Comparative Genomics Reveals Conserved Ophiobolin Biosynthetic Gene Cluster and Necrotrophic Adaptation in Bipolaris oryzae

Bipolaris oryzae, the causal agent of rice brown spot, is a necrotrophic fungus that produces phytotoxic secondary metabolites, yet its genomic basis of pathogenicity remains incompletely defined. We sequenced six South Korean B. oryzae isolates and analyzed them together with publicly available genomes from Bipolaris and related Pleosporaceae, covering 37 Bipolaris isolates across eight species. Phylogenomics based on singlecopy orthologs confirmed the monophyly of Bipolaris and resolved B. oryzae as a distinct lineage. Comparative analyses showed that B. oryzae has a moderately reduced secretome and fewer candidate pathogenicity gene families relative to B. maydis and B. sorokiniana, while retaining a conserved core enriched in carbohydrate and amino acid metabolism. We identified 48 secondary metabolite biosynthetic gene clusters in B. oryzae F1253 and, critically, localized the ophiobolin biosynthetic gene cluster to pseudochromosome 2. The cluster contains conserved core genes, oblA to oblD, which are broadly retained across Bipolaris, and exhibits interspecies variation in synteny and copy number associated with repeat element insertions. These findings reveal the genomic architecture underlying metabolic specialization and toxin biosynthesis in B. oryzae. They also provide actionable targets and markers for management, including diagnostics for oblA to oblD, screening of rice germplasm for ophiobolin tolerance, and RNAi-based suppression of ophiobolin biosynthesis under climate-related stress.