Open Access Highly Accessed Research article

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)*

István Molnár12*, David Lopez3, Jennifer H Wisecaver4, Timothy P Devarenne5, Taylor L Weiss5, Matteo Pellegrini3 and Jeremiah D Hackett24

Author Affiliations

1 Natural Products Center, School of Natural Resources and the Environment, The University of Arizona, 250 E. Valencia Rd, Tucson, AZ, 85739, USA

2 Bio5 Institute, The University of Arizona, 1657 E. Helen St, Tucson, AZ, 85721, USA

3 Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, P. O. Box 951606, Los Angeles, CA, 90095, USA

4 Department of Ecology and Evolutionary Biology, The University of Arizona, 1041 E. Lowell St, Tucson, AZ, 85721, USA

5 Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843, USA

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BMC Genomics 2012, 13:576  doi:10.1186/1471-2164-13-576

Published: 30 October 2012

Additional files

Additional file 1:

Figure S1. – Denaturing agarose gel analyses of purified B. braunii Showa RNA. Figure S2 – RT-PCR analysis using B. braunii Showa RNA from days 0, 3, and 5. Figure S3 – Size distribution of contigs in the assembled B. braunii Showa transcriptome. Table S1 - RNA quantitation from each sample and pooled sample. Table S2 - Machine-assembled contigs with the highest sequence coverage in the B. braunii Showa transcriptome. Table S3 -B. braunii Showa transcript annotations. Table S4 - Top source organisms in the KEGG annotations of the B. braunii Showa transcriptome. Table S6 - Curated contigs for IPP and DMAPP biosynthesis in the B. braunii Showa transcriptome. Table S7 - Curated contigs for polyprenyl diphosphate synthases in the B. braunii Showa transcriptome. Table S8 - Curated contigs for triterpenoid hydrocarbon biosynthesis in the B. braunii Showa transcriptome. Table S9 - Curated contigs for triterpenoid sterol biosynthesis in the B. braunii Showa transcriptome. Table S10 - Curated contigs for tetraterpenoid biosynthesis in the B. braunii Showa transcriptome. Table S11 - Curated contigs for meroterpenoid quinone biosynthesis in the B. braunii Showa transcriptome. Table S12 – Curated contigs for the biosynthesis of gibberellic acid diterpenes in the B. braunii Showa transcriptome. Table S13 – Machine-assembled contigs for S-adenosylmethionine regeneration in the B. braunii Showa transcriptome. Table S14 – Machine-assembled contigs for fatty acid biosynthesis, desaturation, elongation and TAG assembly in the B. braunii Showa transcriptome. Table S15 – Machine-assembled contigs for starch and cellulose biosynthesis in the B. braunii Showa transcriptome. Table S16 – Machine-assembled contigs for putative ABC transporter pumps in the B. braunii Showa transcriptome. Table S17 – Machine-assembled contigs related to autophagy in the B. braunii Showa transcriptome.

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Additional file 2:

Table S5 – Inventory of machine-assembled contigs in the transcriptome of B. braunii Showa with KEGG annotations not shared with proteins encoded in the genomes of C. reinhardtii (v3.0), Ch. variabilis NC64A (v1.0), and Micromonas RC299 (v3.0).

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