BACKGROUND: Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high @entity620 ( @entity7943 ) content in fruits. Pronounced variation in @entity7943 content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to @entity7943 biosynthesis. RESULTS: In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for @entity7943 biosynthesis were identified: animal-like pathway, @entity8580 pathway, L-gulose pathway, @entity3913 / @entity69172 pathway, and @entity13275 pathway. All transcripts coding enzymes involved in the @entity9050 - @entity2041 cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. CONCLUSIONS: This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for @entity7943 production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of @entity7943 , @entity4211 , and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate @entity7943 and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of @entity7943 precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of @entity7943 and their precursors are needed to provide a more comprehensive view of how these pathways for @entity7943 metabolism are regulated and linked in this species.

De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for XXXX biosynthesis.

@entity13275 :: ('CHEBI:27252', 'Chemical') :: ['uronic acid'] @entity8580 :: ('MESH:D007294', 'Chemical') :: ['myo-inositol'] @entity620 :: ('MESH:D001205', 'Chemical') :: ['L-ascorbic acid'] @entity2041 :: ('MESH:D005978', 'Chemical') :: ['glutathione'] @entity3913 :: ('MESH:D008358', 'Chemical') :: ['D-mannose'] @entity69172 :: ('CHEBI:42905', 'Chemical') :: ['L-galactose'] @entity4211 :: ('MESH:D000872', 'Chemical') :: ['anthocyanins'] @entity7943 :: ('D001241', 'Chemical') :: ['AsA'] @entity9050 :: ('CHEBI:38290', 'Chemical') :: ['ascorbate']
@entity620 :: (MESH:D001205,Chemical) :: ['L-ascorbic acid']
