Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

Christian P. Kubicek, Alfredo Herrera-Estrella, Verena Seidl-Seiboth, Diego A. Martinez, Irina S. Druzhinina, Michael Thon, Susanne Zeilinger, Sergio Casas-Flores, Benjamin A. Horwitz, Prasun K. Mukherjee, Mala Mukherjee, L. Kredics, Luis D. Alcaraz, Andrea Aerts, Zsuzsanna Antal, Lea Atanasova, Mayte G. Cervantes-Badillo, Jean Challacombe, Olga Chertkov, Kevin McCluskey & 44 others Fanny Coulpier, Nandan Deshpande, Hans von Döhren, Daniel J. Ebbole, Edgardo U. Esquivel-Naranjo, E. Fekete, M. Flipphi, Fabian Glaser, Elida Y. Gómez-Rodríguez, Sabine Gruber, Cliff Han, Bernard Henrissat, Rosa Hermosa, Miguel Hernández-Oñate, L. Karaffa, Idit Kosti, Stéphane Le Crom, Erika Lindquist, Susan Lucas, Mette Lübeck, Peter S. Lübeck, Antoine Margeot, Benjamin Metz, Monica Misra, Helena Nevalainen, Markus Omann, Nicolle Packer, Giancarlo Perrone, Edith E. Uresti-Rivera, Asaf Salamov, Monika Schmoll, Bernhard Seiboth, Harris Shapiro, Serenella Sukno, Juan Antonio Tamayo-Ramos, Doris Tisch, Aric Wiest, Heather H. Wilkinson, Michael Zhang, Pedro M. Coutinho, Charles M. Kenerley, Enrique Monte, Scott E. Baker, Igor V. Grigoriev

Research output: Contribution to journalArticle

268 Citations (Scopus)

Abstract

Background: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.Results: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.Conclusions: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

Original languageEnglish
Article numberR40
JournalGenome Biology
Volume12
Issue number4
DOIs
Publication statusPublished - Apr 18 2011

Fingerprint

Hypocrea
Trichoderma reesei
Trichoderma
Trichoderma virens
lifestyle
Sequence Analysis
Life Style
sequence analysis
genome
Genome
Trichoderma atroviride
biological control
gene
plant protection
fungus
biocontrol agent
Biological Pest Control
common ancestry
Fungi
plant pests

ASJC Scopus subject areas

  • Genetics
  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Kubicek, C. P., Herrera-Estrella, A., Seidl-Seiboth, V., Martinez, D. A., Druzhinina, I. S., Thon, M., ... Grigoriev, I. V. (2011). Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biology, 12(4), [R40]. https://doi.org/10.1186/gb-2011-12-4-r40

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. / Kubicek, Christian P.; Herrera-Estrella, Alfredo; Seidl-Seiboth, Verena; Martinez, Diego A.; Druzhinina, Irina S.; Thon, Michael; Zeilinger, Susanne; Casas-Flores, Sergio; Horwitz, Benjamin A.; Mukherjee, Prasun K.; Mukherjee, Mala; Kredics, L.; Alcaraz, Luis D.; Aerts, Andrea; Antal, Zsuzsanna; Atanasova, Lea; Cervantes-Badillo, Mayte G.; Challacombe, Jean; Chertkov, Olga; McCluskey, Kevin; Coulpier, Fanny; Deshpande, Nandan; von Döhren, Hans; Ebbole, Daniel J.; Esquivel-Naranjo, Edgardo U.; Fekete, E.; Flipphi, M.; Glaser, Fabian; Gómez-Rodríguez, Elida Y.; Gruber, Sabine; Han, Cliff; Henrissat, Bernard; Hermosa, Rosa; Hernández-Oñate, Miguel; Karaffa, L.; Kosti, Idit; Le Crom, Stéphane; Lindquist, Erika; Lucas, Susan; Lübeck, Mette; Lübeck, Peter S.; Margeot, Antoine; Metz, Benjamin; Misra, Monica; Nevalainen, Helena; Omann, Markus; Packer, Nicolle; Perrone, Giancarlo; Uresti-Rivera, Edith E.; Salamov, Asaf; Schmoll, Monika; Seiboth, Bernhard; Shapiro, Harris; Sukno, Serenella; Tamayo-Ramos, Juan Antonio; Tisch, Doris; Wiest, Aric; Wilkinson, Heather H.; Zhang, Michael; Coutinho, Pedro M.; Kenerley, Charles M.; Monte, Enrique; Baker, Scott E.; Grigoriev, Igor V.

In: Genome Biology, Vol. 12, No. 4, R40, 18.04.2011.

