Polyploidy : Methods and Protocols / edited by Yves Van de Peer.

Format:

Book

Contributor:

Van de Peer, Yves., Editor.

Series:

Methods in Molecular Biology, 1940-6029 ; 2545

Language:

English

Subjects (All):

Genomics.

Local Subjects:

Genomics.

Physical Description:

1 online resource (XVI, 515 p. 139 illus., 131 illus. in color.)

Edition:

1st ed. 2023.

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2023.

Summary:

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.

Contents:

Inference of Ancient Polyploidy from Genomic Data

Navigating the CoGe Online Software Suite for Polyploidy Research

Inference of Ancient Polyploidy Using Transcriptome Data

POInT: Modeling Polyploidy in the Era of Ubiquitous Genomics

Applying Machine Learning to Classify the Origins of Gene Duplications

Phasing gene copies into polyploid subgenomes using a Bayesian phylogeneticapproach

Constraining Whole-Genome Duplication Events in Geological Time

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

Inferring Chromosome Number Changes Along a Phylogeny Using chromEvol

PURC v2.0: A Program for Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem

Analyses of Genome Regulatory Evolution Following Whole-Genome Duplication Using the Phylogenetic EVE Model

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

A Robust Methodology for Assessing Homoeolog-Specific Expression

Analyzing Autopolyploid Genetic Data Using GenoDive

Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data

Population Genomic Analysis of Diploid - Autopolyploid Species

Inferring the Demographic History and Inheritance Mode of Tetraploid Species using ABC

Studying Whole-Genome Duplication Using Experimental Evolution of Chlamydomonas

Studying Whole-Genome Duplication Using Experimental Evolution of Spirodela polyrhiza

Experimental Approaches to Generate and Isolate Human Tetraploid Cells

Measuring Cellular Ploidy In Situ by Light Microscopy

Using Mosaic Cell Labelling to Visualize Polyploid Cells in the Drosophila brain

Sequencing and Assembly of Polyploid Genomes

Genome Editing by CRISPR/Cas9 in Polyploids

Developing a CRISPR system in non-genetic model polyploids

Efficiently Editing Multiple Duplicated Homeologs and Alleles for Recurrent Polyploids. .

ISBN:

9781071625613

1071625616