Genome assembly and comparative genomic analysis of the extracellular polysaccharide-overproducing strain Schizophyllum commune SC-N.

To characterize the genomic features of the extracellular polysaccharide-overproducing strain Schizophyllum commune SC-N, genome assembly and functional annotation were performed using a hybrid sequencing strategy combining Nanopore long reads and Illumina short reads, followed by comparative genomic analyses with S. commune H4-8 and representative basidiomycetes. The SC-N genome was 45.62 Mb in size, with a GC content of 55.45% and a contig N50 of 3.71 Mb. A total of 13,832 protein-coding genes were predicted, and the BUSCO completeness score reached 95.12%. In independent fermentation experiments, SC-N produced 3.91 g/L of extracellular polysaccharide (EPS), and Fourier transform infrared spectroscopy (FTIR) revealed spectral features consistent with a β-glucan-rich EPS. Comparative genomic analyses showed that, within the selected comparative panel, SC-N contained 131 strain-specific orthologous groups comprising 531 predicted protein-coding genes. The composition of carbohydrate-active enzyme families, particularly glycosyltransferases (GTs), glycoside hydrolases (GHs), and carbohydrate esterases (CEs), differed markedly between SC-N and the closely related reference strain S. commune H4-8. In addition, local tandem duplication patterns were observed in genes associated with ORP/Osh proteins, glucose-6-phosphate dehydrogenase (G6PD), GTP cyclohydrolase II, and the E1 component of 2-oxoglutarate dehydrogenase. The copy number of the GT48 family was generally conserved among the compared strains, whereas differences between SC-N and S. commune H4-8 were observed in the predicted transcription factor-binding motif composition of the upstream regions of FKS1 and FKS2 and in local predicted protein structural features. Collectively, these findings reveal distinctive genomic features of SC-N related to carbohydrate metabolism, membrane homeostasis, and β-glucan-associated functional modules, providing a genomic foundation for further elucidation of its enhanced EPS-producing phenotype and for functional validation of key candidate genes.