Polyploidy: Methods and Protocols

ISBN-13: 9781071625606 / Angielski / Twarda / 2023 / 515 str.

Yves Van de Peer

Opis

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.

Spis treści

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