohler, Simone Ottonello, and Francis Martin
