Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels
Background Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofu...
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| Format: | Article |
| Language: | English |
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BioMed Central Ltd
2011
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| Online Access: | http://hdl.handle.net/1721.1/63113 |
| _version_ | 1826197049550307328 |
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| author | Rismani-Yazdi, Hamid Haznedaroglu, Berat Z. Bibby, Kyle Peccia, Jordan Rismani-Yazdi, Hamid Bibby, Kyle Peccia, Jordan |
| author2 | Massachusetts Institute of Technology. Department of Chemical Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Chemical Engineering Rismani-Yazdi, Hamid Haznedaroglu, Berat Z. Bibby, Kyle Peccia, Jordan Rismani-Yazdi, Hamid Bibby, Kyle Peccia, Jordan |
| author_sort | Rismani-Yazdi, Hamid |
| collection | MIT |
| description | Background Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production. Results Next generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) identifiers. These analyses identified the majority of lipid and starch biosynthesis and catabolism pathways in D. tertiolecta. Conclusions The construction of metabolic pathways involved in the biosynthesis and catabolism of fatty acids, triacylglycrols, and starch in D. tertiolecta as well as the assembled transcriptome provide a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock. |
| first_indexed | 2024-09-23T10:41:38Z |
| format | Article |
| id | mit-1721.1/63113 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T10:41:38Z |
| publishDate | 2011 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/631132022-09-27T14:19:23Z Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels Rismani-Yazdi, Hamid Haznedaroglu, Berat Z. Bibby, Kyle Peccia, Jordan Rismani-Yazdi, Hamid Bibby, Kyle Peccia, Jordan Massachusetts Institute of Technology. Department of Chemical Engineering Rismani-Yazdi, Hamid Rismani-Yazdi, Hamid Background Biodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production. Results Next generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology (KO) identifiers. These analyses identified the majority of lipid and starch biosynthesis and catabolism pathways in D. tertiolecta. Conclusions The construction of metabolic pathways involved in the biosynthesis and catabolism of fatty acids, triacylglycrols, and starch in D. tertiolecta as well as the assembled transcriptome provide a foundation for the molecular genetics and functional genomics required to direct metabolic engineering efforts that seek to enhance the quantity and character of microalgae-based biofuel feedstock. National Science Foundation (U.S.) (Grant #0854322) National Institutes of Health (U.S.) (NIH Grant# RR19895) Biomedical High Performance Computing Center 2011-05-25T15:57:18Z 2011-05-25T15:57:18Z 2011-03 2010-11 2011-05-09T18:31:42Z Article http://purl.org/eprint/type/JournalArticle 1471-2164 http://hdl.handle.net/1721.1/63113 Rismani-Yazdi, Hamid et al. "Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels." BMC Genomics. 2011 Mar 14;12(1):148 en http://dx.doi.org/10.1186/1471-2164-12-148 BMC Genomics Creative Commons Attribution http://creativecommons.org/licenses/by/2.0 Rismani-Yazdi et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Rismani-Yazdi, Hamid Haznedaroglu, Berat Z. Bibby, Kyle Peccia, Jordan Rismani-Yazdi, Hamid Bibby, Kyle Peccia, Jordan Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels |
| title | Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels |
| title_full | Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels |
| title_fullStr | Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels |
| title_full_unstemmed | Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels |
| title_short | Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels |
| title_sort | transcriptome sequencing and annotation of the microalgae dunaliella tertiolecta pathway description and gene discovery for production of next generation biofuels |
| url | http://hdl.handle.net/1721.1/63113 |
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