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Chaga mushroom (Inonotus obliquus) is a fungal species in the family Hymenochaetaceae (Basidiomycota) and the causative agent of white rot decay in Betula species. We assembled a high-quality 50.7 Mbp genome from PacBio sequencing and identified a lineage-specific whole genome duplication event approximately 1.3 million years ago, which has contributed to a major increase in biochemical diversity in the species through preferential retention of cytochrome P450 superfamily members. Secondary metabolism has further evolved through small-scale segmental duplications, such as tandem duplications within fungal biosynthetic gene clusters. Metabolomic fingerprinting confirmed increased complexity in terpene biosynthesis chemistry compared to related species that lacked the duplication event. This metabolic diversity may have arisen from co-evolution with the primary host species, which evolved high betulin content in its bark 4–8 million years ago.