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

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

Research output: Contribution to journalArticleScientificpeer-review

711 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)553-560
Number of pages8
JournalNature Biotechnology
Volume26
Issue number5
DOIs
Publication statusPublished - May 2008
MoE publication typeA1 Journal article-refereed

Fingerprint

Hypocrea
Trichoderma
Fungi
Biomass
Genes
Genome
Cellulases
Biofuels
Gene encoding
Carbohydrates
Synteny
Enzymes
Biosynthetic Pathways
Plant Cells
Cell Wall
Polysaccharides
Ecosystem
Metabolites
Ethanol
Soil

Keywords

  • Base Sequence
  • Chromosome Mapping/methods
  • DNA, Fungal/genetics
  • Genome, Fungal/genetics
  • Molecular Sequence Data
  • Sequence Analysis, DNA/methods
  • Trichoderma/classification

Cite this

Martinez, D., Berka, R. M., Henrissat, B., Saloheimo, M., Arvas, M., Baker, S. E., ... Brettin, T. S. (2008). Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology, 26(5), 553-560. https://doi.org/10.1038/nbt1403
Martinez, 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 ; Jackson, Melissa ; Kubicek, Christian P ; Han, Cliff S ; Ho, Isaac ; Larrondo, Luis F ; de Leon, Alfredo Lopez ; Magnuson, Jon K ; Merino, Sandy ; Misra, Monica ; Nelson, Beth ; Putnam, Nicholas ; Robbertse, Barbara ; Salamov, Asaf A ; Schmoll, Monika ; Terry, Astrid ; Thayer, Nina ; Westerholm-Parvinen, Ann ; Schoch, Conrad L ; Yao, Jian ; Barabote, Ravi ; Barbote, Ravi ; Nelson, Mary Anne ; Detter, Chris ; Bruce, David ; Kuske, Cheryl R ; Xie, Gary ; Richardson, Paul ; Rokhsar, Daniel S ; Lucas, Susan M ; Rubin, Edward M ; Dunn-Coleman, Nigel ; Ward, Michael ; Brettin, Thomas S. / Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). In: Nature Biotechnology. 2008 ; Vol. 26, No. 5. pp. 553-560.
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abstract = "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.",
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author = "Diego Martinez and Berka, {Randy M} and Bernard Henrissat and Markku Saloheimo and Mikko Arvas and Baker, {Scott E} and Jarod Chapman and Olga Chertkov and Coutinho, {Pedro M} and Dan Cullen and Danchin, {Etienne G J} and Grigoriev, {Igor V} and Paul Harris and Melissa Jackson and Kubicek, {Christian P} and Han, {Cliff S} and Isaac Ho and Larrondo, {Luis F} and {de Leon}, {Alfredo Lopez} and Magnuson, {Jon K} and Sandy Merino and Monica Misra and Beth Nelson and Nicholas Putnam and Barbara Robbertse and Salamov, {Asaf A} and Monika Schmoll and Astrid Terry and Nina Thayer and Ann Westerholm-Parvinen and Schoch, {Conrad L} and Jian Yao and Ravi Barabote and Ravi Barbote and Nelson, {Mary Anne} and Chris Detter and David Bruce and Kuske, {Cheryl R} and Gary Xie and Paul Richardson and Rokhsar, {Daniel S} and Lucas, {Susan M} and Rubin, {Edward M} and Nigel Dunn-Coleman and Michael Ward and Brettin, {Thomas S}",
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pages = "553--560",
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Martinez, D, Berka, RM, Henrissat, B, Saloheimo, M, Arvas, M, Baker, SE, Chapman, J, Chertkov, O, Coutinho, PM, Cullen, D, Danchin, EGJ, Grigoriev, IV, Harris, P, Jackson, M, Kubicek, CP, Han, CS, Ho, I, Larrondo, LF, de Leon, AL, Magnuson, JK, Merino, S, Misra, M, Nelson, B, Putnam, N, Robbertse, B, Salamov, AA, Schmoll, M, Terry, A, Thayer, N, Westerholm-Parvinen, A, Schoch, CL, Yao, J, Barabote, R, Barbote, R, Nelson, MA, Detter, C, Bruce, D, Kuske, CR, Xie, G, Richardson, P, Rokhsar, DS, Lucas, SM, Rubin, EM, Dunn-Coleman, N, Ward, M & Brettin, TS 2008, 'Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)', Nature Biotechnology, vol. 26, no. 5, pp. 553-560. https://doi.org/10.1038/nbt1403

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). / Martinez, Diego (Corresponding Author); 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; Jackson, Melissa; Kubicek, Christian P; Han, Cliff S; Ho, Isaac; Larrondo, Luis F; de Leon, Alfredo Lopez; Magnuson, Jon K; Merino, Sandy; Misra, Monica; Nelson, Beth; Putnam, Nicholas; Robbertse, Barbara; Salamov, Asaf A; Schmoll, Monika; Terry, Astrid; Thayer, Nina; Westerholm-Parvinen, Ann; Schoch, Conrad L; Yao, Jian; Barabote, Ravi; Barbote, Ravi; Nelson, Mary Anne; Detter, Chris; Bruce, David; Kuske, Cheryl R; Xie, Gary; Richardson, Paul; Rokhsar, Daniel S; Lucas, Susan M; Rubin, Edward M; Dunn-Coleman, Nigel; Ward, Michael; Brettin, Thomas S.

In: Nature Biotechnology, Vol. 26, No. 5, 05.2008, p. 553-560.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

T1 - Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

AU - Martinez, Diego

AU - Berka, Randy M

AU - Henrissat, Bernard

AU - Saloheimo, Markku

AU - Arvas, Mikko

AU - Baker, Scott E

AU - Chapman, Jarod

AU - Chertkov, Olga

AU - Coutinho, Pedro M

AU - Cullen, Dan

AU - Danchin, Etienne G J

AU - Grigoriev, Igor V

AU - Harris, Paul

AU - Jackson, Melissa

AU - Kubicek, Christian P

AU - Han, Cliff S

AU - Ho, Isaac

AU - Larrondo, Luis F

AU - de Leon, Alfredo Lopez

AU - Magnuson, Jon K

AU - Merino, Sandy

AU - Misra, Monica

AU - Nelson, Beth

AU - Putnam, Nicholas

AU - Robbertse, Barbara

AU - Salamov, Asaf A

AU - Schmoll, Monika

AU - Terry, Astrid

AU - Thayer, Nina

AU - Westerholm-Parvinen, Ann

AU - Schoch, Conrad L

AU - Yao, Jian

AU - Barabote, Ravi

AU - Barbote, Ravi

AU - Nelson, Mary Anne

AU - Detter, Chris

AU - Bruce, David

AU - Kuske, Cheryl R

AU - Xie, Gary

AU - Richardson, Paul

AU - Rokhsar, Daniel S

AU - Lucas, Susan M

AU - Rubin, Edward M

AU - Dunn-Coleman, Nigel

AU - Ward, Michael

AU - Brettin, Thomas S

PY - 2008/5

Y1 - 2008/5

N2 - 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.

AB - 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.

KW - Base Sequence

KW - Chromosome Mapping/methods

KW - DNA, Fungal/genetics

KW - Genome, Fungal/genetics

KW - Molecular Sequence Data

KW - Sequence Analysis, DNA/methods

KW - Trichoderma/classification

U2 - 10.1038/nbt1403

DO - 10.1038/nbt1403

M3 - Article

C2 - 18454138

VL - 26

SP - 553

EP - 560

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 5

ER -