Genetic Characterization and Comparative Genomics of Hyperparasitic Ramularia Species

Genetic Characterization and Comparative Genomics of Hyperparasitic Ramularia Species

Jae Sung Lee, Frederick Leo Sossah, Anbazhagan Mageswari, Le Dinh Thao, Daseul Lee, Donghun Kang, Seung-Beom Hong*

Korean Agricultural Culture Collection, Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration Wanju 55365, South Korea

*Corresponding author: Seung-Beom Hong
Email: funguy@korea.kr

Fungal hyperparasites are emerging as promising tools for sustainable disease management. Among them, Ramularia species attacking rust fungi are ecologically important but remain poorly understood. We sequenced two hyperparasitic isolates, R. coleosporii KACC 44077 and R. uredinicola KACC 44079, using PacBio HiFi and Illumina platforms. A non-hyperparasitic isolate, R. pratensis KACC 410531, was included for comparison. The hyperparasite genomes were 25–26 Mb in size, with ~51% GC content, 15–33 contigs, and N50 values of 1.7–1.9 Mb. BUSCO analyses showed >98% completeness. We predicted ~9,200 protein-coding genes, as well as multiple tRNAs and rRNAs. Functional annotation revealed CAZymes, secondary metabolite clusters, and effector-like proteins, while CpG analysis suggested limited but notable methylation events. Comparative analyses with the non-hyperparasitic isolate suggested candidate gene families unique to the hyperparasitic lifestyle, including expansions in CAZyme classes and secondary metabolism pathways. This study provides the first high-quality genomic resources for rust hyperparasites in Ramularia and highlights their evolutionary adaptations, fungal–fungal antagonism, and potential applications in sustainable rust disease management.