Overview

This detailed book presents recent methodologies for the task of inspecting the genomic world of plants, extracting valuable information, and presenting it in a readable way. With a focus on bioinformatics tools, the volume explores phylogenetics and evolution, Omics analysis, as well as experimental procedures for trait characterization. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of vital expert implementation advice that will lead to successful results.  Authoritative and practical, Plant Comparative Genomics serves as an ideal resource for researchers looking to implement comparative tools in order to explore their genomic data for their daily scientific work.

Full Product Details

Author:   Alejandro Pereira-Santana ,  Samuel David Gamboa-Tuz ,  Luis Carlos Rodríguez-Zapata
Publisher:   Springer-Verlag New York Inc.
Imprint:   Springer-Verlag New York Inc.
Edition:   1st ed. 2022
Volume:   2512
Weight:   0.780kg
ISBN:  

9781071624289

ISBN 10:   1071624288
Pages:   294
Publication Date:   13 July 2022
Audience:   Professional and scholarly ,  Professional & Vocational
Format:   Hardback
Publisher's Status:   Active
Availability:   Manufactured on demand  
We will order this item for you from a manufactured on demand supplier.

Table of Contents

Part I: Phylogenetics and Evolution   1. Orthology Prediction and Phylogenetic Analysis Methods in Plants             Abdoallah Sharaf and Sawsan Elateek   2. Species Tree Inference with SNP Data             Michael Matschiner   3. High-Throughput Evolutionary Comparative Analysis of Long Intergenic Non-Coding RNAs in Multiple Organisms             Anna C. Nelson Dittrich and Andrew D.L. Nelson   4. NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data             Julien Boutte, Mark Fishbein, and Shannon C.K. Straub   5. An SGSGeneloss-Based Method for Constructing a Gene Presence/Absence Table Using Mosdepth             Cassandria G. Tay Fernandez, Jacob I. Marsh, Benjamin J. Nestor, Mitchell Gill, Agnieszka A. Golicz, Philipp E. Bayer, and David Edwards   6. POInT: A Tool for Modeling Ancient Polyploidies Using Multiple Polyploid Genomes             Yue Hao and Gavin C. Conant   Part II: Omics Analysis   7. Searching for Homologous Genes Using Daisychain             Philipp E. Bayer and David Edwards   8. Detecting MicroRNAs in Plant Genomes with miRkwood             Sylvain Legrand, Isabelle Guigon, and Hélène Touzet   9. Pangenome Analysis of Plant Transcripts and Coding Sequences             Bruno Contreras-Moreira, Alvaro Rodriguez del Río, Carlos P. Cantalapiedra, Rubén Sancho, and Pablo Vinuesa   10. Metagenomics Bioinformatic Pipeline             Diego Garfias-Gallegos, Claudia Zirión-Martínez, Edder D. Bustos-Díaz, Tania Vanessa Arellano-Fernandez, José Abel Lovaco-Flores, Aarón Espinosa-Jaime, J. Abraham Avelar-Rivas, and Nelly Sélem-Mójica   11. Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach             Victoria Mesa   12. Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants             Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Tao Zhao, and M. Eric Schranz   13. Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis             Francisco J. Pérez-de los Santos, Jesús Emiliano Sotelo-Fonseca, América Ramírez-Colmenero, Hans-Wilhelm Nützmann, Selene L. Fernandez-Valverde, and Katarzyna Oktaba   14. Isolation of Boechera stricta Developing Embryos for Hi-C             Mariana Tiscareño-Andrade, Katarzyna Oktaba, and Jean-Philippe Vielle-Calzada   Part III: Experimental Procedures for Trait Characterization   15. Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens             Oscar Estrada, Stephen M. Richards, and James Breen   16. Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-Aromatic Rice Germplasms             Debarati Chakraborty   17. Efficient Protein Extraction Protocols for NanoLC-MS/MS Proteomics Analysis of Plant Tissues with High Proteolytic Activity: A Case Study with Pineapple Pulp             Esaú Bojórquez-Velázquez, José M. Elizalde-Contreras, Jesús Alejandro Zamora-Briseño, and Eliel Ruiz-May

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