Examinando por Materia "Next-generation sequencing"

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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.
Revealing the complete chloroplast genome of an Andean horticultural crop, sweet cucumber (Solanum muricatum), and its comparison with other Solanaceae species
(MDPI, 2022-09-01) Saldaña Serrano, Carla Lizet; Chávez Galarza, Julio César; De la Cruz, Germán; Jhoncon, Jorge H.; Guerrero Abad, Juan Carlos; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Arbizu Berrocal, Carlos Irvin
Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native to the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes, and tomatoes. To date, molecular tools for this crop remain undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum was 155,681 bp in length and included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 87 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Similar to previous studies, our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect that this first sweet cucumber chloroplast genome will provide potential molecular markers and genomic resources to shed light on the genetic diversity and population studies of S. muricatum, which will allow us to identify varieties and ecotypes. Finally, the features and the structural differentiation will provide us with information about the genes of interest, generating tools for the most precise selection of the best individuals of sweet cucumber, in less time and with fewer resources.
Revealing the Complete Chloroplast Genome of an Andean Horticultural Crop, Sweet Cucumber (Solanum muricatum), and Its Comparison with Other Solanaceae Species
(MDPI, 2022-05-17) Saldaña Serrano, Carla Lizet; Chávez Galarza, Julio César; De la Cruz, Germán; Jhoncon, Jorge H.; Guerrero Abad, Juan Carlos; Vásquez Pérez, Héctor Vladimir; Maicelo Quintana, Jorge Luis; Arbizu Berrocal, Carlos Irvin
Sweet cucumber (Solanum muricatum) sect. Basarthrum is a neglected horticultural crop native of the Andean region. It is naturally distributed very close to other two Solanum crops of high importance, potatoes and tomatoes. To date, molecular tools for this crop are still undetermined. In this study, the complete sweet cucumber chloroplast (cp) genome was obtained and compared with seven Solanaceae species. The cp genome of S. muricatum had a 155,681 bp in length with included a large single copy (LSC) region of 86,182 bp and a small single-copy (SSC) region of 18,360 bp, separated by a pair of inverted repeats (IR) regions of 25,568 bp. The cp genome possessed 88 protein-coding genes (CDS), 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes, and one pseudogene. Furthermore, 48 perfect microsatellites were identified, divided in mononucleotide repeats (32), followed by tetranucleotide (6) and dinucleotides (5). Microsatellites with trinucleotides repeats (3), pentanucleotide (1) and hexanucleotide (1) repeats motifs in these genomes were also identified, but in lower quantity. These repeats were mainly located in the noncoding regions. Whole cp genome comparative analysis revealed that the SSC and LSC regions showed more divergence than IR regions. Our phylogenetic analysis showed that S. muricatum is a sister species to members of sections Petota + Lycopersicum + Etuberosum. We expect to provide useful molecular data to shed light on the genetic diversity within sweet cucumber landrace, and also to determine the evolutionary processes in S. muricatum.