Multilocus derived genetic variability and pathogenicity of Colletotrichum species from the Mid Atlantic United States associated with anthracnose in pepper

Authors: BERNAL-GALEANO, VIVIAN - Oak Ridge Institute For Science And Education (ORISE); Salgado-Salazar, Catalina; WYENANDT, CHRISTIN - Rutgers University; Stommel, John; Clarke, Christopher

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/18/2026
Publication Date: 8/18/2026
Citation: Bernal-Galeano, V., Salgado-Salazar, C., Wyenandt, C.A., Stommel, J.R., Clarke, C.R. 2026. Multilocus derived genetic variability and pathogenicity of Colletotrichum species from the Mid Atlantic United States associated with anthracnose in pepper. Phytopathology. https://doi.org/10.1094/PHYTO-11-25-0371-R.
DOI: https://doi.org/10.1094/PHYTO-11-25-0371-R

Interpretive Summary: Anthracnose, caused by species of the fungus Colletotrichum, results in major losses in pepper and tomato production, with field damage reaching up to 100%, postharvest losses up to 50%, and fungicide resistance reported in some species of the pathogen. Effective management is hindered by limited knowledge of which Colletotrichum species are responsible for the disease across different regions and growing conditions. A collection of 149 Colletotrichum samples from infected pepper and tomato fruits in the Northeastern U.S. was made and characterized by genetic analysis and ability to infect pepper. Eleven distinct Colletotrichum species were identified as causes of anthracnose in bell peppers, including seven not previously reported as causing anthracnose in pepper in the U.S., an unexpectedly high proportion. All were confirmed pathogenic under controlled conditions, underscoring the complexity of this disease and the challenge it poses for effective management. Researchers and advisors will use these findings to improve disease diagnostics and develop more comprehensive management strategies. By guiding resistant crop breeding and optimizing fungicide use, the findings enable development of tools effective against the full spectrum of pathogens, helping farmers reduce fruit rot losses in tomatoes and peppers.

Technical Abstract: Colletotrichum species are important fungal plant pathogens that cause anthracnose and fruit rots leading to pre- and post-harvest losses of a wide variety of crops, including bell pepper and tomato. In this study, we performed a phylogenetic and pathogenic characterization of Colletotrichum isolates collected in the northeastern United States from mature and immature Capsicum annum and Solanum lycopersicum fruits. A total of 149 Colletotrichum sp. isolates were obtained, distributed among 11 recognized Colletotrichum species across four complexes Acutatum, Orchidearum, Truncatum, Gloeosporioides and two singleton groups C. nigrum and C. chlorophyti. Pathogenicity tests demonstrated that out of 61 tested isolates, 59 were able to cause symptoms on mature bell pepper fruits under controlled conditions. Only Colletotrichum scovillei isolates caused disease on immature bell pepper fruits. Selected isolates displayed variable virulence profiles on red pepper, with some of the species being more aggressive than others. Colletotrichum scovillei was consistently the most aggressive of the tested isolates. Represented among the analyzed, pathogenic isolates, there were three species of Colletotrichum not yet reported as pathogens of Capsicum, namely C. melonis, C. changpingense and C. chlorophyti. Four additional Colletotrichum species, C. fioriniae, C. aenigma, C. fructicola and C. sojae, are also reported here for the first time causing disease on Capsicum sp. in the United States. These results demonstrate the extreme heterogeneity of Colletotrichum species on pepper and tomato with the capacity to cause fruit rot in immature and mature bell peppers in the northeastern United States. Accurate identification of the pathogenic species of Colletotrichum causing anthracnose and fruit rot is a critical step for making the most informed disease management decisions.