The Basidiomycete fungus Schizophyllum commune is a wood-decaying fungus and is used as a model system to study lignocellulose degradation. Version 3.0 of the genome assembly filled 269 of 316 sequence gaps and added 680 kb of sequence. This new assembly was reannotated using RNAseq transcriptomics data, and this resulted in 3110 (24percent) more genes.Two additional S. commune strains with different wood-decaying properties were sequenced, from Tattone (France) and Loenen (The Netherlands). Sequence comparison shows remarkably high sequence diversity between the strains. The overall SNP rate of > 100 SNPs/kb is among the highest rates of within-species polymorphisms in Basidiomycetes. Some well-described proteins like hydrophobins and transcription factors have less than 70percent sequence identity among the strains. Some chromosomes are better conserved than others and in some cases large parts of chromosomes are missing from one or more strains.Gene expression on glucose, cellulose and wood was analyzed in two S. commune strains. Overall, gene expression correlated between the two strains, but there were some notable exceptions. Of particular interest are CAZymes (carbohydrate-active enzymes) that are regulated in different ways in the different strains.In both strains the transcription factor Fsp1 was strongly up-regulated during growth on cellulose and wood, when compared to glucose. Over-expression of Fsp1 using a constitutive promoter resulted in higher cellulose and xylose-degrading enzyme activity, which suggests that Fsp1 is involved in regulating CAZyme gene expression.Two CAZyme genes (of family GH61 and GH11) were shown to be strongly up-regulated during growth on cellulose, compared to glucose. Proteomics on the secreted proteins in the growth medium confirmed this. A promoter analysis revealed the shortest active promoters for these two genes, as well as putative transcription factor binding sites.