Quantifying Re-association of a Facultative Endohyphal Bacterium with a Filamentous Fungus -- Characterizing Mycoviruses -- Analysis of Secondary Metabolites from Plant Endophytic Fungi -- Protocols for Investigating the Leaf Mycobiome using High throughput DNA Sequencing -- Characterizing Small RNAs in Filamentous Fungi using the Rice Blast Fungus, Magnaporthe oryzae, as an Example -- Plant Small RNAs Responsive to Fungal Pathogen Infection -- Sequential Phosphopeptide Enrichment for phosphoproteome Analysis of Filamentous Fungi: A Test Case using Magnaporthe oryzae -- Assays for MAP kinase Activation in Magnaporthe oryzae and other Plant Pathogenic Fungi -- Visualizing the Movement of Magnaporthe oryzae Effector Proteins in Rice Cells during Infection -- Illuminating Phytophthora Biology with Fluorescent Protein Tags -- Methods for Transient Gene Expression in Wild Relatives of Potato -- Host-induced Gene Silencing (HIGS) for Elucidating Puccinia Gene Function in Wheat -- From Short Reads to Chromosome-scale Genome Assemblies -- BLASTmap: A Shiny-based Application to Visualise BLAST Results as Interactive Heat Maps and a Tool to Design Gene Specific Baits for Bespoke Target Enrichment Sequencing -- A Computational Protocol to Analyze Meta-transcriptomic Data Capturing Fungal-host Interactions -- Application of the Cre/lox System to Construct Auxotrophic Markers for Quantitative Genetic Analyses in Fusarium graminearum -- Protocol of Phytophthora capsici Transformation using the CRISPR-Cas9 System -- Generating Gene Silenced Mutants in Phytophthora sojae. .

This book describes approaches for the analysis of plant pathogenic fungi that range from ecosystem composition to in vitro and wet-lab to computational analyses. Chapters detail bioinformatics protocols for genome assembly, transcriptome analysis and small RNA profiling, characterization of secondary metabolome, analysis of post-translational modification and localization of proteins, examination of virulence function and interaction with plants or other microorganisms, and targeted mutagenesis using various approaches. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Plant Pathogenic Fungi and Oomycetes: Methods and Protocols aims to provide techniques developed through a wide range of perspectives to facilitate research on a comprehensive understanding of these important filamentous pathogens.