Polyploidy

Methods and Protocols

Buch | Softcover

515 Seiten

2024 | 1st ed. 2023
Springer-Verlag New York Inc.
978-1-0716-2563-7 (ISBN)

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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.

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.

Erscheinungsdatum	07.02.2024
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	131 Illustrations, color; 8 Illustrations, black and white; XVI, 515 p. 139 illus., 131 illus. in color.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	allopolyploids • autopolyploids • collinearity analysis in plants • Endopolyploidy • whole-genome duplication
ISBN-10	1-0716-2563-2 / 1071625632
ISBN-13	978-1-0716-2563-7 / 9781071625637
Zustand	Neuware