Epicoccum Associated with Soybean in Russia: Species Diversity, Pathogenic Potential, and Genomic Features

Species of the genus Epicoccum are widespread plant-associated fungi; however, their phytopathological significance in soybean remains insufficiently studied. In the present study, 15 Epicoccum isolates obtained in 2024–2026 from symptomatic soybean leaves and seeds in four regions of Russia were characterized using multilocus phylogenetic analysis, whole-genome sequencing, controlled inoculation assays, assessment of extracellular enzymatic activity, and fungicide sensitivity testing. Nine isolates were identified as E. tobaicum, five as E. mezzettii, and one as E. oryzae. The five sequenced genomes ranged from 32.84 to 34.62 Mb in size, with BUSCO completeness of 97.1–98.9%. In the mycelial-plug assay, performed without needle puncturing of the leaf blade, the largest mean necrotic lesion diameter was 12.75 ± 5.03 mm; in a separate wound-assisted assay, in which an E. tobaicum conidial suspension was applied to standardized needle wounds, the highest mean proportion of necrotic leaflet area was 26.17 ± 8.93% at 7 days after inoculation. Following artificial seed inoculation with E. tobaicum isolate 152H, no normal seedlings developed, and visible signs of fungal colonization were recorded on 100% of the seeds, indicating substantial adverse effects on seedling development under the experimental conditions. For 14 of the 15 isolates, 50% inhibition of mycelial growth by azoxystrobin was not reached at the highest tested concentration (EC50 > 1000 µg/mL), indicating low sensitivity under the test conditions, whereas EC50 values ranged from 0.0448 to 0.3837 µg/mL for boscalid, from 0.0760 to 0.2736 µg/mL for fludioxonil, and from 3.735 to 49.542 µg/mL for tebuconazole. These findings demonstrate substantial variation in fungicide sensitivity among the tested isolates, although further comparative studies are required to establish resistance status. To our knowledge, this study reports the first molecularly confirmed detection of E. tobaicum, E. mezzettii, and E. oryzae associated with soybean in Russia, as well as the first experimental evidence of the pathogenic potential of E. tobaicum toward soybean leaves in the country under controlled inoculation conditions. Because the conidial assay was performed on wounded leaflets, it does not establish the ability of these isolates to infect intact leaves under natural conditions.