title: Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels.
abstract: 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.
authors.affiliation: Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511, USA.
authors.forename: Hamid
authors.initials: H
authors.lastname: Rismani-Yazdi
authors.forename: Berat Z
authors.initials: BZ
authors.lastname: Haznedaroglu
authors.forename: Kyle
authors.initials: K
authors.lastname: Bibby
authors.forename: Jordan
authors.initials: J
authors.lastname: Peccia
mesh_terms: D056804:Biofuels; D000460:Chlorophyta / Q000201:enzymology / Q000235:genetics*; D002874:Chromosome Mapping; D018744:DNA, Plant / Q000235:genetics; D000431:Ethanol / Q000378:metabolism; D005227:Fatty Acids / Q000096:biosynthesis; D020869:Gene Expression Profiling; D015723:Gene Library; D017343:Genes, Plant; D023281:Genomics; D053858:Metabolic Networks and Pathways; D058977:Molecular Sequence Annotation; D017422:Sequence Analysis, DNA; D013213:Starch / Q000096:biosynthesis; D014280:Triglycerides / Q000096:biosynthesis
chemical_list: D056804:Biofuels; D018744:DNA, Plant; D005227:Fatty Acids; D014280:Triglycerides; D000431:Ethanol; D013213:Starch