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Fungal Genomics

Methods and Protocols

  • Book
  • © 2018

Overview

Editors:
  1. Ronald P. de Vries

    1. Fungal Physiology, Westerdijk Fungal, Biodiversity Institute, Utrecht, The Netherlands

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    You can also search for this editor in PubMed   Google Scholar

  2. Adrian Tsang

    1. Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada

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    You can also search for this editor in PubMed   Google Scholar

  3. Igor V. Grigoriev

    1. US Department of Energy, Joint Genome Institute, Walnut Creek, USA

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1775)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Introduction: Overview of Fungal Genomics

    • Ronald P. de Vries, Igor V. Grigoriev, Adrian Tsang
    Pages 1-7

  3. Technical Aspects of Genomics

    1. Front Matter

      Pages 9-9
      Download chapter PDF

    2. Fungal Genomic DNA Extraction Methods for Rapid Genotyping and Genome Sequencing

      • Annie Bellemare, Tricia John, Sandrine Marqueteau
      Pages 11-20

    3. Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples

      • Laure Fauchery, Stéphane Uroz, Marc Buée, Annegret Kohler
      Pages 21-35

    4. Genome Sequencing

      • Yuko Yoshinaga, Christopher Daum, Guifen He, Ronan O’Malley
      Pages 37-52

    5. Methods for Genomic Characterization and Maintenance of Anaerobic Fungi

      • Xuefeng Peng, Candice L. Swift, Michael K. Theodorou, Michelle A. O’Malley
      Pages 53-67

    6. Efficient Extraction Method for High Quality Fungal RNA from Complex Lignocellulosic Substrates

      • Miia R. Mäkelä, Kristiina Hildén
      Pages 69-73

    7. Isolation of High Quality RNA for Metatranscriptomic Analysis of Lignocellulose Digestion in the Rumen

      • R. J. Gruninger, R. J. Forster, T. A. McAllister
      Pages 75-82

    8. Fungal Transcriptomics

      • Vasanth R. Singan, Rita C. Kuo, Cindy Chen
      Pages 83-92

    9. Mass Spectrometry-Based Proteomics

      • Marcos Rafael Di Falco
      Pages 93-106

    10. Mass Spectrometry-Based Metabolomics

      • Young-Mo Kim, Heino M. Heyman
      Pages 107-118

    11. Genome Editing: CRISPR-Cas9

      • Jakob B. Hoof, Christina S. Nødvig, Uffe H. Mortensen
      Pages 119-132

    12. Evolutionary Adaptation to Generate Mutants

      • Ronald P. de Vries, Ronnie Lubbers, Aleksandrina Patyshakuliyeva, Ad Wiebenga, Isabelle Benoit-Gelber
      Pages 133-137

  4. Data Processing and Analysis

    1. Front Matter

      Pages 139-139
      Download chapter PDF

    2. Genome Assembly

      • Alicia Clum
      Pages 141-153

    3. Fungal Epigenomics: Detection and Analysis

      • Stephen J. Mondo, Rita C. Kuo, Vasanth R. Singan
      Pages 155-170

    4. Fungal Genome Annotation

      • Sajeet Haridas, Asaf Salamov, Igor V. Grigoriev
      Pages 171-184

    5. Manual Gene Curation and Functional Annotation

      • Erin McDonnell, Kimchi Strasser, Adrian Tsang
      Pages 185-208

    6. Evaluating Programs for Predicting Genes and Transcripts with RNA-Seq Support in Fungal Genomes

      • Ian Reid
      Pages 209-227
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Keywords

About this book

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.

Editors and Affiliations

  • Fungal Physiology, Westerdijk Fungal, Biodiversity Institute, Utrecht, The Netherlands

    Ronald P. de Vries

  • Centre for Structural and Functional Genomics, Concordia University, Montreal, Canada

    Adrian Tsang

  • US Department of Energy, Joint Genome Institute, Walnut Creek, USA

    Igor V. Grigoriev

Bibliographic Information

  • Book Title: Fungal Genomics

  • Book Subtitle: Methods and Protocols

  • Editors: Ronald P. de Vries, Adrian Tsang, Igor V. Grigoriev

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-7804-5

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2018

  • Hardcover ISBN: 978-1-4939-7803-8Published: 07 June 2018

  • Softcover ISBN: 978-1-4939-9290-4Published: 25 July 2019

  • eBook ISBN: 978-1-4939-7804-5Published: 06 June 2018

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XI, 291

  • Number of Illustrations: 9 b/w illustrations, 48 illustrations in colour

  • Topics: Microbiology

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