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Polyploidy

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Yves Van de Peer

    1. Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

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  • 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 2545)

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xvi
    Download chapter PDF

  2. Comparative Genomics to Study (Paleo-)Polyploidy

    1. Front Matter

      Pages 1-1
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    2. Inference of Ancient Polyploidy from Genomic Data

      • Hengchi Chen, Arthur Zwaenepoel
      Pages 3-18

    3. Navigating the CoGe Online Software Suite for Polyploidy Research

      • Victor A. Albert, Trevor J. Krabbenhoft
      Pages 19-45

    4. Inference of Ancient Polyploidy Using Transcriptome Data

      • Jia Li, Yves Van de Peer, Zhen Li
      Pages 47-76

    5. POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics

      • Gavin C. Conant
      Pages 77-90

    6. Applying Machine Learning to Classify the Origins of Gene Duplications

      • Michael T. W. McKibben, Michael S. Barker
      Pages 91-119

  3. Phylogenetics to Study Polyploidy

    1. Front Matter

      Pages 121-121
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    2. Phasing Gene Copies into Polyploid Subgenomes Using a Bayesian Phylogenetic Approach

      • William A. Freyman, Carl J. Rothfels
      Pages 123-138

    3. Constraining Whole-Genome Duplication Events in Geological Time

      • James W. Clark, Philip C. J. Donoghue
      Pages 139-154

    4. SCORPiOs, a Novel Method to Reconstruct Gene Phylogenies in the Context of a Known WGD Event

      • Elise Parey, Hugues Roest Crollius, Camille Berthelot
      Pages 155-173

    5. Inferring Chromosome Number Changes Along a Phylogeny Using chromEvol

      • Anna Rice, Itay Mayrose
      Pages 175-187

    6. PURC Provides Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem

      • Peter Schafran, Fay-Wei Li, Carl J. Rothfels
      Pages 189-206

  4. Analysis of Gene Expression and Regulation in Polyploids

    1. Front Matter

      Pages 207-207
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    2. Analyses of Genome Regulatory Evolution Following Whole-Genome Duplication Using the Phylogenetic EVE Model

      • Ksenia Arzumanova, Rori V. Rohlfs, Lars Grønvold, Marius A. Strand, Torgeir R. Hvidsten, Simen R. Sandve
      Pages 209-225

    3. Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses per Biomass, per Genome, and per Cell with RNA-Seq

      • Jeremy E. Coate
      Pages 227-250

    4. A Robust Methodology for Assessing Homoeolog-Specific Expression

      • J. Lucas Boatwright
      Pages 251-258

  5. Population Genomics Approaches to Study Polyploidy

    1. Front Matter

      Pages 259-259
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    2. Analyzing Autopolyploid Genetic Data Using GenoDive

      • Patrick G. Meirmans
      Pages 261-277

    3. Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data

      • Alison Dawn Scott, Jozefien D. Van de Velde, Polina Yu Novikova
      Pages 279-295
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Keywords

About this book

This volume provides protocols on evidence for polyploidy and how it can be unveiled. Chapters guide readers through evolutionary experiments, measure effects of polyploidy, evidence for (remnants of) ancient WGDs, models of chromosome number evolution, population genomics approaches to study polyploidy, analysing genetic data from polyploid populations, Phylogenetic and phylogenomic methods, gene expression, gene regulation, unicellular alga (Chlamydomonas),  and a fast-growing duckweed (Spirodela). Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

 

Authoritative and cutting-edge, Polyploidy: Method and Protocols aims to be of interest to experimental and computational (evolutionary) biologists, molecular biologists, and biotechnologists.

Editors and Affiliations

  • Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium

    Yves Van de Peer

Bibliographic Information

  • Book Title: Polyploidy

  • Book Subtitle: Methods and Protocols

  • Editors: Yves Van de Peer

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2561-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2560-6Published: 02 February 2023

  • Softcover ISBN: 978-1-0716-2563-7Published: 02 February 2024

  • eBook ISBN: 978-1-0716-2561-3Published: 01 February 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 515

  • Number of Illustrations: 8 b/w illustrations, 131 illustrations in colour

  • Topics: Genetics and Genomics

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