Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

By Diego Martinez, R. Berka, Bernard Henrissat, M. Saloheimo, M. Arvas, S. Baker, J. Chapman, O. Chertkov, Pedro M. Coutinho, Dan Cullen and 35 more. Nature Biotechnology, 2008

807 citations recorded by the source corpus.

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.

Subfields: Biomedical Engineering, Biotechnology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e6dd2309a9fc1b95c1fbe3ea04849d912c0c1b85

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In Biomedical Engineering

1. C. Ivanova
2. Thomas W. Jeffries
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4. André Schuster
5. M. Schmoll
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In Biotechnology

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8. T. Suryanarayanan

Citations in the corpus

• Trichoderma reesei: A Fungal Enzyme Producer for Cellulosic Biofuels (2011, methodology): “The genome sequence of T. reesei QM6a was published in 2008 (Martinez et al., 2008) and currently two further annotated genome sequences of Trichoderma species i.e. the mycoparasitic and biocontrol fungi T. atroviride and T. virens (Kubicek et al., 2011) are available via the Joint Genome Institute…”
• Fueling the future with fungal genomics (2011, methodology): “Another industrially utilized and sequenced fungus, Trichoderma reesei (Martinez et al. 2008), produces large amounts of enzymes employed in breaking cellulose into simple sugars (glucose and xylose).”
• Fungal endophytes: an untapped source of biocatalysts (2012, background): “…some plant pathogenic fungi have more cellulases, hemicellulases, pectinases, carbohydrate-binding modules, carbohydrate esterases, and polysaccharide lyases; notably, they also produce unique glycosyl hydrolases that are not coded by T. reesei (Paper et al. 2007; Martinez et al. 2008 ).”
• Biology and biotechnology of Trichoderma (2010, background): “…the genomes of three strains representing the most important applications of this genus: The genome sequence of T. reesei, the industrial workhorse (Martinez et al. 2008; http://genome.jgi-psf.org/ Trire2/Trire2.home.html), surprisingly revealed that, despite its importance in industrial cellulase…”