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Plant Comparative Genomics

  • Book
  • © 2022

Overview

Editors:
  1. Alejandro Pereira-Santana

    1. Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Mexico

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  2. Samuel David Gamboa-Tuz

    1. Unidad de Biotecnología, Centro de Investigación CientÚfica de Yucatán, Mérida, Mexico

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  3. Luis Carlos Rodríguez-Zapata

    1. Unidad de Biotecnología., Centro de Investigación Científica de Yucatán, Mérida, Mexico

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  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2512)

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xi
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  2. Phylogenetics and Evolution

    1. Front Matter

      Pages 1-1
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    2. Orthology Prediction and Phylogenetic Analysis Methods in Plants

      • Abdoallah Sharaf, Sawsan Elateek
      Pages 3-22

    3. Species Tree Inference with SNP Data

      • Michael Matschiner
      Pages 23-44

    4. High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms

      • Anna C. Nelson Dittrich, Andrew D. L. Nelson
      Pages 45-60

    5. NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data

      • Julien Boutte, Mark Fishbein, Shannon C. K. Straub
      Pages 61-72

    6. 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 et al.
      Pages 73-80

    7. POInT: A Tool for Modeling Ancient Polyploidies Using Multiple Polyploid Genomes

      • Yue Hao, Gavin C. Conant
      Pages 81-91

  3. Omics Analysis

    1. Front Matter

      Pages 93-93
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    2. Searching for Homologous Genes Using Daisychain

      • Philipp E. Bayer, David Edwards
      Pages 95-101

    3. Detecting MicroRNAs in Plant Genomes with miRkwood

      • Sylvain Legrand, Isabelle Guigon, Hélène Touzet
      Pages 103-120

    4. Pangenome Analysis of Plant Transcripts and Coding Sequences

      • Bruno Contreras-Moreira, Álvaro Rodríguez del Río, Carlos P. Cantalapiedra, Rubén Sancho, Pablo Vinuesa
      Pages 121-152

    5. Metagenomics Bioinformatic Pipeline

      • Diego Garfias-Gallegos, Claudia Zirión-Martínez, Edder D. Bustos-Díaz, Tania Vanessa Arellano-Fernández, José Abel Lovaco-Flores, Aarón Espinosa-Jaime et al.
      Pages 153-179

    6. Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach

      • Victoria Mesa
      Pages 181-197

    7. Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants

      • Samuel David Gamboa-Tuz, Alejandro Pereira-Santana, Tao Zhao, M. Eric Schranz
      Pages 199-215

    8. 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, Katarzyna Oktaba
      Pages 217-247

    9. Isolation of Boechera stricta Developing Embryos for Hi-C

      • Mariana Tiscareño-Andrade, Katarzyna Oktaba, Jean-Philippe Vielle-Calzada
      Pages 249-257

  4. Experimental Procedures for Trait Characterization

    1. Front Matter

      Pages 259-259
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    2. Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens

      • Oscar Estrada, Stephen M. Richards, James Breen
      Pages 261-267

    3. Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-aromatic Rice Germplasms

      • Debarati Chakraborty
      Pages 269-279
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Keywords

About this book

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.

Editors and Affiliations

  • Unidad de Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Zapopan, Mexico

    Alejandro Pereira-Santana

  • Unidad de Biotecnología, Centro de Investigación CientÚfica de Yucatán, Mérida, Mexico

    Samuel David Gamboa-Tuz

  • Unidad de Biotecnología., Centro de Investigación Científica de Yucatán, Mérida, Mexico

    Luis Carlos Rodríguez-Zapata

Bibliographic Information

  • Book Title: Plant Comparative Genomics

  • Editors: Alejandro Pereira-Santana, Samuel David Gamboa-Tuz, Luis Carlos Rodríguez-Zapata

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2429-6

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-2428-9Published: 13 July 2022

  • Softcover ISBN: 978-1-0716-2431-9Published: 13 July 2023

  • eBook ISBN: 978-1-0716-2429-6Published: 11 July 2022

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 294

  • Number of Illustrations: 9 b/w illustrations, 54 illustrations in colour

  • Topics: Plant Genetics and Genomics, Biological Techniques, Bioinformatics

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