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Title: The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Abstract

SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in severalmore » signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.« less


Citation Formats

Schmoll, Monika, Dattenböck, Christoph, Carreras-Villaseñor, Nohemí, Mendoza-Mendoza, Artemio, Tisch, Doris, Alemán, Mario Ivan, Baker, Scott E., Brown, Christopher, Cervantes-Badillo, Mayte Guadalupe, Cetz-Chel, José, Cristobal-Mondragon, Gema Rosa, Delaye, Luis, Esquivel-Naranjo, Edgardo Ulises, Frischmann, Alexa, Gallardo-Negrete, Jose de Jesus, García-Esquivel, Monica, Gomez-Rodriguez, Elida Yazmin, Greenwood, David R., Hernández-Oñate, Miguel, Kruszewska, Joanna S., Lawry, Robert, Mora-Montes, Hector M., Muñoz-Centeno, Tania, Nieto-Jacobo, Maria Fernanda, Nogueira Lopez, Guillermo, Olmedo-Monfil, Vianey, Osorio-Concepcion, Macario, Piłsyk, Sebastian, Pomraning, Kyle R., Rodriguez-Iglesias, Aroa, Rosales-Saavedra, Maria Teresa, Sánchez-Arreguín, J. Alejandro, Seidl-Seiboth, Verena, Stewart, Alison, Uresti-Rivera, Edith Elena, Wang, Chih-Li, Wang, Ting-Fang, Zeilinger, Susanne, Casas-Flores, Sergio, and Herrera-Estrella, Alfredo. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. United States: N. p., 2016. Web. doi:10.1128/MMBR.00040-15.
Schmoll, Monika, Dattenböck, Christoph, Carreras-Villaseñor, Nohemí, Mendoza-Mendoza, Artemio, Tisch, Doris, Alemán, Mario Ivan, Baker, Scott E., Brown, Christopher, Cervantes-Badillo, Mayte Guadalupe, Cetz-Chel, José, Cristobal-Mondragon, Gema Rosa, Delaye, Luis, Esquivel-Naranjo, Edgardo Ulises, Frischmann, Alexa, Gallardo-Negrete, Jose de Jesus, García-Esquivel, Monica, Gomez-Rodriguez, Elida Yazmin, Greenwood, David R., Hernández-Oñate, Miguel, Kruszewska, Joanna S., Lawry, Robert, Mora-Montes, Hector M., Muñoz-Centeno, Tania, Nieto-Jacobo, Maria Fernanda, Nogueira Lopez, Guillermo, Olmedo-Monfil, Vianey, Osorio-Concepcion, Macario, Piłsyk, Sebastian, Pomraning, Kyle R., Rodriguez-Iglesias, Aroa, Rosales-Saavedra, Maria Teresa, Sánchez-Arreguín, J. Alejandro, Seidl-Seiboth, Verena, Stewart, Alison, Uresti-Rivera, Edith Elena, Wang, Chih-Li, Wang, Ting-Fang, Zeilinger, Susanne, Casas-Flores, Sergio, & Herrera-Estrella, Alfredo. The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species. United States. doi:10.1128/MMBR.00040-15.
Schmoll, Monika, Dattenböck, Christoph, Carreras-Villaseñor, Nohemí, Mendoza-Mendoza, Artemio, Tisch, Doris, Alemán, Mario Ivan, Baker, Scott E., Brown, Christopher, Cervantes-Badillo, Mayte Guadalupe, Cetz-Chel, José, Cristobal-Mondragon, Gema Rosa, Delaye, Luis, Esquivel-Naranjo, Edgardo Ulises, Frischmann, Alexa, Gallardo-Negrete, Jose de Jesus, García-Esquivel, Monica, Gomez-Rodriguez, Elida Yazmin, Greenwood, David R., Hernández-Oñate, Miguel, Kruszewska, Joanna S., Lawry, Robert, Mora-Montes, Hector M., Muñoz-Centeno, Tania, Nieto-Jacobo, Maria Fernanda, Nogueira Lopez, Guillermo, Olmedo-Monfil, Vianey, Osorio-Concepcion, Macario, Piłsyk, Sebastian, Pomraning, Kyle R., Rodriguez-Iglesias, Aroa, Rosales-Saavedra, Maria Teresa, Sánchez-Arreguín, J. Alejandro, Seidl-Seiboth, Verena, Stewart, Alison, Uresti-Rivera, Edith Elena, Wang, Chih-Li, Wang, Ting-Fang, Zeilinger, Susanne, Casas-Flores, Sergio, and Herrera-Estrella, Alfredo. Wed . "The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species". United States. doi:10.1128/MMBR.00040-15.
