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ARS Home » Northeast Area » Frederick, Maryland » Foreign Disease-Weed Science Research » Research » Publications at this Location » Publication #428623
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: Phylogenomic analysis supports the transfer of Coniothyrium glycines, a soybean pathogen and USDA Select Agent, to the genus Aristastoma

Author
item GREATENS, NICHOLAS - Oak Ridge Institute For Science And Education (ORISE)
item Koch Bach, Rachel

Submitted to: Mycologia
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/15/2026
Publication Date: 8/18/2026
Citation: Greatens, N., Koch Bach, R.A. 2026. Phylogenomic analysis supports the transfer of Coniothyrium glycines, a soybean pathogen and USDA Select Agent, to the genus Aristastoma. Mycologia. https://doi.org/10.1080/00275514.2026.2677228.
DOI: https://doi.org/10.1080/00275514.2026.2677228

Interpretive Summary: A devastating foreign soybean disease, caused by the fungus Coniothyrium glycines, threatens a U.S. crop valued at over $58 billion annually, making it a top concern for plant health regulators, farmers, industry partners, and other ARS stakeholders. Its confusing classification history—marked by repeated name changes—has hindered clear communication across science and agriculture. Using DNA data from hundreds of related fungi, ARS scientists traced the pathogen’s family tree and determined it fits within a group of fungi known as Aristastoma. They proposed a new name—Aristastoma glycines—to reflect its true genetic identity. This clarified identity will support more accurate diagnostics and strengthen coordination in early detection and biosecurity planning. This updated scientific name provides a stable reference point for researchers, diagnostic labs, and regulatory agencies, reinforcing the foundation for early warning systems and coordinated efforts to keep the pathogen out of U.S. soybean fields.

Technical Abstract: Red leaf blotch is a major leaf spot disease of soybean in Africa. It is caused by a fungus in the Pleosporales, Coniothyrium glycines. The pathogen could be highly destructive if introduced to other soybean-growing regions and is classified as a USDA APHIS PPQ Select Agent. Because of its unique suite of morphological characteristics, C. glycines has been placed in numerous genera since its description in 1957, which complicates communication, literature searches and diagnostic development. To provide nomenclatural stability to this high-consequence plant pathogen, we utilized a phylogenomic approach to re-evaluate the evolutionary history and taxonomy of this pathogen. We generated draft genomes for thirteen close relatives of C. glycines, performed phylogenomic analyses that included these newly sequenced species with over 300 other species of Dothideomycetes, and produced a consensus tree from 4,643 single-copy ortholog gene trees. We find that Coniothyrium is not a monophyletic genus and C. glycines is not resolved to the same lineage as the type species, Coniothyrium palmarum. We show that C. glycines is sister to Aristastoma oeconomicum, a once prevalent leaf spot pathogen of cowpea in the eastern United States that causes remarkably similar symptoms as C. glycines does on soybean. Genome distance estimations and a phylogeny based on ITS and 28S data support the transfer of C. glycines and another species, Coniothyrium dolichi, to Aristastoma. The inclusion of A. glycines in Aristastoma expands the morphological concept of this genus to include species that not only form erumpent pycnidia with setose ostioles and septate conidia, and, usually, have a host preference for legumes, to now include those that can produce sclerotia and have aseptate conidia. The improved systematics and genomic resources generated with this study will advance the development of diagnostics and detection assays of this high-consequence plant pathogen.