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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Food Quality Laboratory » Research » Research Project #438142

Research Project: Whole Genome, Transcriptome and Comparative Genomics of Postharvest Fungal Plant Pathogens

Location: Food Quality Laboratory

Project Number: 8042-42430-003-010-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Apr 27, 2020
End Date: Apr 26, 2023

The overall purpose of the project is to provide publicly available, high quality genomics resources for fungal postharvest pathogens of fruit that are economically significant and contribute greatly to food loss and waste. Fungal genomics resources will provide new information on pathogen genes controlling fruit decay, molecular regulators of antimicrobial resistance, and toxin gene clusters that can be targeted to inhibit decay, combat fungicide resistance, prevent mycotoxin contamination and allow for high quality fruit to be maintained during prolonged storage, shipping and transport.

Multiple bioinformatics approaches will be executed and combined using Linux command line programs like (Shovil and SPADES) to assemble, annotate and analyze fungal genome and transcriptome data. Genomes will be verified for quality using programs that assess completeness of conserved fungal genes including Benchmark Universal Single Copy Orthologues, contig number, length, and depth of coverage. After genomes are assembled comparative analyses will be conducted that include phylogenomics to compare sequences from Genbank that are associated with type species. Established pipelines and tools will be implemented to determine transposon number, type and gene location. AntiSMash and SMURF will help to determine toxin gene cluster identity and type. Transcription factors and Single Nucleotide Polymorphism calling will be conducted between isolates with different fungicide-resistant profiles to ascertain genetic markers associated with fungicide resistance to be used to design rapid detection tools.