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This volume details protocols covering nearly all aspects of fungal genomics. New and updated chapters guide the reader through experimental genomics, biotechnologies, and the analysis and processing of data. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Fungal Genomics : Methods and Protocols, Second Edition aims to ensure successful results in the further study of this vital field.

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1. Introduction to the Book: Overview of Fungal Genomics

Ronald 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 Bl‘sbjerg Hoof, Christina N›dvig, and Uffe H. Mortensen

12.Evolutionary Adaptation to Generate Mutants

Ronald 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. Grigoriev

16.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 Family

Letian 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

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