title: The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species.
abstract: 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.
authors: Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria monika.schmoll@ait.ac.at aherrera@langebio.cinvestav.mx.
authors: Monika
authors: M
authors: Schmoll
authors: Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria.
authors: Christoph
authors: C
authors: Dattenböck
authors: LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico.
authors: Nohemí
authors: N
authors: Carreras-Villaseñor
authors: Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand.
authors: Artemio
authors: A
authors: Mendoza-Mendoza
authors: Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria.
authors: Doris
authors: D
authors: Tisch
authors: Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico.
authors: Mario Ivan
authors: MI
authors: Alemán
authors: Pacific Northwest National Laboratory, Richland, Washington, USA.
authors: Scott E
authors: SE
authors: Baker
authors: University of Otago, Department of Biochemistry and Genetics, Dunedin, New Zealand.
authors: Christopher
authors: C
authors: Brown
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Mayte Guadalupe
authors: MG
authors: Cervantes-Badillo
authors: LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico.
authors: José
authors: J
authors: Cetz-Chel
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Gema Rosa
authors: GR
authors: Cristobal-Mondragon
authors: Cinvestav, Department of Genetic Engineering, Irapuato, Guanajuato, Mexico.
authors: Luis
authors: L
authors: Delaye
authors: LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico.
authors: Edgardo Ulises
authors: EU
authors: Esquivel-Naranjo
authors: Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria.
authors: Alexa
authors: A
authors: Frischmann
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Jose de Jesus
authors: Jde J
authors: Gallardo-Negrete
authors: LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico.
authors: Monica
authors: M
authors: García-Esquivel
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Elida Yazmin
authors: EY
authors: Gomez-Rodriguez
authors: The University of Auckland, School of Biological Sciences, Auckland, New Zealand.
authors: David R
authors: DR
authors: Greenwood
authors: LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico.
authors: Miguel
authors: M
authors: Hernández-Oñate
authors: Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland.
authors: Joanna S
authors: JS
authors: Kruszewska
authors: Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand.
authors: Robert
authors: R
authors: Lawry
authors: University of Guanajuato, Department of Biology, Guanajuato, Guanajuato, Mexico.
authors: Hector M
authors: HM
authors: Mora-Montes
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Tania
authors: T
authors: Muñoz-Centeno
authors: Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand.
authors: Maria Fernanda
authors: MF
authors: Nieto-Jacobo
authors: Lincoln University, Bio-Protection Research Centre, Lincoln, Canterbury, New Zealand.
authors: Guillermo
authors: G
authors: Nogueira Lopez
authors: University of Guanajuato, Department of Biology, Guanajuato, Guanajuato, Mexico.
authors: Vianey
authors: V
authors: Olmedo-Monfil
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Macario
authors: M
authors: Osorio-Concepcion
authors: Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Laboratory of Fungal Glycobiology, Warsaw, Poland.
authors: Sebastian
authors: S
authors: Piłsyk
authors: Pacific Northwest National Laboratory, Richland, Washington, USA.
authors: Kyle R
authors: KR
authors: Pomraning
authors: Austrian Institute of Technology, Department Health and Environment, Bioresources Unit, Tulln, Austria.
authors: Aroa
authors: A
authors: Rodriguez-Iglesias
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Maria Teresa
authors: MT
authors: Rosales-Saavedra
authors: LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico.
authors: J Alejandro
authors: JA
authors: Sánchez-Arreguín
authors: Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria.
authors: Verena
authors: V
authors: Seidl-Seiboth
authors: Marrone Bio Innovations, Davis, California, USA.
authors: Alison
authors: A
authors: Stewart
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Edith Elena
authors: EE
authors: Uresti-Rivera
authors: National Chung-Hsing University, Department of Plant Pathology, Taichung, Taiwan.
authors: Chih-Li
authors: CL
authors: Wang
authors: Academia Sinica, Institute of Molecular Biology, Taipei, Taiwan.
authors: Ting-Fang
authors: TF
authors: Wang
authors: Research Division Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, Vienna, Austria University of Innsbruck, Institute of Microbiology, Innsbruck, Austria.
authors: Susanne
authors: S
authors: Zeilinger
authors: IPICYT, Molecular Biology Division, San Luis Potosí, Mexico.
authors: Sergio
authors: S
authors: Casas-Flores
authors: LANGEBIO, National Laboratory of Genomics for Biodiversity, Cinvestav-Irapuato, Guanajuato, Mexico monika.schmoll@ait.ac.at aherrera@langebio.cinvestav.mx.
authors: Alfredo
authors: A
authors: Herrera-Estrella
mesh_terms: D042002:Chromatin Assembly and Disassembly; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D051548:Histone Acetyltransferases / Q000235:genetics / Q000378:metabolism; D006655:Histone Deacetylases / Q000235:genetics / Q000378:metabolism; D006657:Histones / Q000235:genetics / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics; D010802:Phylogeny; D011499:Protein Processing, Post-Translational; D017434:Protein Structure, Tertiary; D015398:Signal Transduction; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014242:Trichoderma / Q000145:classification / Q000235:genetics* / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D006657:Histones; D014157:Transcription Factors; D051548:Histone Acetyltransferases; D006655:Histone Deacetylases