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

Martínez, Diego; Berka, Randy M.; Henrissat, Bernard; Saloheimo, Markku; Arvas, Mikko; Baker, Scott E.; Chapman, Jarod; Chertkov, Olga; Coutinho, Pedro M.; Cullen, Dan; Danchin, Etienne G. J.; Grigoriev, Igor V.; Harris, Paul V.; Jackson, Melissa F.; Kubicek, Christian P.; Han, Cliff; Ho, Isaac; Larrondo, Luis F.; Leon, Alfredo Lopez de; Magnuson, Jon; Merino, Sandy; Misra, Monica; Nelson, Beth A.; Putnam, Nicholas H.; Robbertse, Barbara; Salamov, Asaf; Schmoll, Monika; Terry, Astrid; Thayer, Nina; Westerholm-Parvinen, Ann; Schoch, Conrad L.; Yao, Jian; Barabote, Ravi D.; Nelson, Mary Anne; Detter, Chris; Bruce, David; Kuske, Cheryl R.; Xie, Gary; Richardson, Paul; Rokhsar, Daniel S.; Lucas, Susan; Rubin, Edward M.; Dunn-Coleman, Nigel; Ward, Michael P.; Brettin, Thomas

doi:10.1038/nbt1403

Cited by 1,092 publications

(976 citation statements)

References 49 publications

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“…We have selected (a) 14 popular white rot fungal strains – Ceriporiopsis subvermispora B (Fernandez-Fueyo et al 2012), Heterobasidion annosum v2.0 (Olson et al 2012), Fomitiporia mediterranea v1.0 (Floudas et al 2012), Phanerochaete carnosa HHB-10118 (Suzuki et al 2012), Pycnoporus cinnabarinus BRFM 137 (Levasseur et al 2014), Phanerochaete chrysosporium R78 v2.2 (Martinez et al 2004; Ohm et al 2014), Dichomitus squalens LYAD-421 SS1 (Floudas et al 2012), Trametes versicolor v1.0 (Floudas et al 2012), Punctularia strigosozonata v1.0 (Floudas et al 2012), Phlebia brevispora HHB-7030 SS6 (Binder et al 2013), Botrytis cinerea v1.0 (Amselem et al 2011), Pleurotus ostreatus PC15 v2.0 (Riley et al 2014; Alfaro et al 2016; Castanera et al 2016), Stereum hirsutum FP-91666 SS1 v1.0 (Floudas et al 2012), Pleurotus eryngii ATCC90797 (Guillen et al 1992; Camarero et al 1999; Ruiz‐Dueñas et al 1999; Matheny et al 2006); (b) 15 popular brown rot fungal strains – Postia placenta MAD 698-R v1.0 (Martinez et al 2009), Fibroporia radiculosa TFFH 294 (Tang et al 2012), Wolfiporia cocos MD-104 SS10 v1.0 (Floudas et al 2012), Dacryopinax primogenitus DJM 731 SSP1 v1.0 (Floudas et al 2012), Daedalea quercina v1.0 (Nagy et al 2015), Laetiporus sulphureus var v1.0 (Nagy et al 2015), Postia placenta MAD-698-R-SB12 v1.0 (Martinez et al 2009), Neolentinus lepideus v1.0 (Nagy et al 2015), Serpula lacrymans S7.9 v2.0 (Eastwood et al 2011), Calocera cornea v1.0 (Eastwood et al 2011), Gloeophyllum trabeum v1.0 (Floudas et al 2012), Fistulina hepatica v1.0 (Floudas et al 2015), Fomitopsis pinicola FP-58527 SS1 (Floudas et al 2015), Hydnomerulius pinastri v2.0 (Kohler et al 2015) and Coniophora puteana v1.0 (Kohler et al 2015); (c) 13 popular soft rot fungal strains – Trichoderma reesei v 2.0 (Martinez et al 2008), Rhizopus oryzae 99-880 from Broad (Ma et al 2009), Aspergillus wentii v1.0 (De Vries et al 2017), Penicillium chrysogenum Wisconsin 54-1255 (Van Den Berg et al 2008), Daldinia eschscholzii EC12 v1.0, Hypoxylon sp. CI-4A v1.0 (Wu et al 2017), Aspergillus niger ATCC 1015 v4.0 (Andersen et al 2011), Hypoxylon sp.…”

Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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We have conducted a genome-level comparative study of basidiomycetes wood-rotting fungi (white, brown and soft rot) to understand the total plant biomass (lignin, cellulose, hemicellulose and pectin) -degrading abilities. We have retrieved the genome-level annotations of well-known 14 white rot fungi, 15 brown rot fungi and 13 soft rot fungi. Based on the previous literature and the annotations obtained from CAZy (carbohydrate-active enzyme) database, we have separated the genome-wide CAZymes of the selected fungi into lignin-, cellulose-, hemicellulose- and pectin-degrading enzymes. Results obtained in our study reveal that white rot fungi, especially Pleurotus eryngii and Pleurotus ostreatus potentially possess high ligninolytic ability, and soft rot fungi, especially Botryosphaeria dothidea and Fusarium oxysporum sp., potentially possess high cellulolytic, hemicellulolytic and pectinolytic abilities. The total number of genes encoding for cytochrome P450 monooxygenases and metabolic processes were high in soft and white rot fungi. We have tentatively calculated the overall lignocellulolytic abilities among the selected wood-rotting fungi which suggests that white rot fungi possess higher lignin and soft rot fungi potentially possess higher cellulolytic, hemicellulolytic and pectinolytic abilities. This approach can be applied industrially to efficiently find lignocellulolytic and aromatic compound-degrading fungi based on their genomic abilities.

