Gap-free genome assembly and comparative analysis reveal the evolution and lignin degradation mechanisms of Cylindrobasidium torrendii.

The Physalacriaceae family comprises numerous saprophytic edible and medicinal fungi with significant ecological and economic importance. However, the lack of high-quality genomic data has hindered systematic studies of this family. Here, we report the chromosome-level genome assembly of Cylindrobasidium torrendii, a species identified in China, using a combination of Illumina, PacBio HiFi, and Hi-C sequencing technologies. The 33.67 Mb genome, featuring a GC content of 52.00 %, demonstrates enhanced continuity and completeness. Phylogenetic analysis based on 1685 single-copy orthologous gene families places C. torrendii in close evolutionary proximity to Armillaria mellea and Gymnopus necrorhizus, with a divergence time of 112.39 Mya. Comparative genomics reveals conserved syntenic blocks between chromosomes of C. torrendii and those of Pleurotus ostreatus and Lentinula edodes. Gene family analysis identified 980 expanded and 487 contracted gene families, with expanded genes significantly enriched in secondary metabolite biosynthesis pathways. CAZyme, P450, and laccase gene family comparisons highlighted the evolutionary dynamics of these gene families in C. torrendii. Transcriptomic analysis under fungal dark stress revealed significant upregulation of genes such as CtoLAC7 and CAZymes (GH and CE families). This study provides a high-quality genomic resource and novel insights into the genetic and functional characteristics of C. torrendii and the Physalacriaceae family.