Orthology Prediction and Phylogenetic Analysis Methods in Plants -- Species Tree Inference with SNP Data -- High-Throughput Evolutionary Comparative Analysis of Long Intergenic Non-Coding RNAs in Multiple Organisms -- NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data -- An SGSGeneloss-Based Method for Constructing a Gene Presence/Absence Table Using Mosdepth -- POInT: A Tool for Modeling Ancient Polyploidies Using Multiple Polyploid Genomes -- Searching for Homologous Genes Using Daisychain -- Detecting MicroRNAs in Plant Genomes with miRkwood -- Pangenome Analysis of Plant Transcripts and Coding Sequences -- Metagenomics Bioinformatic Pipeline -- Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach -- Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants -- Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis -- Isolation of Boechera stricta Developing Embryos for Hi-C -- Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens -- Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-Aromatic Rice Germplasms -- Efficient Protein Extraction Protocols for NanoLC-MS/MS Proteomics Analysis of Plant Tissues with High Proteolytic Activity: A Case Study with Pineapple Pulp.

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.