Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments
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Date
2020
Publication Type
Book Chapter
ETH Bibliography
no
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Abstract
Genome sequencing of fungal pathogens have documented extensive variation in genome structure and composition between species and in many cases between individuals of the same species. This type of genomic variation can be adaptive for pathogens to rapidly evolve new virulence phenotypes. Analyses of genome-wide variation in fungal pathogen genomes rely on high quality assemblies and methods to detect and quantify structural variation. Population genomic studies in fungi have addressed the underlying mechanisms whereby structural variation can be rapidly generated. Transposable elements, high mutation and recombination rates as well as incorrect chromosome segregation during mitosis and meiosis contribute to extensive variation observed in many species. We here summarize key findings in the field of fungal pathogen genomics and we discuss methods to detect and characterize structural variants including an alignment-based pipeline to study variation in population genomic data.
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Publication status
published
Book title
Population Genomics of Fungal Plant Pathogens and the Analyses of Rapidly Evolving Genome Compartments
Journal / series
Volume
2090
Pages / Article No.
337 - 355
Publisher
Humana
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
Fungal pathogens; Genome compartments; Transposable elements; De novo assembly; Multiple genome alignments
Organisational unit
03516 - McDonald, Bruce (emeritus) / McDonald, Bruce (emeritus)