1. Introduction to the Book: Overview of Fungal GenomicsRonald P. de Vries, Igor V. Grigoriev,and Adrian Tsang Part I: Technical Aspects of Genomics 2.Fungal Genomic DNA Extraction Methods for Rapid Genotyping and Genome Sequencing Annie Bellemare, Tricia John, and Sandrine Marqueteau 3.Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples Laure Fauchery, Stéphane Uroz, Marc Buée, and Annegret Kohler 4.Genome Sequencing Yuko Yoshinaga, Christopher Daum, Guifen He, and Ronan O'Malley 5.Methods for Genomic Characterization and Maintenance of Anaerobic Fungi Xuefeng Peng, Candice L. Swift, Michael K. Theodorou, and Michelle A. O'Malley 6.Efficient Extraction Method for High Quality Fungal RNA from Complex Lignocellulosic Substrates Miia R. Mäkelä and Kristiina Hildén 7.Isolation of high quality RNA for Metatranscriptome Analysis of Lignocellulose Digestion in the Rumen Gruninger R.J., Forster, R. J., and McAllister T.A. 8.Fungal Transcriptomics Vasanth R. Singan, Rita C. Kuo, and Cindy Chen 9.Mass Spectrometrybased Proteomics Marcos Rafael Di Falco 10.Mass Spectrometry Based Metabolomics Young-Mo Kim and Heino M Heyman 11.Genome Editing - CRISPR/cas9 Jakob Blæsbjerg Hoof, Christina Nødvig, and Uffe H. Mortensen 12.Evolutionary Adaptation to Generate MutantsRonald P. de Vries, Ronnie Lubbers, Aleksandrina Patyshakuliyeva, Ad Wiebenga, and Isabelle Benoit-Gelber Part II: Data Processing and Analysis 13. Genome Assembly Alicia Clum 14. Fungal Epigenomics: Detection and Analysis Stephen J. Mondo, Rita C. Kuo, and Vasanth R. Singan 15.Fungal Genome Annotation Sajeet Haridas, Asaf Salamov, and Igor V. Grigoriev16.Manual Gene Curation and Functional Annotation Erin McDonnell, Kimchi Strasser, and Adrian Tsang 17.Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes Ian Reid 18.Genomic Sequence Variation Analysis by Resequencing Joel Martin, Wendy Schackwitz, and Anna Lipzen 19.ChIP-seq Analysis in Neurospora crassa Aileen R. Ferraro and Zachary A. Lewis 20.Fungal Phylogenomics Robert Riley and Laszlo Nagy 21.Phylogenetic Analysis of Protein FamilyLetian Song, Sherry Wu, and Adrian Tsang 22.Parasexual Crossings for Bulk Segregant Analysis in Aspergillus Niger To Facilitate Mutant Identification Via Whole Genome Sequencing Mark Arentshorst and Arthur F.J. Ram... Mehr