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Section: Methodsmentioning

confidence: 99%

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

2017

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“…Trichoderma reesei is the major fungus used for industrial cellulase production. The secreted cellulases comprise two cellobiohydrolases and eight endoglucanases from six glycoside hydrolase families [3] which act in a synergistic manner to degrade the plant biomass, together with beta-glucosidases and hemicellulases. In total, the T. reesei genome contains 200 glycoside hydrolases and more than 20 of them can be found in the secretome [3,4].…”

Section: Introductionmentioning

confidence: 99%

“…The secreted cellulases comprise two cellobiohydrolases and eight endoglucanases from six glycoside hydrolase families [3] which act in a synergistic manner to degrade the plant biomass, together with beta-glucosidases and hemicellulases. In total, the T. reesei genome contains 200 glycoside hydrolases and more than 20 of them can be found in the secretome [3,4]. It is supposed that the presence of multiple enzymes displaying the same type of activity (as is the case for endoglucanases) is necessary for efficient biomass hydrolysis, but the precise role of the individual enzymes is still not well understood.…”

Section: Introductionmentioning

confidence: 99%

Optimization of a synthetic mixture composed of major Trichoderma reesei enzymes for the hydrolysis of steam-exploded wheat straw

Billard

Faraj

Ferreira

et al. 2012

Biotechnol Biofuels

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BackgroundAn efficient hydrolysis of lignocellulosic substrates to soluble sugars for biofuel production necessitates the interplay and synergistic interaction of multiple enzymes. An optimized enzyme mixture is crucial for reduced cost of the enzymatic hydrolysis step in a bioethanol production process and its composition will depend on the substrate and type of pretreatment used. In the present study, an experimental design was used to determine the optimal composition of a Trichoderma reesei enzyme mixture, comprising the main cellulase and hemicellulase activities, for the hydrolysis of steam-exploded wheat straw.MethodsSix enzymes, CBH1 (Cel7a), CBH2 (Cel6a), EG1 (Cel7b), EG2 (Cel5a), as well as the xyloglucanase Cel74a and the xylanase XYN1 (Xyl11a) were purified from a T. reesei culture under lactose/xylose-induced conditions. Sugar release was followed in milliliter-scale hydrolysis assays for 48 hours and the influence of the mixture on initial conversion rates and final yields is assessed.ResultsThe developed model could show that both responses were strongly correlated. Model predictions suggest that optimal hydrolysis yields can be obtained over a wide range of CBH1 to CBH2 ratios, but necessitates a high proportion of EG1 (13% to 25%) which cannot be replaced by EG2. Whereas 5% to 10% of the latter enzyme and a xylanase content above 6% are required for highest yields, these enzymes are predicted to be less important in the initial stage of hydrolysis.ConclusionsThe developed model could reliably predict hydrolysis yields of enzyme mixtures in the studied domain and highlighted the importance of the respective enzyme components in both the initial and the final hydrolysis phase of steam-exploded wheat straw.

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“…The Trichoderma karyotype was shown to be comprised of six large chromosomes (Gilly & Sands 1991) similar to karyotypes of Neurospora (Orbach et al 1988) and other filamentous ascomycetes (Mills & McCluskey 1990). The genome sequence for the reference strain of T. reesei (Martinez et al 2008) indicated that biomass degraded enzymes were clustered in the genome and served as the basis for early resequencing studies on high cellulase-producing strains (Le Crom et al 2009; Koike et al 2013). …”

Section: Pathogenic Aspergillimentioning

confidence: 99%

“…Similarly, to facilitate the understanding of Trichoderma , a public taxonomy database at http://www.isth.info/spans the transition from morphological taxonomy to molecular taxonomy and includes barcode sequences and protocols, although it has not been updated recently. Genome data supporting the Trichoderma research community include publicly available assembled genome sequences for several species (Martinez et al 2008; Druzhinina et al 2011; Kubicek et al 2011). While not as prolific as for other fungi, public sequence resources at the NCBI Short Read Archive include 76 genome sequence and one transcriptome sequence.…”

Section: Pathogenic Aspergillimentioning

confidence: 99%

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

McCluskey

Baker

2017

Mycology

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Filamentous fungi have been important as model organisms since the beginning of modern biological inquiry and have benefitted from open data since the earliest genetic maps were shared. From early origins in simple Mendelian genetics of mating types, parasexual genetics of colony colour, and the foundational demonstration of the segregation of a nutritional requirement, the contribution of research systems utilising filamentous fungi has spanned the biochemical genetics era, through the molecular genetics era, and now are at the very foundation of diverse omics approaches to research and development. Fungal model organisms have come from most major taxonomic groups although Ascomycete filamentous fungi have seen the most major sustained effort. In addition to the published material about filamentous fungi, shared molecular tools have found application in every area of fungal biology. Similarly, shared data has contributed to the success of model systems. The scale of data supporting research with filamentous fungi has grown by 10 to 12 orders of magnitude. From genetic to molecular maps, expression databases, and finally genome resources, the open and collaborative nature of the research communities has assured that the rising tide of data has lifted all of the research systems together.

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

Cited by 1,092 publications

References 49 publications

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Comparative study of genome-wide plant biomass-degrading CAZymes in white rot, brown rot and soft rot fungi

Optimization of a synthetic mixture composed of major Trichoderma reesei enzymes for the hydrolysis of steam-exploded wheat straw

Diverse data supports the transition of filamentous fungal model organisms into the post-genomics era

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