Ilex paraguariensis Genome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB36685 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| CAJIXV01.dat.gz | Other | |||
| CAJIXV01.fasta.gz | Fasta.gz | |||
| CAJIXV01.master.dat | Other |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Ilex paraguariensis multiple library de novo transcriptome assembly
| PRJNA315513 | ENA
Project description:UNLABELLED: PREMISE OF THE STUDY:Ilex paraguariensis is a native tree species from Brazil, Argentina, and Paraguay that is used in the production of beverages, medicines, and cosmetics. Primers flanking microsatellites were developed to investigate genetic parameters in the species. • METHODS AND RESULTS:Using microsatellites cloned from an I. paraguariensis shotgun genomic library, 25 pairs of primers were designed and synthesized. Levels of polymorphism were evaluated in 24 individuals from two populations. Twenty loci were polymorphic, and an average of 4.8 and 4.5 alleles per locus were detected in the two populations, respectively. The mean observed heterozygosity was lower than the expected heterozygosity (0.54 vs. 0.60), indicating a departure from Hardy-Weinberg equilibrium and suggesting endogamy in both populations. • CONCLUSIONS:The reported set of markers is highly informative and constitutes a powerful tool for the development of genetic characterization studies in I. paraguariensis.
| S-EPMC4105281 | biostudies-literature
Project description:In this work, a methodology for determination of As(III), As(V), dimethylarsinic acid (DMA), Fe(II) and Fe(III) in fifty-eight samples (forty-nine products of thirteen brands from three countries) commercial yerba mate (Ilex paraguariensis) was performed. The hyphenated high performance liquid chromatography inductively coupled plasma optical emission spectrometry (HPLC-ICP OES) technique was used. Arsenic was determined below the quantification limit in 38 samples of yerba mate. As(III) was found at the level 0.09 and 0.08 mg kg-1. The As(V) content was in the range: 0.21 to 0.28 mg kg-1. The content of DMA was found the highest of the three arsenic species in the range: 0.21 to 0.47 mg kg-1. The content of Fe(II) and Fe(III) was found in the range: 0.61 to 15.4 mg kg-1 and 0.66 to 43.1 mg kg-1, respectively and the dominance of Fe(III) was observed. Moreover, total and extractable content of 16 elements were determined. The results have been subjected to statistical analysis in order to establish relationships between samples of the same origin (country), kind (type) and composition (purity).
| S-EPMC8700693 | biostudies-literature
Project description:Ilex paraguariensis strain:Pg538 Transcriptome or Gene expression
| PRJNA251985 | ENA
Project description:Obesity is a major health problem. A food field research that has recently aroused considerable interest is the potential of natural products to counteract obesity. Yerba Mate may be helpful in reducing body weight and fat. The aim of this study was to investigate the efficacy and safety of Yerba Mate supplementation in Korean subjects with obesity.A randomized, double-blind, placebo-controlled trial was conducted. Subjects with obesity (body mass index (BMI)???25 but?<?35 kg/m(2) and waist-hip ratio (WHR)???0.90 for men and???0.85 for women) were given oral supplements of Yerba Mate capsules (n?=?15) or placebos (n?=?15) for 12 weeks. Subjects take three capsules per each meal, total three times in a day (3 g/day). Measured outcomes were efficacy (abdominal fat distribution, anthropometric parameters and blood lipid profiles) and safety (adverse events, laboratory test results and vital signs).During 12 weeks of Yerba Mate supplementation, decreases in body fat mass (P?=?0.036) and percent body fat (P?=?0.030) compared to the placebo group were statistically significant. WHR was significantly decreased (P?=?0.004) in the Yerba Mate group compared to the placebo group. No clinically significant changes in any safety parameters were observed.Yerba Mate supplementation decreased body fat mass, percent body fat and WHR. Yerba Mate was a potent anti-obesity reagent that did not produce significant adverse effects. These results suggested that Yerba Mate supplementation may be effective for treating obese individuals.ClinicalTrials.gov: (NCT01778257).
