title: Bio-crude transcriptomics: gene discovery and metabolic network reconstruction for the biosynthesis of the terpenome of the hydrocarbon oil-producing green alga, Botryococcus braunii race B (Showa).
abstract: BACKGROUND
  Microalgae hold promise for yielding a biofuel feedstock that is sustainable, carbon-neutral, distributed, and only minimally disruptive for the production of food and feed by traditional agriculture. Amongst oleaginous eukaryotic algae, the B race of Botryococcus braunii is unique in that it produces large amounts of liquid hydrocarbons of terpenoid origin. These are comparable to fossil crude oil, and are sequestered outside the cells in a communal extracellular polymeric matrix material. Biosynthetic engineering of terpenoid bio-crude production requires identification of genes and reconstruction of metabolic pathways responsible for production of both hydrocarbons and other metabolites of the alga that compete for photosynthetic carbon and energy.
  
  
  RESULTS
  A de novo assembly of 1,334,609 next-generation pyrosequencing reads form the Showa strain of the B race of B. braunii yielded a transcriptomic database of 46,422 contigs with an average length of 756 bp. Contigs were annotated with pathway, ontology, and protein domain identifiers. Manual curation allowed the reconstruction of pathways that produce terpenoid liquid hydrocarbons from primary metabolites, and pathways that divert photosynthetic carbon into tetraterpenoid carotenoids, diterpenoids, and the prenyl chains of meroterpenoid quinones and chlorophyll. Inventories of machine-assembled contigs are also presented for reconstructed pathways for the biosynthesis of competing storage compounds including triacylglycerol and starch. Regeneration of S-adenosylmethionine, and the extracellular localization of the hydrocarbon oils by active transport and possibly autophagy are also investigated.
  
  
  CONCLUSIONS
  The construction of an annotated transcriptomic database, publicly available in a web-based data depository and annotation tool, provides a foundation for metabolic pathway and network reconstruction, and facilitates further omics studies in the absence of a genome sequence for the Showa strain of B. braunii, race B. Further, the transcriptome database empowers future biosynthetic engineering approaches for strain improvement and the transfer of desirable traits to heterologous hosts.
authors.affiliation: Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, Tucson, 85739, USA. imolnar@email.arizona.edu
authors.forename: István
authors.initials: I
authors.lastname: Molnár
authors.forename: David
authors.initials: D
authors.lastname: Lopez
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Wisecaver
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Devarenne
authors.forename: Taylor L
authors.initials: TL
authors.lastname: Weiss
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.forename: Jeremiah D
authors.initials: JD
authors.lastname: Hackett
mesh_terms: D056804:Biofuels; D001692:Biological Transport / Q000235:genetics; D001704:Biopolymers / Q000096:biosynthesis; D002734:Chlorophyll / Q000378:metabolism; D000460:Chlorophyta / Q000235:genetics* / Q000378:metabolism*; D020224:Expressed Sequence Tags; D059014:High-Throughput Nucleotide Sequencing; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D055442:Metabolome / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010788:Photosynthesis / Q000235:genetics; D010938:Plant Oils / Q000378:metabolism; D010940:Plant Proteins / Q000096:biosynthesis / Q000235:genetics*; D017434:Protein Structure, Tertiary; D012436:S-Adenosylmethionine / Q000378:metabolism; D017422:Sequence Analysis, DNA; D013213:Starch / Q000096:biosynthesis; D013729:Terpenes / Q000378:metabolism*; D059467:Transcriptome; D014280:Triglycerides / Q000096:biosynthesis
chemical_list: D056804:Biofuels; D001704:Biopolymers; D010938:Plant Oils; D010940:Plant Proteins; D013729:Terpenes; D014280:Triglycerides; D002734:Chlorophyll; D012436:S-Adenosylmethionine; D013213:Starch