Cronartium ribicola is a globally distributed fungal pathogen that infects Pinus armandii Franch., causing widespread tree mortality. In this study, we report a chromosomal-level genome assembly of C. ribicola LQ (262.51 Mb, N50 = 15.4 Mb, GC content = 38.4%) using integrated Illumina short-read, PacBio long-read, and Hi-C sequencing technologies. Ultimately, a total of 94.83% of the assembled sequences were anchored onto 17 pseudo-chromosomes. Genome annotation predicted 10,222 protein-coding genes, and repetitive sequences accounted for 91.67% of the genome. Benchmarking Universal Single-Copy Ortholog (BUSCO) analysis demonstrated 94.03% genome completeness, with functional annotations covering 88.32% of the genes. A total of 352 carbohydrate-active enzyme (CAZyme) genes, predominantly glycoside hydrolases (45.17%), and 8 secondary metabolite biosynthetic gene clusters were identified, indicating strong host tissue degradation capability and diverse virulence factors. Overall, this study provides valuable genomic resources for dissecting the pathogenicity, host interaction mechanisms, and resistance gene discovery of C. ribicola and establishes a foundation for developing virulence-targeted disease control strategies.
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