CiNii Books - Plant cytogenetics and cytogenomics : methods and protocols

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.

Table of Contents

Part I: Introduction 1. Plant Cytogenetics: From Chromosomes to Cytogenomics Trude Schwarzacher, Qing Liu, and J.S. (Pat) Heslop-Harrison Part II: Sizing the Nucleus: Methods for Genome Size and Ploidy Level Estimation 2. The Use of Flow Cytometry for Estimating Genome Sizes and DNA Ploidy Levels in Plants Joao Loureiro, Martin Certner, Magdalena Lucanova, Elwira Sliwinska, Filip Kolar, Jaroslav Dolezel, Sonia Garcia, Silvia Castro, and David W. Galbraith 3. Nuclear DNA Content Estimation of Seaweed by Fluorimetry Analysis Rafael P. Martin-Martin, Noemi Salvador-Soler, Jordi Rull Lluch, and Amelia Gomez Garreta 4. K-Mer-Based Genome Size Estimation in Theory and Practice Uljana Hesse 5. A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens Juan Viruel, Oriane Hidalgo, Lisa Pokorny, Felix Forest, Barbara Gravendeel, Paul Wilkin, and Ilia J. Leitch Part III: Getting to the Chromosomes: Methods for Chromosome Fixation, Preparation, and Manipulation 6. Nitrous Oxide-Induced Metaphase Arrest: A Technique for Somatic Chromosome Analysis Patrice S. Albert and James A. Birchler 7. Preparation of Mitotic Chromosomes with the Squash Technique Alexis J. Maravilla, Marcela Rosato, and Josep A. Rossello 8. Preparation of Mitotic Chromosomes with the Dropping Technique Nicola Schmidt, Beatrice Weber, Jessica Klekar, Susan Liedtke, Sarah Breitenbach, and Tony Heitkam 9. Laser Capture Microdissection: From Genomes to Chromosomes, from Complex Tissue to Single-Cell Analysis Tomas Janicek, Roman Hobza, and Vojtech Hudzieczek 10. Flow Cytometric Analysis and Sorting of Plant Chromosomes Petr Capal, Mahmoud Said, Istvan Molnar, and Jaroslav Dolezel Part IV: Putting on Color: Banding and Staining Techniques 11. C-Banding of Plant Chromosomes Adam J. Lukaszewski 12. CMA/DAPI Banding of Plant Chromosomes Ana Emilia Barros e Silva and Marcelo Guerra 13. Silver Nitrate Staining of Nucleolar Organizer Regions (Ag-NORs) in Plant Chromosomes Claudio Palma-Rojas, Pedro Jara-Seguel, and Cristian Araya-Jaime 14. Chromatin Immunostaining of Plant Nuclei Nobuko Ohmido and Aqwin Polosoro Part V: Labeling DNA: In Situ Hybridization and Other Methods Using Fluorescent Labels 15. Critical Steps in DAPI and FISH Imaging of Chromosome Spread Preparations Hans de Jong, Jose van de Belt, and Paul Fransz 16. Formamide-Free Genomic In Situ Hybridization (ff-GISH) Hanna Weiss-Schneeweiss and Tae-Soo Jang 17. The Use of Ribosomal DNA for Comparative Cytogenetics Gulru Yucel, Magdalena Senderowicz, and Bozena Kolano 18. Identification of the Sequence and the Length of Telomere DNA Martin Lycka, Petr Fajkus, Leon P. Jenner, Eva Sykorova, Miloslava Fojtova, and Vratislav Peska 19. Chromosome Painting Using Chromosome-Specific BAC Clones Terezie M. Mandakova and Martin A. Lysak 20. CRISPR-FISH: A CRISPR/Cas9-Based In Situ Labeling Method Bhanu Prakash Potlapalli, Takayoshi Ishii, Kiyotaka Nagaki, Saravanakumar Somasundaram, and Andreas Houben 21. Preparation of Male Meiotic Chromosomes for Fluorescence In Situ Hybridization and Immunodetection with Major Focus on Dogroses Jana Lunerova and Radka Vozarova 22. Extended DNA Fibers for High-Resolution Mapping Paul Fransz, Jose van de Belt, and Hans de Jong 23. Visualizing Chromosome Territories and Nuclear Architecture of Large Plant Genomes Using Alien Introgressions Katerina Pernickova and David Kopecky 24. Visualization of the Nucleolus Using 5Ethynyl Uridine Martina Dvorackova and Jiri Fajkus Part VI: Leveraging Data onto Nuclei: Genomics-Informed Methods 25. Bioinformatics Prediction of Bulked Oligonucleotide Probes for FISH Using Chorus2 Guanqing Liu and Tao Zhang 26. Visualization of Oligonucleotide-Based Probes along Pseudochromosomes Using RIdeogram, KaryoploteR, and Circlize (Circos) Ludwig Mann and Sophie Maiwald 27. Bulked Oligo-FISH for Chromosome Painting and Chromosome Barcoding Denisa Berankova and Eva Hribova 28. Flow Sorting-Assisted Optical Mapping Hana Simkova, Zuzana Tulpova, and Petr Capal 29. Chromosome Conformation Capture of Mitotic Chromosomes Petr Capal 30. Analysis of 5S rDNA Genomic Organization through the RepeatExplorer2 Pipeline: A Simplified Protocol Sonia Garcia, Joan Pere Pascual-Diaz, Alice Krumpolcova, and Ales Kovarik Part VII: Software and Online Plant Cytogenetics & Genomics Resources 31. Tools for Drawing Informative Idiograms Shoaeib Mahmoudi and Ghader Mirzaghaderi 32. Using ChromEvol to Determine the Mode of Chromosomal Evolution Marcial Escudero, Enrique Maguilla, Jose Ignacio Marquez-Corro, Santiago Martin-Bravo, Itay Mayrose, Anat Shafir, Lu Tan, Carrie Tribble, and Rosana Zenil-Ferguson 33. Online Resources Useful for Plant Cytogenetics and Cytogenomics Research Maria Luisa Gutierrez, Roi Rodriguez-Gonzalez, Joan Pere Pascual-Diaz, Ines Fuentes, and Sonia Garcia

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Plant cytogenetics and cytogenomics : methods and protocols

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