| S-EPMC4583719 | biostudies-literature
Project description:Gene expression changes triggered by drought stress
| PRJNA375923 | ENA
Project description:The aim of this study was to assess the risk of exposure to polycyclic aromatic hydrocarbons (PAH) from yerba mate infusions in Uruguay using the margin of exposure approach (MOE) and a probabilistic method (Monte Carlo simulation). Servings/day, portion size, weekly frequency of mate consumption and body weight were the factors considered. The amount in infusions of benz[a]pyrene (B[a]P), PAH2 (sum of chrysene and B[a]P), and PAH4 (sum of benz[a]anthracene, chrysene, benz[b]fluoranthene and B[a]P) were used as markers of PAH exposure. Total content of PAH in infusions had large inter-brand variability (48-54 %) with significant differences among brands. PAH content in infusions prepared as habitually consumed was about 40 % of total content. The probability of occurrence of MOE < 10,000 varied according to the infusion preparation and the marker of exposure used, being higher for infusions prepared for total content and when B[a]P was used as marker of exposure. When the average B[a]P amount in infusion as habitually consumed was used in the simulation model, the probability of MOE < 10,000 was 9 %. The main factors contributing to B[a]P MOE variance were B[a]P amount (28.4 %), servings/day (17.3 %), and portion size (9.6 %). Heavy drinkers of yerba mate with high B[a]P content are those at risk to PAH exposure from mate infusions.
| S-EPMC7875766 | biostudies-literature
Project description:BACKGROUND:The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration currently consumed in >?90% of homes in Argentina, in Paraguay and Uruguay. The economy of entire provinces heavily relies on the production, collection and manufacture of Ilex paraguariensis, the fifth plant species with highest antioxidant activity. Polyphenols are associated to relevant health benefits including strong antioxidant properties. Despite its regional relevance and potential biotechnological applications, little is known about functional genomics and genetics underlying phenotypic variation of relevant traits. By generating tissue specific transcriptomic profiles, we aimed to comprehensively annotate genes in the Ilex paraguariensis phenylpropanoid pathway and to evaluate differential expression profiles. RESULTS:In this study we generated a reliable transcriptome assembly based on a collection of 15 RNA-Seq libraries from different tissues of Ilex paraguariensis. A total of 554 million RNA-Seq reads were assembled into 193,897 transcripts, where 24,612 annotated full-length transcripts had complete ORF. We assessed the transcriptome assembly quality, completeness and accuracy using BUSCO and TransRate; consistency was also evaluated by experimentally validating 11 predicted genes by PCR and sequencing. Functional annotation against KEGG Pathway database identified 1395 unigenes involved in biosynthesis of secondary metabolites, 531 annotated transcripts corresponded to the phenylpropanoid pathway. The top 30 differentially expressed genes among tissue revealed genes involved in photosynthesis and stress response. These significant differences were then validated by qRT-PCR. CONCLUSIONS:Our study is the first to provide data from whole genome gene expression profiles in different Ilex paraguariensis tissues, experimentally validating in-silico predicted genes key to the phenylpropanoid (antioxidant) pathway. Our results provide essential genomic data of potential use in breeding programs for polyphenol content. Further studies are necessary to assess if the observed expression variation in the phenylpropanoid pathway annotated genes is related to variations in leaves' polyphenol content at the population scale. These results set the current reference for Ilex paraguariensis genomic studies and provide a substantial contribution to research and biotechnological applications of phenylpropanoid secondary metabolites.
| S-EPMC6286616 | biostudies-literature
Project description:Yerba mate (Ilex paraguariensis A. St.-Hil.) is an important subtropical tree crop cultivated on 326,000 ha in Argentina, Brazil and Paraguay, with a total yield production of more than 1,000,000 t. Yerba mate presents a strong limitation regarding sequence information. The NCBI GenBank lacks an EST database of yerba mate and depicts only 80 DNA sequences, mostly uncharacterized. In this scenario, in order to elucidate the yerba mate gene landscape by means of NGS, we explored and discovered a vast collection of I. paraguariensis transcripts. Total RNA from I. paraguariensis was sequenced by Illumina HiSeq-2000 obtaining 72,031,388 pair-end 100 bp sequences. High quality reads were de novo assembled into 44,907 transcripts encompassing 40 million bases with an estimated coverage of 180X. Multiple sequence analysis allowed us to predict that yerba mate contains ∼ 32,355 genes and 12,551 gene variants or isoforms. We identified and categorized members of more than 100 metabolic pathways. Overall, we have identified ∼ 1,000 putative transcription factors, genes involved in heat and oxidative stress, pathogen response, as well as disease resistance and hormone response. We have also identified, based in sequence homology searches, novel transcripts related to osmotic, drought, salinity and cold stress, senescence and early flowering. We have also pinpointed several members of the gene silencing pathway, and characterized the silencing effector Argonaute1. We predicted a diverse supply of putative microRNA precursors involved in developmental processes. We present here the first draft of the transcribed genomes of the yerba mate chloroplast and mitochondrion. The putative sequence and predicted structure of the caffeine synthase of yerba mate is presented. Moreover, we provide a collection of over 10,800 SSR accessible to the scientific community interested in yerba mate genetic improvement. This contribution broadly expands the limited knowledge of yerba mate genes, and is presented as the first genomic resource of this important crop.
| S-EPMC4199719 | biostudies-literature