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Colletotrichum fructicola is a plant pathogenic fungus with a broad host range. It causes significant losses to important crops including apple, pear, strawberry and other Rosaceae and non-Rosaceae species. To date, two short-read based C. fructicola genomes are publicly available, but both are fragmented. In this study we re-sequenced the genome of C. fructicola using nanopore long read technology and refined the assembly with Hi-C map data. The resulting high-quality assembly is an important resource for further comparative and experim