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

Abstract

BackgroundMyrciaria 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.ResultsIn 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.ConclusionsThis 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.Electron...

Valorization of byproducts from tropical fruits: Extraction methodologies, applications, environmental, and economic assessment: A review (Part 1: General overview of the byproducts, traditional biorefinery practices, and possible applications)

“…Camu‐camu is a rich source of ascorbic acid (0.96 to 2.99 g per 100 g), which is approximately 60 times higher than that of orange juice. This is attributed to the presence of five metabolic pathways for ascorbic acid biosynthesis (Castro, Maddox, & Imán, ; Castro et al., ). The main byproduct of camu‐camu is the peel, representing around 40% of the fruit, while the seeds are a minimum part of the fruit, eaten together with the fruit but also being part of the byproducts when its industrially processed, as summarized in Table .…”

“…Camu-camu is a rich source of ascorbic acid (0.96 to 2.99 g per 100 g), which is approximately 60 times higher than that of orange juice. This is attributed to the presence of five metabolic pathways for ascorbic acid biosynthesis (Castro, Maddox, & Imán, 2018;Castro et al, 2015). The main byproduct of camu-camu is the peel, representing around 40% of the fruit, while the seeds are a minimum part of the fruit, eaten together with the fruit but also being part of the byproducts when its industrially processed, as summarized in Table 2. In general, flavonoids, ellagic, and syringic acid were identified and quantified in extracts obtained with different solvents in different steps to extract bioactive compounds from hot-air-dried and fresh residue of camu-camu, consisting mainly of seeds and peels (Table 3).…”

Myrciaria dubia “Camu Camu” Fruit: Health-Promoting Phytochemicals and Functional Genomic Characteristics

“…We identified more than 3200 SSR motifs that would be appropriate for developing a comprehensive set of genic-SSR markers. Also, the transcriptome contained a large number (>23,000) of high-quality singlenucleotide polymorphisms (SNPs) and marks the highest number of SNP markers discovered to date for camu camu using transcriptome sequencing [48]. Both types of potential molecular markers, however, will require validation.…”

Gene-to-Gene Network Analysis of the Mediation of Plant Innate Immunity by the Eliciting Plant Response-Like 1 (Epl1) Elicitor of Trichoderma formosa

“…However, most of the important problems in plant disease occur in crops that might not have genomic or transcriptomic information available, the so-called nonmodel organisms. Currently, nextgeneration sequencing (NGS) is widely applied to study the whole-transcriptome profiles of model and nonmodel organisms and to understand gene expression from a genome-wide perspective (Gao et al 2014;Kim et al 2014;Liu et al 2014;Castro et al 2015;Lin et al 2015). Although NGS can easily generate contigs for genomes or transcriptomes, the bottleneck is how to efficiently analyze these high-throughput genomic profiles.…”