Plant comparative genomics / edited by Alejandro Pereira-Santana, Samuel David Gamboa-Tuz, Luis Carlos Rodriguez-Zapata. -- New York, NY : Springer, 2022. – (58.17/M592/v.2512)

Contents

Preface
Contributors
PART I  PHYLOGENETICS AND EVOLUTION
1  Orthology Prediction and Phylogenetic Analysis Methods in Plants
2  Species Tree Inference with SNP Data
3  High-Throughput Evolutionary Comparative Analysis of Long Intergenic Noncoding RNAs in Multiple Organisms
4  NGS-Indel Coder v2.0: A Streamlined Pipeline to Code Indel Characters in Phylogenomic Data
5  An SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth
6  POINT: A Tool for Modeling Ancient Polyploidies Using Multiple Polyploid Genomes
PART II  OMICS ANALYSIS
7  Searching for Homologous Genes Using Daisychain
8  Detecting MicroRNAs in Plant Genomes with miRkwood
9  Pangenome Analysis of Plant, Transcripts and Coding Sequences
10  Metagenomics Bioinformatic Pipeline
11  Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach
12  Applying Synteny Networks (SynNet) to Study Genomic Arrangements of Protein-Coding Genes in Plants
13  Plant In Situ Hi-C Experimental Protocol and Bioinformatic Analysis
14  Isolation of Boechera stricta Developing Embryos for Hi-C
PART III  EXPERIMENTAL PROCEDURES FOR TRAIT CHARACTERIZATION
15  Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens
16  Use of Allele-Specific Amplification for Rapid Identification of Aromatic and Non-aromatic Rice Germplasms
17  Efficient Protein Extraction Protocols for NanoLC-MS/MS Proteomics Analysis of Plant Tissues with High Proteolytic Activity: A Case Study with Pineapple Pulp
Index