By: Nicholas Greatens1,2 and Rachel A. Koch Bach2 |
04/30/2025
1SCINet Program and ARS AI Center of Excellence, Office of National Programs, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America
2Foreign Disease-Weed Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Fort Detrick, Maryland, United States of America
Coniothyrium glycines causes red leaf blotch, a major disease of soybean in Africa (Figure 1). It is one of two fungal pathogens listed on the USDA APHIS Plant Protection and Quarantine Select Agents and Toxins list owing to its likely destructive potential if it spreads to major soybean growing regions.
At the USDA-ARS Foreign Disease-Weed Science Research Unit, based in Fort Detrick, Maryland, SCINet/AI-COE Postdoctoral Fellow Nicholas Greatens and Research Plant Pathologist Rachel Koch Bach study this carefully regulated pathogen in containment research facilities. Drawing from recent collections of the red leaf blotch pathogen from across southern and eastern Africa, ARS researchers have published the first annotated genome of C. glycines and provided new insights into how it causes disease in soybean. Genome assembly and annotation and comparative genomics analyses were made possible by SCINet’s Ceres supercomputer and the personnel and educational resources of SCINet.
Many leaf spot fungi produce compounds that are toxic to plants, and these phytotoxins can play key roles in causing disease. Often, the enzymes that synthesize phytotoxins are encoded by closely linked genes that act together and are inherited as a cluster. This close linkage enables detection of these gene clusters and helps to predict their chemical products.
Examination of the C. glycines genome with antiSMASH software revealed a gene cluster similar in structure to well-studied clusters that produce cercosporin and elsinochrome, light-activated, disease-causing toxins produced by pathogens like Cercospora beticola, causing Cercospora leaf spot of beet, and Parastagonospora nodorum, causing Septoria leaf blotch of wheat. The red leaf blotch symptom caused by C. glycines resembles the distinct reddish leaf spots of Cercospora diseases.
In cultures of C. glycines grown under light conditions, the gene cluster was upregulated, and in leaves inoculated under light, more lesions developed and at a faster rate. Liquid chromatography and mass spectrometry confirmed production of elsinochrome in field-collected specimens and pure cultures.
Remarkably, similar gene clusters likely synthesizing elsinochrome or related compounds were detected for the first time in other important plant pathogens and fungi using BLAST, phylogenetic approaches, and the software CAGECAT, a user-friendly tool useful for exploring biosynthetic gene clusters. As it turns out, elsinochrome and related compounds may have broader importance to fungal ecology than was previously understood.
This study lays the groundwork for understanding the molecular machinery required for plant pathogenicity by the Select Agent C. glycines. Understanding the molecular basis of disease is an important step toward the development of effective management strategies for red leaf blotch of soybean. The study is in press at PLOS One as “Production of the light-activated elsinochrome phytotoxin in the soybean pathogen Coniothyrium glycines hints at virulence factor”.
Figure 1. Red leaf blotch disease in soybean.