Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

Khodadadi, Fatemeh; Luciano-Rosario, Dianiris; Gottschalk, Christopher; Jurick, Wayne M.; Aćimović, Srđan G.

doi:10.3390/jof10070493

Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

Journal Article · Tue Jul 16 00:00:00 EDT 2024 · Journal of Fungi

DOI:https://doi.org/10.3390/jof10070493· OSTI ID:2469764

Khodadadi, Fatemeh ^[1]; Luciano-Rosario, Dianiris ^[2]; ^[3]; Jurick, Wayne M. ^[2]; ^[4]

University of California, Riverside, CA (United States)
U.S. Department of Agriculture, Beltsville, MD (United States)
U.S. Department of Agriculture, Kearneysville, WV (United States)
Virginia Polytechnic Institute and State University, Winchester, VA (United States)

The bitter rot of apple is caused by Colletotrichum spp. and is a serious pre-harvest disease that can manifest in postharvest losses on harvested fruit. In this study, we obtained genome sequences from four different species, C. chrysophilum, C. noveboracense, C. nupharicola, and C. fioriniae, that infect apple and cause diseases on other fruits, vegetables, and flowers. Our genomic data were obtained from isolates/species that have not yet been sequenced and represent geographic-specific regions. Genome sequencing allowed for the construction of phylogenetic trees, which corroborated the overall concordance observed in prior MLST studies. Bioinformatic pipelines were used to discover CAZyme, effector, and secondary metabolic (SM) gene clusters in all nine Colletotrichum isolates. We found redundancy and a high level of similarity across species regarding CAZyme classes and predicted cytoplastic and apoplastic effectors. SM gene clusters displayed the most diversity in type and the most common cluster was one that encodes genes involved in the production of alternapyrone. Our study provides a solid platform to identify targets for functional studies that underpin pathogenicity, virulence, and/or quiescence that can be targeted for the development of new control strategies. With these new genomics resources, exploration via omics-based technologies using these isolates will help ascertain the biological underpinnings of their widespread success and observed geographic dominance in specific areas throughout the country.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC); Bowman Trust Startup Fund; National Institute of Food and Agriculture; New York State Department of Agriculture and Markets (NYSDAM); Apple Research and Development Program (ARDP); USDA

Grant/Contract Number:: SC0014664

OSTI ID:: 2469764

Journal Information:: Journal of Fungi, Journal Name: Journal of Fungi Journal Issue: 7 Vol. 10; ISSN 2309-608X

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Unveiling the Arsenal of Apple Bitter Rot Fungi: Comparative Genomics Identifies Candidate Effectors, CAZymes, and Biosynthetic Gene Clusters in Colletotrichum Species

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