Publication - Journal Article The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

Microbiology and Molecular Biology Reviews, vol. 80, iss. 1, pp. 205-327, 2016

Monika Schmoll, Christoph Dattenböck, Nohemí Carreras-Villaseñor, Artemio Mendoza-Mendoza, Doris Tisch, Mario Ivan Alemán, Scott E. Baker, Christopher Brown, Mayte Guadalupe Cervantes-Badillo, José Cetz-Chel, Gema Rosa Cristobal-Mondragon, Luis Delaye, Edgardo Ulises Esquivel-Naranjo, Alexa Frischmann, Jose de Jesus Gallardo-Negrete, Monica García-Esquivel, Elida Yazmin Gomez-Rodriguez, David R. Greenwood, Miguel Hernández-Oñate, Joanna S. Kruszewska, Robert Lawry, Hector M. Mora-Montes, Tania Muñoz-Centeno, Maria Fernanda Nieto-Jacobo, Guillermo Nogueira Lopez, Vianey Olmedo-Monfil, Macario Osorio-Concepcion, Sebastian Piłsyk, Kyle R. Pomraning, Aroa Rodriguez-Iglesias, Maria Teresa Rosales-Saavedra, J. Alejandro Sánchez-Arreguín, Verena Seidl-Seiboth, Alison Stewart, Edith Elena Uresti-Rivera, Chih-Li Wang, Ting-Fang Wang, Susanne Zeilinger, Sergio Casas-Flores, Alfredo Herrera-Estrella

SUMMARY The genus Trichoderma contains 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 in T. reesei , T. atroviride , and T. 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 each Trichoderma species 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 in N -linked glycosylation was detected, as were indications for the ability of Trichoderma spp. to generate hybrid galactose-containing N -linked glycans. The genomic inventory of effector proteins revealed numerous compounds unique to Trichoderma , and these warrant further investigation. We found interesting expansions in the Trichoderma genus in several signaling pathways, such as G-protein-coupled receptors, RAS GTPases, and casein kinases. A particularly interesting feature absolutely unique to T. atroviride is the duplication of the alternative sulfur amino acid synthesis pathway.