Examinando por Autor "Maddox, J. Dylan"

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Bioactive Compounds of Camu-Camu (Myrciaria dubia (Kunth) McVaugh)
(Hosakatte Niranjana Murthy, 2019-10-24) Castro Gómez, Juan Carlos; Maddox, J. Dylan; Cobos Ruiz, Marianela; Paredes, Jae D.; Marapara del Aguila, Jorge Luis; Braga, Janeth; Imán Correa, Sixto Alfredo; Rodríguez, Hicler N.; Castro, Carlos G.
Camu-camu is a shrub, native to the Amazon that thrives in areas where flooding is frequent. Genetically, the plant is characterized by a diploid genome and moderate genetic diversity. Several parts of the plant are used in traditional folk medicine to treat a variety of acute and chronic diseases. For over 50 years, the exceptionally high vitamin C content of camu-camu has attracted worldwide attention that continues today because of the recent discovery of several health-promoting phytochemicals with corroborated biological activities (e.g., antioxidant, anti-obesity, antidiabetic). All of these beneficial attributes are well supported by in vitro and in vivo studies as well as human clinical trials. The metabolic precursors of these phytochemicals are synthesized in key metabolic pathways (i.e., the shikimate pathway, the mevalonate pathway). Of these metabolic pathways, we show details for the biosynthesis of betulinic acid, trans-resveratrol, and syringic acid. In conclusion, camu-camu is an exceptional plant for its ability to produce and accumulate significant amounts of a variety of health-promoting phytochemicals. Although several metabolic pathways responsible for the biosynthesis of these phytochemicals have been reconstructed based on fruit and seedling transcriptomes, detailed knowledge of the vast majority of metabolic pathways and their molecular regulatory mechanisms is lacking. Consequently, we must increase our knowledge of the metabolic processes using multi-omic approaches so that we can acquire the skills necessary to develop genetically improved varieties of camu-camu and implement biotechnological applications for the production of these bioactive phytochemicals.
Camu-camu - Myrciaria dubia (Kunth) McVaugh
(Academic Press, 2018-02-02) Castro Gómez, Juan Carlos; Maddox, J. Dylan; Imán Correa, Sixto Alfredo
Myrciaria dubia (Kunth) McVaugh (common name camu-camu) is an Amazonian fruit shrub that produces several nutritional compounds such as essential amino acids, essential fatty acids, vitamins, and minerals. Also, it contains several health-promoting phytochemicals with powerful antioxidant and antiinflammatory properties, due to phenolics, vitamin C, and betulinic acid. In addition, it has been shown to have hepatoprotective, antimicrobial, and antimalarial activity. Finally, it is best known for its high content of vitamin C.
Dataset of de novo assembly and functional annotation of the transcriptome during germination and initial growth of seedlings of Myrciaria Dubia “camu-camu”
(Elsevier, 2020-06-11) Castro Gómez, Juan Carlos; Maddox, J. Dylan; Rodríguez, Hicler N.; Castro, Carlos G.; Imán Correa, Sixto Alfredo; Cobos Ruiz, Marianela; Paredes, Jae D.; Marapara del Aguila, Jorge Luis; Braga, Janeth; Adrianzén Julca, Pedro M.
Myrciaria dubia “camu-camu” is a native shrub of the Amazon that is commonly found in areas that are flooded for three to four months during the annual hydrological cycle. This plant species is exceptional for its capacity to biosynthesize and accumulate important quantities of a variety of health-promoting phytochemicals, especially vitamin C [1], yet few genomic resources are available [2]. Here we provide the dataset of a de novo assembly and functional annotation of the transcriptome from a pool of samples obtained from seeds during the germination process and seedlings during the initial growth (until one month after germination). Total RNA/mRNA was purified from different types of plant materials (i.e., imbibited seeds, germinated seeds, and seedlings of one, two, three, and four weeks old), pooled in equimolar ratio to generate the cDNA library and RNA paired-end sequencing was conducted on an Illumina HiSeq™2500 platform. The transcriptome was de novo assembled using Trinity v2.9.1 and SuperTranscripts v2.9.1. A total of 21,161 transcripts were assembled ranging in size from 500 to 10,001 bp with a N50 value of 1,485 bp. Completeness of the assembly dataset was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) software v2/v3. Finally, the assembled transcripts were functionally annotated using TransDecoder v3.0.1 and the web-based platforms Kyoto Encyclopedia of Genes and Genomes (KEGG) Automatic Annotation Server (KAAS), and FunctionAnnotator.
De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis
(BioMed Central, 2015-11-24) Castro Gómez, Juan Carlos; Maddox, J. Dylan; Cobos Ruiz, Marianela; Requena Anicama, David Ruben; Zimic Peralta, Mirko Juan; Bombarely Gomez, Aureliano; Imán Correa, Sixto Alfredo; Cerdeira Gutiérrez, Luis Alexander; Medina Bardales, Anderson E.
