Genomic resources of four colletotrichum species (c. fioriniae, c. chrysophilum, c. noveborasense and c. nupharicola) threatening commercial apple production in the eastern United States

Authors: KHODADADI, FATEMEH - Virginia Tech; GIROUX, EMILY - Canadian Food Inspection Agency; BILODEAU, GUILLAUME - Canadian Food Inspection Agency; Jurick, Wayne; ACIMOVIC, SRDJAN - Virginia Tech

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/3/2023
Publication Date: 9/11/2023
Citation: Khodadadi, F., Giroux, E., Bilodeau, G., Jurick II, W.M., Acimovic, S.G. 2023. Genomic resources of four colletotrichum species (c. fioriniae, c. chrysophilum, c. noveborasense and c. nupharicola) threatening commercial apple production in the eastern United States. Molecular Plant-Microbe Interactions. 36(8):529–532. https://doi.org/10.1094/MPMI-10-22-0204-A.
DOI: https://doi.org/10.1094/MPMI-10-22-0204-A

Interpretive Summary: Fruit quality deterioration and losses are attributed to fungal diseases. In the mid-Atlantic area, bitter rot is a predominant pre- and postharvest problem for pome fruit growers. Bitter rot is caused by a fungus that is controlled by fungicides. However, fruit that survive the growing season and enter storage, often come out with bitter rot symptoms. Hence, new tools and detection methods need to be developed to help the industry identify and manage this disease. Thus, we used genomics to decode the genomes of bitter rot fungi to aid in rapid detection methods. We envision our data will be directly useful for designing tests to screen fruit for the pathogen, increase our understanding of the factors needed for this pathogen to cause disease, and enable development of novel control strategies to ensure fruit quality while reducing food loss and waste.

Technical Abstract: Colletotrichum spp. are one of the top fungal plant pathogens causing anthracnose and pre- and post-harvest fruit rot on a wide range of economically important crops. Apple (Malus domestica Borkh.) is a major agricultural product cultivated in temperate regions worldwide and significantly contributes to the human nutrition and global economy. Orchards can suffer devastating losses by bitter rot of apple, which is a serious disease caused by several species of Colletotrichum. Bitter rot was also first described as a major postharvest pathogen in the mid-Atlantic region, and it was found that C. fioriniae caused bitter rot in commercial apple storages leading to 2 – 14 % of unmarketable fruit. Correct species-level detection and identification is critical for developing effective disease control practices in apple orchards in the U.S. In this study, we performed whole genome sequencing, de novo assembly, and annotation of two isolates of C. fioriniae, three isolates of C. chrysophilum, and two isolates of C. noveboracense collected from bitter rot-infected apple fruit in New York, Pennsylvania, and Virginia. The C. noveboracense Coll940 isolate was collected from Juglans nigra in Oklahoma and two isolates of C. nupharicola (CBS470 and Coll922) were obtained from yellow waterlily (Nuphar lutea) in Washington and New Jersey, respectively. This work provides new genomic resources for Colletotrichum spp. that were previously not available and significantly contributes to the expansion of existing resources for Colletotrichum genus which has species complexes and designing species-specific diagnostic assays is challenging. Thus, the whole genome sequencing data, obtained from the dominant disease-causing species, will provide the genome resources needed to identify species-specific gene targets for molecular marker development to complement existing diagnostic/detection tools. It is envisioned that these tools will also facilitate many comparative genomics studies that aim to understand the nature of host-pathogen interactions and factors impacting disease resistance in the host.