Plant Comparative Genomics

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 H幨鋝e Touzet

9. Pangenome Analysis of Plant Transcripts and Coding Sequences

Bruno Contreras-Moreira, Alvaro Rodriguez del R甐, Carlos P. Cantalapiedra, Rub幯 Sancho, and Pablo Vinuesa

10. Metagenomics Bioinformatic Pipeline

Diego Garfias-Gallegos, Claudia Ziri鏮-Mart璯ez, Edder D. Bustos-D燰z, Tania Vanessa Arellano-Fernandez, Jos?Abel Lovaco-Flores, Aar鏮 Espinosa-Jaime, J. Abraham Avelar-Rivas, and Nelly S幨em-M鎩ica

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. P廨ez-de los Santos, Jes Emiliano Sotelo-Fonseca, Am廨ica Ram甏ez-Colmenero, Hans-Wilhelm Nzmann, Selene L. Fernandez-Valverde, and Katarzyna Oktaba

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

Mariana Tiscare隳-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

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