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Full Description
This book provides an up-to-date account of the most widespread methods used by specialists in the field of plant cytogenetics and the emerging field of cytogenomics that will likely soon be adapted by more labs. From the classical basic karyological approaches to the most recent genomics-informed and computational methods, the volume explores genome size and ploidy level estimation, chromosome fixation, preparation, and manipulation, banding and staining techniques, in situ hybridization, as well as numerous methods that integrate cytogenetics with bioinformatics and computational genomics. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step and readily reproducible laboratory protocols, as well as tips on troubleshooting and avoiding known pitfalls.
Authoritative and practical, Plant Cytogenetics and Cytogenomics: Methods and Protocols serves as an ideal resource for plant scientists interested in molecular and evolutionary biology, breeding, systematics, and plant -omics in general.
Contents
Plant Cytogenetics: From Chromosomes to Cytogenomics.- The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants.- Nuclear DNA Content Estimation of Seaweed by Fluorimetry Analysis.- K-Mer-Based Genome Size Estimation in Theory and Practice.- A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens.- Nitrous Oxide-Induced Metaphase Arrest: A Technique for Somatic Chromosome Analysis.- Preparation of Mitotic Chromosomes with the Squash Technique.- Preparation of Mitotic Chromosomes with the Dropping Technique.- Laser Capture Microdissection: From Genomes to Chromosomes, from Complex Tissue to Single-Cell Analysis.- Flow Cytometric Analysis and Sorting of Plant Chromosomes.- C-Banding of Plant Chromosomes.- CMA/DAPI Banding of Plant Chromosomes.- Silver Nitrate Staining of Nucleolar Organizer Regions (Ag-NORs) in Plant Chromosomes.- Chromatin Immunostaining of Plant Nuclei.- Critical Steps in DAPI and FISH Imaging of Chromosome Spread Preparations.- Formamide-Free Genomic In Situ Hybridization (ff-GISH).- The Use of Ribosomal DNA for Comparative Cytogenetics.- Identification of the Sequence and the Length of Telomere DNA.- Chromosome Painting Using Chromosome-Specific BAC Clones.- CRISPR-FISH: A CRISPR/Cas9-Based In Situ Labeling Method.- Preparation of Male Meiotic Chromosomes for Fluorescence In Situ Hybridization and Immunodetection with Major Focus on Dogroses.- Extended DNA Fibers for High-Resolution Mapping.- Visualizing Chromosome Territories and Nuclear Architecture of Large Plant Genomes Using Alien Introgressions.- Visualization of the Nucleolus Using 5'Ethynyl Uridine.- Bioinformatics Prediction of Bulked Oligonucleotide Probes for FISH Using Chorus2.- Visualization of Oligonucleotide-Based Probes along Pseudochromosomes Using RIdeogram, KaryoploteR, and Circlize (Circos).- Bulked Oligo-FISH for Chromosome Painting and Chromosome Barcoding.- Flow Sorting-Assisted Optical Mapping.- Chromosome Conformation Capture of Mitotic Chromosomes.- Analysis of 5S rDNA Genomic Organization through the RepeatExplorer2 Pipeline: A Simplified Protocol.- Tools for Drawing Informative Idiograms.- Using ChromEvol to Determine the Mode of Chromosomal Evolution.- Online Resources Useful for Plant Cytogenetics and Cytogenomics Research.
