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ARS Home » Northeast Area » Frederick, Maryland » Foreign Disease-Weed Science Research » Research » Publications at this Location » Publication #427623
Research Project: Integrative Genomic and Biological Approaches to Detect and Manage Emerging Foreign Fungal and Oomycete Plant Pathogens

Location: Foreign Disease-Weed Science Research

Title: A chromosome-level genome assembly of Thecaphora frezzii, cause of peanut smut, reveals the largest genome among the true smut fungi

Author
item GREATENS, NICHOLAS - Oak Ridge Institute For Science And Education (ORISE)
item COUGER, BRAIN - Brigham & Women'S Hospital
item MAESTRO, MARIANO - Foundation For The Study Of Invasive Species
item CABRERA WALSH, GUILLERMO - Foundation For The Study Of Invasive Species
item MORICHETTI, SERGIO - Sanchez Farms
item TALLON, LUKE - University Of Maryland School Of Medicine
item Bennett, Rebecca
item CLEVENGER, JOSH - Hudsonalpha Institute For Biotechnology
item Chamberlin, Kelly
item Koch Bach, Rachel

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 2/2/2026
Publication Date: N/A
Citation: N/A
DOI: https://doi.org/10.64898/2026.02.02.703329

Interpretive Summary: Peanut smut, caused by the fungus Thecaphora frezzii, severely damages peanut crops in Argentina by replacing the developing nuts with masses of dark spores, reducing both yield and quality. Several countries have restricted peanut imports from Argentina to prevent the fungus from spreading—especially to the United States where peanuts are a $1.4 billion crop and a cornerstone of the agricultural economy. In this study, scientists decoded the complete genome sequence of T. frezzii, revealing the largest and most repetitive genome among 50 related smut fungi. This breakthrough provides vital information for developing rapid diagnostic tools to prevent the fungus from entering U.S. borders, thereby protecting domestic production and agricultural biosecurity. It also helps scientists understand how the pathogen causes disease and enables breeders to assess the durability of peanut varieties that have been used to manage the disease in affected regions.

Technical Abstract: Peanut smut, caused by the fungus Thecaphora frezzii, is a significant disease of peanuts in Argentina. Infected plants have seeds replaced by a mass of dark teliospores, reducing yield and seed quality. To prevent the spread of the pathogen, several countries have limited import of raw peanuts from Argentina, a major grower and exporter. Following successful in vitro culture of the fungus in its haploid stage, we produced a chromosome-level assembly of the species for the first time. We compare the genome with those of 49 other species of true smut fungi, or Ustilaginomycetes, including species of medical, agricultural, and industrial importance, some of which are known as pathogens, and others only as saprotrophic yeasts. At 39 Mb, T. frezzii has the largest genome of the smut fungi sequenced to date and the most repetitive content. While it shares some core effectors with the distantly related and better studied Ustilago and related fungi, predicted effectors only found in T. frezzii or in Thecaphora suggest unique infection strategies. Comparisons among the 50 smut genomes also show that the 14 smut fungi observed only as yeasts share genomic traits such as low repeat content and generally smaller genomes. This supports the hypothesis that some smut fungi are adapted to saprotrophic growth as yeasts. The high-quality, annotated genome for T. frezzii will be a valuable resource for investigating the population dynamics and evolution of an economically important pathogen, as well as illuminating an understudied clade of smut fungi.