Haplotype-Phased Chromosome-Level Genome Assembly of Floccularia luteovirens Provides Insights into Its Taxonomy, Adaptive Evolution, and Biosynthetic Potential

<i>Floccularia luteovirens</i> is a valuable medicinal and edible ectomycorrhizal fungus that is endemic to alpine meadows on the Qinghai-Tibet Plateau. It is of significant ecological and pharmacological importance. To overcome the genomic limitations of previous fragmented assemblies, we present the first haplotype-phased, chromosome-scale genome of the Qinghai-derived QHU-1 strain using an integrated approach of PacBio HiFi, Hi-C, and Illumina sequencing. The high-contiguity assembly spans 13 chromosomes with 97.6% BUSCO completeness. Phylogenomic analysis of 31 basidiomycetes clarified a historical misclassification by placing <i>F. luteovirens</i> closest to <i>Mycocalia denudata/Crucibulum laeve</i>, thus confirming its distinct lineage from <i>Armillaria</i> spp. through low synteny and divergent gene family dynamics. Analyses of adaptive evolution revealed strong purifying selection and stable transposable elements, suggesting genomic adaptations to extreme UV/cold stress. AntiSMASH identified 15 biosynthetic gene clusters (BGCs), which encode diverse terpenoids (7), NRPS-like enzymes (4), PKSs (2), and a hybrid synthase with unique KS-AT-PT-A domains, which have the potential to generate novel metabolites. This chromosome-level resource sheds light on the genetic basis of <i>F. luteovirens</i>' taxonomy, alpine survival, and symbiotic functions while also unlocking its potential for bioprospecting bioactive compounds.