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.
Gene expression and enzyme activities of the D-mannose/L-galactose pathway influence L-ascorbic acid content in Myrciaria dubia
(Springer Nature, 2015-12-01) Castro Gómez, Juan Carlos; Cobos Ruiz, Marianela; Maddox, J. Dylan; Imán Correa, Sixto Alfredo; Egoavil Reátegui, Alina del Carmen; Torres, Juan; Gutierrez, F.
The aim of this work was to elucidate the molecular and biochemical mechanisms that control L-ascorbic acid (AsA) content variation in Myrciaria dubia. The AsA was quantified by high-performance liquid chromatography, gene expression by real-time quantitative PCR, and enzyme activities by spectrophotometric methods from leaves and immature fruits of two genotypes (Md-60,06 and Md-02,04) with pronounced (about 2 times) differences in the AsA content. In either genotype, the fruit peel had ∼ 1.5 times more AsA than the fruit pulp and ∼ 15.0 times more than the leaf. All tissues examined demonstrated the capability for AsA biosynthesis through the D-mannose/L-galactose pathway because mRNAs of the six key genes [GDP-D-mannose pyrophosphorylase (GMP), GDP-D-mannose-3′,5′-epimerase (GME), GDP-L-galactose phosphorylase (GGP), L-galactose-1-phosphate phosphatase (GPP), L-galactose dehydrogenase (GDH), and L-galactono-1-4-lactone dehydrogenase (GLDH)] and catalytic activities of the corresponding enzymes (GMP, GDH, and GLDH) were detected. The differential expressions of genes and enzyme activities mostly correlated with the respective AsA content. Thus, the expression of several genes of the D-mannose/L-galactose pathway determined the AsA content variation in tissues of M. dubia.
Isolation and molecular cloning of genes from Myrciaria dubia “camu-camu” with potential use for biotechnological production of vitamin C
(Society for Biology and Biotechnology, 2016-11-03) Castro Gómez, Juan Carlos; Cobos Ruiz, Marianela; Maddox, J. Dylan; Imán Correa, Sixto Alfredo; Marapara del Aguila, Jorge Luis
Myrciaria dubia “camu-camu” is a rich source of several bioactive phytochemicals and vitamin C (L-ascorbic acid, AsA). To gain insights about the genes involved in AsA biosynthesis in this plant species and consequently with potential use for its biotechnological production, here we report the isolation and molecular cloning of partial gene sequences of the D-mannose/L-galactose pathway. Degenerate primers designed by the multiple sequence alignment of related plant species were used to isolate in M. dubia the partial sequences of the six D-mannose/L-galactose pathway genes (GMP, GME, GGP, GPP, GDH and GLDH). The deduced protein sequences of the six genes have more than 81% sequence identity to rosids and asterids species, with a closer phylogenetic relationship to Eucalyptus grandis. In conclusion, gene sequences of the D-mannose/L-galactose pathway involved in AsA biosynthesis of M. dubia were successfully isolated and cloned and the phylogenetic analysis indicated that these genes have been relatively well conserved throughout of plant evolution, reflecting the importance of the enzymes of this metabolic pathway for plant growth and survival. Additionally, the isolation and cloning of these genes allow us to implement systems for biotechnological production of AsA.
Myrciaria dubia “Camu Camu” Fruit: Health-Promoting Phytochemicals and Functional Genomic Characteristics
(IntechOpen, 2018-06-13) Castro Gómez, Juan Carlos; Maddox, J. Dylan; Cobos Ruiz, Marianela; Imán Correa, Sixto Alfredo
Camu camu is a typical Amazon native fruit shrub that possesses a diploid genome, moderate genetic diversity, and population structure. The fruits accumulate several essential nutrients and synthesize L-ascorbic acid (vitamin C) in great quantities and an array of diverse secondary metabolites with corroborated in vitro and in vivo health-promoting activities. These beneficial effects include antioxidative and antiinflammatory activities, antiobesity, hypolipidemic, antihypertensive and antidiabetic effects, DNA damage and cancer protection effects, and other bioactivities. Many health-promoting phytochemicals are biosynthesized in several metabolic pathways of camu camu. Their reconstruction from the fruit transcriptome database was accomplished by our research group. These include basic metabolic pathways such as glycolysis and pentose phosphate pathway, vitamin C biosynthesis pathways, and pathways involved in secondary metabolites production. Due to their agronomic potential and fruits growing demand, recently, based on an ideotype, programs were initiated for their domestication and genetic improvement, but so far with very negligible achievements. Consequently, we propose new strategies to accelerate the processes of domestication and genetic improvement based on state of the art technologies for multiomic data analysis and innovative molecular tools.