Plant Comparative Genomics

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