Hybrid Genome Assembly and Annotation of the Basidiomycete Fungus Candolleomyces candolleanus Strain CMU-8613 Using a Cost-Effective Iterative Pipeline

The recently described genus <i>Candolleomyces</i> (Basidiomycota, Agaricales, Psathyrellaceae) is now recognized as a distinct taxonomic group separate from <i>Psathyrella</i>. Currently, no fully assembled and accurately annotated genomes of <i>Candolleomyces</i> species are available, limiting our understanding of their physiological traits and biotechnological potential. Numerous tools exist for fungal genome assembly and annotation, each using different algorithms, resulting in substantial variation in gene content and distribution within the same genome. In this work, a hybrid assembly and annotation of the genome of strain CMU-8613 were performed using pipelines that combine different assembly and annotation tools. Phylogenetic analysis showed that the analyzed strain CMU-8613 belongs to <i>Candolleomyces candolleanus</i>. The assembled genome size ranged from 46.8 Mb (NECAT + Racon) to 59.3 Mb (Canu + <i>Coprinellus micaceus</i> genome assembly), depending on the assembly and polishing strategy. The analysis identified 15-25 secondary metabolite gene clusters (BGCs), depending on the genome assembly and the tools used for BGC prediction. In strain CMU-8613, CAZyme-encoding genes varied across assemblies: 494 genes were detected in the Flye assembly and 453 in NECAT; in both cases, the AA (Auxiliary Activities) and GH (Glycoside Hydrolases) families were the most represented. The diversity of CAZymes observed among <i>Candolleomyces</i> species suggests differences in their saprophytic capacities. Analysis of the MAT-A/MAT-B loci revealed that <i>C. candolleanus</i> possesses a tetrapolar mating system. This study provides the first annotated genome of <i>C. candolleanus</i>, highlighting its enzymatic potential to degrade plant biomass and its capacity to synthesize diverse secondary metabolites. The combination of assembly and annotation tools employed here offers robust alternative strategies for characterizing non-model fungi or species lacking high-quality reference genomes.