title: Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides.
abstract: The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels. Endophytes represent a promising group of organisms, as they are a mostly untapped reservoir of metabolic diversity. They are often able to degrade cellulose, and they can produce an extraordinary diversity of metabolites. The filamentous fungal endophyte Ascocoryne sarcoides was shown to produce potential-biofuel metabolites when grown on a cellulose-based medium; however, the genetic pathways needed for this production are unknown and the lack of genetic tools makes traditional reverse genetics difficult. We present the genomic characterization of A. sarcoides and use transcriptomic and metabolomic data to describe the genes involved in cellulose degradation and to provide hypotheses for the biofuel production pathways. In total, almost 80 biosynthetic clusters were identified, including several previously found only in plants. Additionally, many transcriptionally active regions outside of genes showed condition-specific expression, offering more evidence for the role of long non-coding RNA in gene regulation. This is one of the highest quality fungal genomes and, to our knowledge, the only thoroughly annotated and transcriptionally profiled fungal endophyte genome currently available. The analyses and datasets contribute to the study of cellulose degradation and biofuel production and provide the genomic foundation for the study of a model endophyte system.
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: Tara A
authors.initials: TA
authors.lastname: Gianoulis
authors.forename: Meghan A
authors.initials: MA
authors.lastname: Griffin
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Spakowicz
authors.forename: Brian F
authors.initials: BF
authors.lastname: Dunican
authors.forename: Cambria J
authors.initials: CJ
authors.lastname: Alpha
authors.forename: Andrea
authors.initials: A
authors.lastname: Sboner
authors.forename: A Michael
authors.initials: AM
authors.lastname: Sismour
authors.forename: Chinnappa
authors.initials: C
authors.lastname: Kodira
authors.forename: Michael
authors.initials: M
authors.lastname: Egholm
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.forename: Mark B
authors.initials: MB
authors.lastname: Gerstein
authors.forename: Scott A
authors.initials: SA
authors.lastname: Strobel
mesh_terms: D001203:Ascomycota / Q000235:genetics / Q000254:growth & development / Q000378:metabolism; D056804:Biofuels; D002482:Cellulose / Q000378:metabolism; D060026:Endophytes / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006838:Hydrocarbons / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D055432:Metabolomics; D022661:RNA, Untranslated / Q000235:genetics; D059386:Reverse Genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D056804:Biofuels; D006838:Hydrocarbons; D022661:RNA, Untranslated; D002482:Cellulose