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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Disease and Pest Management Research Unit » Research » Research Project #445131

Research Project: Whole Genome Sequencing for Epidemiology, Population Structure, and Fungicide Resistance of Botrytis spp. in the Pacific Northwest

Location: Horticultural Crops Disease and Pest Management Research Unit

Project Number: 2072-22000-045-036-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 1, 2023
End Date: Aug 31, 2025

1. Sequence genomes of Botrytis cinerea and related species. 2. Compare genomes for evolutionary relationships. 3. Examine similarities in biosynthetic pathways associated with fungicide tolerance.

This effort is intended to leverage existing and ongoing research on the population structure, epidemiology, and characterization of fungicide resistance profiles of Botrytis spp. collected from vineyards and other small fruit crops throughout the western United States. Whole genome DNA will be prepared from 50-100 Botrytis isolates from grape, blueberry, caneberries, and nursery crops. Isolates will be hierarchically sampled and selected to maximize diversity in plant host and geographic range across the Western US. Whole genomes will be sequenced using long read Nanopore technology. Genomes will be assembled and annotated prior to examining evolutionary relationships. Newly sequenced genomes will be analyzed in the context of previously sequenced Botrytis spp. to generate a phylogenetic framework. Phylogenetic analysis based on marker genes (MLSA/MLST), and whole genome single nucleotide polymorphism (SNP) analysis will be used to infer genotypes and characterize evolutionary relationships between isolates. Whole genome analysis provides the highest resolution of evolutionary relationships and will be used to characterize epidemiological patterns. Analysis will be made at multiple hierarchies and scales, comparing multiple isolates from individual vineyards/nurseries, across locations, and on different hosts. Phylogenetic analysis will also be used to assess evolutionary relationships between isolates from agricultural and native systems. Based on initial sequencing results, additional strains may be isolated and sequenced to investigate epidemiological patterns in vineyards and nurseries. Whole genome sequences will be analyzed to infer Botrytis population structure. Population structure analysis will be used to characterize distinct populations of Botrytis and recombination between these populations. Highly contiguous assemblies built from long reads will also inform on chromosomal structural variation and evolution. Pangenome analysis and comparative genomics will be used to identify genetic differences associated with plant host, fungicide resistance, and other phenotypes of interest.