title: Analysis of genomic regions of Trichoderma harzianum IOC-3844 related to biomass degradation.
abstract: Trichoderma harzianum IOC-3844 secretes high levels of cellulolytic-active enzymes and is therefore a promising strain for use in biotechnological applications in second-generation bioethanol production. However, the T. harzianum biomass degradation mechanism has not been well explored at the genetic level. The present work investigates six genomic regions (~150 kbp each) in this fungus that are enriched with genes related to biomass conversion. A BAC library consisting of 5,760 clones was constructed, with an average insert length of 90 kbp. The assembled BAC sequences revealed 232 predicted genes, 31.5% of which were related to catabolic pathways, including those involved in biomass degradation. An expression profile analysis based on RNA-Seq data demonstrated that putative regulatory elements, such as membrane transport proteins and transcription factors, are located in the same genomic regions as genes related to carbohydrate metabolism and exhibit similar expression profiles. Thus, we demonstrate a rapid and efficient tool that focuses on specific genomic regions by combining a BAC library with transcriptomic data. This is the first BAC-based structural genomic study of the cellulolytic fungus T. harzianum, and its findings provide new perspectives regarding the use of this species in biomass degradation processes.
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
authors.forename: Aline
authors.initials: A
authors.lastname: Crucello
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
authors.forename: Danilo Augusto
authors.initials: DA
authors.lastname: Sforça
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
authors.forename: Maria Augusta Crivelente
authors.initials: MA
authors.lastname: Horta
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
authors.forename: Clelton Aparecido
authors.initials: CA
authors.lastname: dos Santos
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
authors.forename: Américo José Carvalho
authors.initials: AJ
authors.lastname: Viana
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
authors.forename: Lilian Luzia
authors.initials: LL
authors.lastname: Beloti
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.
authors.forename: Marcelo Augusto Szymanski
authors.initials: MA
authors.lastname: de Toledo
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil; Instituto de Biologia (IB), Universidade Estadual de Campinas, Departamento de Biologia Vegetal, Campinas, São Paulo, Brazil.
authors.forename: Michel
authors.initials: M
authors.lastname: Vincentz
authors.affiliation: Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo, São José dos Campos, São Paulo, Brazil.
authors.forename: Reginaldo Massanobu
authors.initials: RM
authors.lastname: Kuroshu
authors.affiliation: Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas, Campinas, São Paulo, Brazil; Instituto de Biologia (IB), Universidade Estadual de Campinas, Departamento de Biologia Vegetal, Campinas, São Paulo, Brazil.
authors.forename: Anete Pereira
authors.initials: AP
authors.lastname: de Souza
mesh_terms: D001673:Biodegradation, Environmental; D056804:Biofuels; D018533:Biomass; D001709:Biotechnology; D002480:Cellulase / Q000235:genetics / Q000378:metabolism; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D000431:Ethanol / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D006868:Hydrolysis; D014242:Trichoderma / Q000235:genetics* / Q000378:metabolism*
chemical_list: D056804:Biofuels; D005656:Fungal Proteins; D000431:Ethanol; D002480:Cellulase
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