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ARS Home » Plains Area » Fargo, North Dakota » Edward T. Schafer Agricultural Research Center » Sunflower and Plant Biology Research » Research » Publications at this Location » Publication #385503
Research Project: Sclerotinia Initiative

Location: Sunflower and Plant Biology Research

Title: Population genomics of filamentous plant pathogens—a brief overview of research questions, approaches, and pitfalls

Author
item EVERHART, SYDNEY - University Of Nebraska
item GAMBHIR, NIKITA - University Of Nebraska
item STAM, REMCO - Technical University Of Munich

Submitted to: Phytopathology
Publication Type: Review Article
Publication Acceptance Date: 12/1/2020
Publication Date: 12/18/2020
Citation: Everhart, S., Gambhir, N., Stam, R. 2020. Population genomics of filamentous plant pathogens—a brief overview of research questions, approaches, and pitfalls. Phytopathology. 111:12-22. https://doi.org/10.1094/PHYTO-11-20-0527-FI.
DOI: https://doi.org/10.1094/PHYTO-11-20-0527-FI

Interpretive Summary:

Technical Abstract: With ever-decreasing sequencing costs, research on the population biology of plant pathogens is transitioning from population genetics—using dozens of genetic markers or polymorphism data of several genes—to population genomics—using several hundred to tens of thousands of markers or whole-genome sequence data. The field of population genomics is characterized by rapid theoretical and methodological advances and by numerous steps and pitfalls in its technical and analytical workflow. In this article, we aim to provide a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens and direct readers to more extensive reviews for in-depth understanding. We briefly discuss different types of population genomics-inspired research questions and give insights into the sampling strategies that can be used to answer such questions. We then consider different sequencing strategies, the various options available for data processing, and some of the currently available tools for population genomic data analysis. We conclude by highlighting some of the hurdles along the population genomic workflow, providing cautionary warnings relative to assumptions and technical challenges, and presenting our own future perspectives of the field of population genomics for filamentous plant pathogens.