Overview

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.

Full Product Details

Author:   Yves Van de Peer
Publisher:   Springer-Verlag New York Inc.
Imprint:   Springer-Verlag New York Inc.
Edition:   1st ed. 2023
Volume:   2545
Weight:   1.186kg
ISBN:  

9781071625606

ISBN 10:   1071625608
Pages:   515
Publication Date:   02 February 2023
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   Manufactured on demand  
We will order this item for you from a manufactured on demand supplier.

Table of Contents

PART I Comparative genomics to study (paleo)polyploidy   1. Inference of Ancient Polyploidy from Genomic Data Hengchi Chen and Arthur Zwaenepoel   2. Navigating the CoGe Online Software Suite for Polyploidy Research Victor A. Albert and Trevor J. Krabbenhoft   3. Inference of Ancient Polyploidy Using Transcriptome Data Jia Li, Yves Van de Peer, and Zhen Li   4. POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics Gavin C. Conant   5. Applying Machine Learning to Classify the Origins of Gene Duplications Michael T.W. McKibben and Michael S. Barker     PART II Phylogenetics to study Polyploidy   6. Phasing gene copies into polyploid subgenomes using a Bayesian phylogenetic approach William A. Freyman and Carl J. Rothfels   7. Constraining Whole-Genome Duplication Events in Geological Time James W. Clark and Philip C. J. Donoghue   8. SCORPiOs, a Novel Method to Reconstruct Gene Phylogenies in the Context of a Known WGD Event Elise Parey, Hugues Roest Crollius, and Camille Berthelot   9. Inferring Chromosome Number Changes Along a Phylogeny Using chromEvol Anna Rice and Itay Mayrose   10 PURC v2.0: A Program for Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem Peter Schafran, Fay-Wei Li, and Carl J. Rothfels     PART III Analysis of Gene Expression and Regulation in Polyploids   11 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, and Simen R. Sandve   12 Beyond Transcript Concentrations: Quantifying Polyploid Expression Responses Per Biomass, Per Genome, and Per Cell with RNA-Seq Jeremy Coate   13 A Robust Methodology for Assessing Homoeolog-Specific Expression J. Lucas Boatwright     PART IV Population Genomics Approaches to study Polyploidy   14 Analyzing Autopolyploid Genetic Data Using GenoDive Patrick G. Meirmans   15 Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data Alison Dawn Scott, Jozefien D. Van de Velde, and Polina Yu. Novikova   16 Population Genomic Analysis of Diploid - Autopolyploid Species Magdalena Bohutinská, Jakub Vlček, Patrick Monnahan, and Filip Kolář   17 Inferring the Demographic History and Inheritance Mode of Tetraploid Species using ABC Camille Roux, Xavier Vekemans, and John Pannell     PART V Experimental Approaches to Study Polyploidy   18 Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas Quinten Bafort, Lucas Prost, Eylem Aydogdu, Antoine Van de Vloet, Griet Casteleyn, Yves Van de Peer, and Olivier De Clerck   19 Studying Whole-Genome Duplication Using Experimental Evolution of Spirodela polyrhiza Tian Wu, Annelore Natran, Lucas Prost, Eylem Aydogdu, Yves Van de Peer, and Quinten Bafort   20 Experimental Approaches to Generate and Isolate Human Tetraploid Cells Sara Vanessa Bernhard, Simon Gemble, Renata Basto, and Zuzana Storchova   21 Measuring Cellular Ploidy In Situ by Light Microscopy Delisa E. Clay, Benjamin M. Stormo, and Donald T. Fox   22 Using Mosaic Cell Labelling to Visualize Polyploid Cells in the Drosophila brain Shyama Nandakumar, and Laura Buttitta     PART VI Sequencing, Assembling, Editing and Engineering Polyploid Genomes   23 Sequencing and Assembly of Polyploid Genomes Yibin Wang, Jiaxin Yu, Mengwei Jiang, Wenlong Lei, Xingtan Zhang, and Haibao Tang   24 Genome Editing by CRISPR/Cas9 in Polyploids Carlos Sánchez-Gómez, David Posé, and Carmen Martín-Pizarro   25 Developing a CRISPR system in non-genetic model polyploids Shengchen Shan, Bing Yang, Bernard A. Hauser, Pamela S. Soltis, and Douglas E. Soltis   26 Efficiently Editing Multiple Duplicated Homeologs and Alleles for Recurrent Polyploids Rui-Hai Gan, Li Zhou, and Jian-Fang Gui      

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