@article{osti_1333999,
title = {The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species},
author = {Schmoll, Monika and Dattenböck, Christoph and Carreras-Villaseñor, Nohemí and Mendoza-Mendoza, Artemio and Tisch, Doris and Alemán, Mario Ivan and Baker, Scott E. and Brown, Christopher and Cervantes-Badillo, Mayte Guadalupe and Cetz-Chel, José and Cristobal-Mondragon, Gema Rosa and Delaye, Luis and Esquivel-Naranjo, Edgardo Ulises and Frischmann, Alexa and Gallardo-Negrete, Jose de Jesus and García-Esquivel, Monica and Gomez-Rodriguez, Elida Yazmin and Greenwood, David R. and Hernández-Oñate, Miguel and Kruszewska, Joanna S. and Lawry, Robert and Mora-Montes, Hector M. and Muñoz-Centeno, Tania and Nieto-Jacobo, Maria Fernanda and Nogueira Lopez, Guillermo and Olmedo-Monfil, Vianey and Osorio-Concepcion, Macario and Piłsyk, Sebastian and Pomraning, Kyle R. and Rodriguez-Iglesias, Aroa and Rosales-Saavedra, Maria Teresa and Sánchez-Arreguín, J. Alejandro and Seidl-Seiboth, Verena and Stewart, Alison and Uresti-Rivera, Edith Elena and Wang, Chih-Li and Wang, Ting-Fang and Zeilinger, Susanne and Casas-Flores, Sergio and Herrera-Estrella, Alfredo},
abstractNote = {SUMMARYThe genusTrichodermacontains fungi with high relevance for humans, with applications in enzyme production for plant cell wall degradation and use in biocontrol. Here, we provide a broad, comprehensive overview of the genomic content of these species for “hot topic” research aspects, including CAZymes, transport, transcription factors, and development, along with a detailed analysis and annotation of less-studied topics, such as signal transduction, genome integrity, chromatin, photobiology, or lipid, sulfur, and nitrogen metabolism inT. reesei,T. atroviride, andT. virens, and we open up new perspectives to those topics discussed previously. In total, we covered more than 2,000 of the predicted 9,000 to 11,000 genes of eachTrichodermaspecies discussed, which is >20% of the respective gene content. Additionally, we considered available transcriptome data for the annotated genes. Highlights of our analyses include overall carbohydrate cleavage preferences due to the different genomic contents and regulation of the respective genes. We found light regulation of many sulfur metabolic genes. Additionally, a new Golgi 1,2-mannosidase likely involved inN-linked glycosylation was detected, as were indications for the ability ofTrichodermaspp. to generate hybrid galactose-containingN-linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique toTrichoderma, and these warrant further investigation. We found interesting expansions in theTrichodermagenus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique toT. atrovirideis the duplication of the alternative sulfur amino acid synthesis pathway.},
doi = {10.1128/MMBR.00040-15},
journal = {Microbiology and Molecular Biology Reviews},
number = 1,
volume = 80,
place = {United States},
year = {Wed Feb 10 00:00:00 EST 2016},
month = {Wed Feb 10 00:00:00 EST 2016}
}