Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production.

Trichoderma reesei (teleomorph Hypocrea jecorina) is a mesophilic soft-rot ascomycete fungus that is widely used in industry as a source of cellulases and hemicellulases for the hydrolysis of plant cell wall polysaccharides. For many years after its discovery during World War II1, T. reesei was believed to reproduce asexually. However, although it was subsequently shown to be the anamorph of the pantropical ascomycete Hypocrea jecorina2, the organism remains most widely recognized by its former name. It has enjoyed a long history of safe use for industrial enzyme production3 and as an important model system for studying lignocellulose degradation. Lignocellulosic biomass from agricultural crop residues, grasses, wood and municipal solid waste represents an abundant renewable