Plant Comparative Genomics

Alejandro Pereira-Santana, Samuel David Gamboa-Tuz, Luis Carlos Rodríguez-Zapata (Herausgeber)

Buch | Softcover

294 Seiten

2023 | 1st ed. 2022
Springer-Verlag New York Inc.
978-1-0716-2431-9 (ISBN)

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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.

lt;p>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

Erscheinungsdatum	18.07.2023
Reihe/Serie	Methods in Molecular Biology
Zusatzinfo	54 Illustrations, color; 9 Illustrations, black and white; XI, 294 p. 63 illus., 54 illus. in color.
Verlagsort	New York, NY
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Naturwissenschaften ► Biologie ► Botanik
Themenwelt	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	Bioinformatic tools • Data Visualization • Genomic Information • Next-generation sequencing technologies • Phylogenomics • Trait characterization
ISBN-10	1-0716-2431-8 / 1071624318
ISBN-13	978-1-0716-2431-9 / 9781071624319
Zustand	Neuware