The phylogenomic and molecular clock analysis of saprophytic (straw-degrading and wood-degrading) basidiomycota including 21 fungal genomes showed that wood-degrading fungi was more ancient and the divergence time occurred 346 million years ago ; Analysis of gene family showed that compared to the large-scale gene loss (average contraction size of 1899) in pathogenic fungi, saprophytic basidiomycota have the small size change; Comparison on gene families showed that there was a significant expansion of large size gene families (> 161) in straw-degrading fungi, such as F-box domain genes that play a role in protein ubiquitination.