Universidad Peruana Cayetano Heredia

De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis

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dc.contributor.author Castro, Juan C.
dc.contributor.author Maddox, J. Dylan
dc.contributor.author Cobos, Marianela
dc.contributor.author Requena, David
dc.contributor.author Zimic-Peralta, Mirko Juan
dc.contributor.author Bombarely, Aureliano
dc.contributor.author Iman, Sixto A.
dc.contributor.author Cerdeira, Luis A.
dc.contributor.author Medina, Andersson E.
dc.date.accessioned 2019-02-06T14:52:14Z
dc.date.available 2019-02-06T14:52:14Z
dc.date.issued 2015
dc.identifier.uri https://hdl.handle.net/20.500.12866/5279
dc.description.abstract Background. Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA 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 AsA 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 AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione 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 AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, 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 AsA 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 AsA 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 AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. en_US
dc.language.iso eng
dc.publisher BioMed Central
dc.relation.ispartofseries BMC Genomics
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Transcriptome en_US
dc.subject Ascorbic Acid/biosynthesis/genetics en_US
dc.subject Biosynthetic Pathways en_US
dc.subject High-Throughput Nucleotide Sequencing/methods en_US
dc.subject M Phase Cell Cycle Checkpoints en_US
dc.subject Molecular Sequence Annotation en_US
dc.subject Myrtaceae/enzymology/genetics en_US
dc.subject Plant Proteins/genetics en_US
dc.subject Sequence Analysis, RNA/methods en_US
dc.title De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1186/s12864-015-2225-6
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#1.06.07
dc.relation.issn 1471-2164


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