Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides.
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 t...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS Genetics |
| Online Access: | http://europepmc.org/articles/PMC3291568?pdf=render |
| _version_ | 1811209827344449536 |
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| author | Tara A Gianoulis Meghan A Griffin Daniel J Spakowicz Brian F Dunican Cambria J Alpha Andrea Sboner A Michael Sismour Chinnappa Kodira Michael Egholm George M Church Mark B Gerstein Scott A Strobel |
| author_facet | Tara A Gianoulis Meghan A Griffin Daniel J Spakowicz Brian F Dunican Cambria J Alpha Andrea Sboner A Michael Sismour Chinnappa Kodira Michael Egholm George M Church Mark B Gerstein Scott A Strobel |
| author_sort | Tara A Gianoulis |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T04:45:32Z |
| format | Article |
| id | doaj.art-297d9f07f06345879fe0bca937effb97 |
| institution | Directory Open Access Journal |
| issn | 1553-7390 1553-7404 |
| language | English |
| last_indexed | 2024-04-12T04:45:32Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj.art-297d9f07f06345879fe0bca937effb972022-12-22T03:47:30ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042012-01-0183e100255810.1371/journal.pgen.1002558Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides.Tara A GianoulisMeghan A GriffinDaniel J SpakowiczBrian F DunicanCambria J AlphaAndrea SbonerA Michael SismourChinnappa KodiraMichael EgholmGeorge M ChurchMark B GersteinScott A StrobelThe 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.http://europepmc.org/articles/PMC3291568?pdf=render |
| spellingShingle | Tara A Gianoulis Meghan A Griffin Daniel J Spakowicz Brian F Dunican Cambria J Alpha Andrea Sboner A Michael Sismour Chinnappa Kodira Michael Egholm George M Church Mark B Gerstein Scott A Strobel Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. PLoS Genetics |
| title | Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. |
| title_full | Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. |
| title_fullStr | Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. |
| title_full_unstemmed | Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. |
| title_short | Genomic analysis of the hydrocarbon-producing, cellulolytic, endophytic fungus Ascocoryne sarcoides. |
| title_sort | genomic analysis of the hydrocarbon producing cellulolytic endophytic fungus ascocoryne sarcoides |
| url | http://europepmc.org/articles/PMC3291568?pdf=render |
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