Examinando por Autor "Castro, Carlos G."

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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.
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 Marcelino
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.
Decoding the chloroplast genome of the Amazonian fruit Myrciaria dubia (camu-camu): molecular evolution and comparative genomics across the order Myrtales
(Springer Nature, 2026-08-14) Castro, Juan C.; Leonardo, Diego A.; Cobos, Marianela; Vargas, Jhon A.; Paredes, Jae D.; Adrianzén, Pedro M.; Castro, Carlos G.; Imán Correa, Sixto Alfredo; Rodriguez, Hicler N.; Marapara, Jorge L.; Maddox , J. Dylan
Myrciaria dubia (camu-camu) is an economically important Amazonian fruit species with severely limited genomic resources despite growing commercial interest and conservation needs. This study sequenced, assembled, and comprehensively analyzed the complete chloroplast (cp) genome of M. dubia and performed comparative genomic analyses across the order Myrtales, including codon usage, codon decoding mechanisms, repetitive elements, nucleotide diversity, and phylogenetic reconstruction. The cp genome spanned 158,664 bp with a typical quadripartite organization: a large single-copy region (LSC = 87,640 bp), a small single-copy region (SSC = 18,324 bp), and paired inverted repeats (IRA/IRB = 26,350 bp each). Functional annotation identified 135 genomic features, comprising 84 protein-coding genes, 37 tRNA genes, eight rRNA genes, and five pseudogenes. Codon usage analysis revealed a strong AT bias (62.50%), with 30 preferred codons (RSCU >1.0) predominantly ending with A/T nucleotides. Codon decoding analysis assigned all 61 sense codons to five mechanistic categories, collectively achieving complete codon coverage across all 23 Myrtales accessions. Repetitive element analysis identified 69 simple sequence repeats in M. dubia (91.3% mononucleotide, predominantly adenine motifs in LSC intergenic spacers) and 439 long dispersed repeat pairs (97.5% palindromic, concentrated in the inverted repeat regions). Nucleotide diversity varied significantly across structural regions (SSC, mean π = 0.173; LSC, mean π = 0.084; IRA/IRB, mean π = 0.010–0.015), with the highest diversity window (π = 0.240) located in the SSC at approximately 117.7 kb. SWAN analysis of 78 protein-coding genes identified rpl22, ycf1, matK, ndhF, and ndhD as the most variable loci, with no gene exceeding ω = 1.0, indicating a pervasive purifying selection. Comparative analysis across 19 Myrtaceae accessions demonstrated complete gene collinearity and conserved IR boundary arrangement, with divergence concentrated in the SSC intergenic regions. Phylogenetic analysis positioned M. dubia as a sister species to Plinia trunciflora within the Myrteae tribe, nested in a well-supported monophyletic Myrtaceae clade (bootstrap = 100%).
Development and application of microsatellite markers for genetic diversity assessment and construction of a core collection of Myrciaria dubia (Kunth) Mcvaugh germplasm from the peruvian Amazon
(MDPI, 2024-10-25) Castro, Juan C.; Vasquez Guizado, Stalin Juan; Vigil Santillan, Bianca Estefani; Ascue, Francisco; Rojas Villa, Naysha; Paredes, Jae D.; Cobos, Marianela; Castro, Carlos G.; Motta, Daniel E.; Adrianzén, Pedro M.; Imán Correa, Sixto Alfredo; Maddox, J. Dylan
The Amazonian shrub Myrciaria dubia (camu-camu) produces vitamin C-rich fruits of growing commercial interest. However, sustainable utilization requires assessment and protection of the genetic diversity of the available germplasm. This study aimed to develop and apply microsatellite markers to assess genetic diversity and construct a core collection of M. dubia germplasm from the Peruvian Amazon. Sixteen polymorphic microsatellite loci were developed using an enrichment approach. The evaluation of 336 genotypes from 43 accessions of the germplasm bank, originating from eight river basins, was conducted using these newly developed markers. Genetic diversity parameters, including observed and expected heterozygosity, were calculated. Analysis of molecular variance (AMOVA) was performed to assess the distribution of genetic variation within and among accessions and river basins. Bayesian clustering analysis was employed to infer population structure. A core collection was constructed to maximize allelic richness. High genetic diversity was observed, with heterozygosity values ranging from 0.468 to 0.644 (observed) and 0.684 to 0.817 (expected) at the river basin level. AMOVA indicated significant genetic variation within (73–86%) compared to among (14–27%) accessions and river basins. Bayesian clustering detected ten genetic clusters, with several degrees of admixture among river basins, except for the genetically homogeneous Putumayo River basin. A core collection comprising 84 plant genotypes (25% of the full collection) was established, representing 90.82% of the overall allelic diversity. These results have important implications for M. dubia conservation strategies and breeding programs, in demonstrating a need for genetic connectivity between populations but preserving unique genetic resources in isolated basins. These results validate the expected levels of diversity and population subdivision in a crop and stress the need to secure genetically diverse germplasms, underscoring the importance of thorough genetic characterization for ex situ germplasm management.