Population Genomics of Filamentous Plant Pathogens—A Brief Overview of Research Questions, Approaches, and Pitfalls
| Autor: | Sydney E. Everhart, Remco Stam, Nikita Gambhir |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0301 basic medicine education.field_of_study Genomic data Population Genomics Plant Science Population biology Plants Biology 01 natural sciences Data science Population genomics 03 medical and health sciences Genetics Population 030104 developmental biology Workflow Data sequences Research questions Metagenomics education Agronomy and Crop Science Plant Diseases 010606 plant biology & botany |
| Zdroj: | Phytopathology®. 111:12-22 |
| ISSN: | 1943-7684 0031-949X |
| DOI: | 10.1094/phyto-11-20-0527-fi |
| Popis: | 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. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
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