| Summary: | <i>Floccularia luteovirens</i> is a famous and precious edible mushroom (Huang Mogu) on the Qinghai–Tibet plateau that has a unique flavor and remarkable medical functions. Herein, we report a reference-grade 27 Mb genome of <i>F. luteovirens</i> containing 7068 protein-coding genes. The genome component and gene functions were predicted. Genome ontology enrichment and pathway analyses indicated the potential production capacity for terpenoids, polyketides and polysaccharides. Moreover, 16 putative gene clusters and 145 genes coding for secondary metabolites were obtained, including guadinomine and melleolides. In addition, phylogenetic and comparative genomic analyses shed light on the precise classification of <i>F. luteovirens</i> suggesting that it belongs to the genus <i>Floccularia</i> instead of <i>Armillaria</i>. RNA-sequencing and comparative transcriptomic analysis revealed differentially expressed genes during four developmental stages of <i>F. luteovirens</i>, that of which helps to identify important genes regulating fruiting body formation for strain modification. This study will provide insight into artificial cultivation and increase the production of useful metabolites.
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