Research output: Contribution to journalArticle

Kubicek, CP, Herrera-Estrella, A, Seidl-Seiboth, V, Martinez, DA, Druzhinina, IS, Thon, M, Zeilinger, S, Casas-Flores, S, Horwitz, BA, Mukherjee, PK, Mukherjee, M, Kredics, L, Alcaraz, LD, Aerts, A, Antal, Z, Atanasova, L, Cervantes-Badillo, MG, Challacombe, J, Chertkov, O, McCluskey, K, Coulpier, F, Deshpande, N, von Döhren, H, Ebbole, DJ, Esquivel-Naranjo, EU, Fekete, E, Flipphi, M, Glaser, F, Gómez-Rodríguez, EY, Gruber, S, Han, C, Henrissat, B, Hermosa, R, Hernández-Oñate, M, Karaffa, L, Kosti, I, Le Crom, S, Lindquist, E, Lucas, S, Lübeck, M, Lübeck, PS, Margeot, A, Metz, B, Misra, M, Nevalainen, H, Omann, M, Packer, N, Perrone, G, Uresti-Rivera, EE, Salamov, A, Schmoll, M, Seiboth, B, Shapiro, H, Sukno, S, Tamayo-Ramos, JA, Tisch, D, Wiest, A, Wilkinson, HH, Zhang, M, Coutinho, PM, Kenerley, CM, Monte, E, Baker, SE & Grigoriev, IV 2011, 'Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma', Genome Biology, vol. 12, no. 4, R40. https://doi.org/10.1186/gb-2011-12-4-r40
Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M et al. Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. Genome Biology. 2011 Apr 18;12(4). R40. https://doi.org/10.1186/gb-2011-12-4-r40
Kubicek, Christian P. ; Herrera-Estrella, Alfredo ; Seidl-Seiboth, Verena ; Martinez, Diego A. ; Druzhinina, Irina S. ; Thon, Michael ; Zeilinger, Susanne ; Casas-Flores, Sergio ; Horwitz, Benjamin A. ; Mukherjee, Prasun K. ; Mukherjee, Mala ; Kredics, L. ; Alcaraz, Luis D. ; Aerts, Andrea ; Antal, Zsuzsanna ; Atanasova, Lea ; Cervantes-Badillo, Mayte G. ; Challacombe, Jean ; Chertkov, Olga ; McCluskey, Kevin ; Coulpier, Fanny ; Deshpande, Nandan ; von Döhren, Hans ; Ebbole, Daniel J. ; Esquivel-Naranjo, Edgardo U. ; Fekete, E. ; Flipphi, M. ; Glaser, Fabian ; Gómez-Rodríguez, Elida Y. ; Gruber, Sabine ; Han, Cliff ; Henrissat, Bernard ; Hermosa, Rosa ; Hernández-Oñate, Miguel ; Karaffa, L. ; Kosti, Idit ; Le Crom, Stéphane ; Lindquist, Erika ; Lucas, Susan ; Lübeck, Mette ; Lübeck, Peter S. ; Margeot, Antoine ; Metz, Benjamin ; Misra, Monica ; Nevalainen, Helena ; Omann, Markus ; Packer, Nicolle ; Perrone, Giancarlo ; Uresti-Rivera, Edith E. ; Salamov, Asaf ; Schmoll, Monika ; Seiboth, Bernhard ; Shapiro, Harris ; Sukno, Serenella ; Tamayo-Ramos, Juan Antonio ; Tisch, Doris ; Wiest, Aric ; Wilkinson, Heather H. ; Zhang, Michael ; Coutinho, Pedro M. ; Kenerley, Charles M. ; Monte, Enrique ; Baker, Scott E. ; Grigoriev, Igor V. / Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma. In: Genome Biology. 2011 ; Vol. 12, No. 4.
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abstract = "Background: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.Results: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96{\%}), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.Conclusions: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.",
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T1 - Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

AU - Kubicek, Christian P.

AU - Herrera-Estrella, Alfredo

AU - Seidl-Seiboth, Verena

AU - Martinez, Diego A.

AU - Druzhinina, Irina S.

AU - Thon, Michael

AU - Zeilinger, Susanne

AU - Casas-Flores, Sergio

AU - Horwitz, Benjamin A.

AU - Mukherjee, Prasun K.

AU - Mukherjee, Mala

AU - Kredics, L.

AU - Alcaraz, Luis D.

AU - Aerts, Andrea

AU - Antal, Zsuzsanna

AU - Atanasova, Lea

AU - Cervantes-Badillo, Mayte G.

AU - Challacombe, Jean

AU - Chertkov, Olga

AU - McCluskey, Kevin

AU - Coulpier, Fanny

AU - Deshpande, Nandan

AU - von Döhren, Hans

AU - Ebbole, Daniel J.

AU - Esquivel-Naranjo, Edgardo U.

AU - Fekete, E.

AU - Flipphi, M.

AU - Glaser, Fabian

AU - Gómez-Rodríguez, Elida Y.

AU - Gruber, Sabine

AU - Han, Cliff

AU - Henrissat, Bernard

AU - Hermosa, Rosa

AU - Hernández-Oñate, Miguel

AU - Karaffa, L.

AU - Kosti, Idit

AU - Le Crom, Stéphane

AU - Lindquist, Erika

AU - Lucas, Susan

AU - Lübeck, Mette

AU - Lübeck, Peter S.

AU - Margeot, Antoine

AU - Metz, Benjamin

AU - Misra, Monica

AU - Nevalainen, Helena

AU - Omann, Markus

AU - Packer, Nicolle

AU - Perrone, Giancarlo

AU - Uresti-Rivera, Edith E.

AU - Salamov, Asaf

AU - Schmoll, Monika

AU - Seiboth, Bernhard

AU - Shapiro, Harris

AU - Sukno, Serenella

AU - Tamayo-Ramos, Juan Antonio

AU - Tisch, Doris

AU - Wiest, Aric

AU - Wilkinson, Heather H.

AU - Zhang, Michael

AU - Coutinho, Pedro M.

AU - Kenerley, Charles M.

AU - Monte, Enrique

AU - Baker, Scott E.

AU - Grigoriev, Igor V.

PY - 2011/4/18

Y1 - 2011/4/18

N2 - Background: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.Results: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.Conclusions: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

AB - Background: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma.Results: Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis) and Trichoderma virens (formerly Gliocladium virens, teleomorph Hypocrea virens), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride. The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei.Conclusions: The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.

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