Elettaria cardamomum cultivar:Appangala 1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA474822 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7280098_1.fastq.gz | Fastqsanger.gz | |||
| SRR7280098_2.fastq.gz | Fastqsanger.gz | |||
| SRR7280099_1.fastq.gz | Fastqsanger.gz | |||
| SRR7280099_2.fastq.gz | Fastqsanger.gz |
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Project description:Elettaria cardamomum Transcriptome or Gene expression
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Project description:Elettaria cardamomum cultivar:MCC-260 Raw sequence reads
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Project description:Elettaria cardamomum (L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild) and SRX1141276 (cultivars). The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.
| S-EPMC5219599 | biostudies-literature
Project description:Elettaria cardamomum (L.) Maton, or small cardamom referred as 'queen of spices', is a perennial herbaceous rhizomatous monocot of the family Zingiberaceae. Cardamom seeds and fruits are the economically significant parts and effectively used as a traditional medicine, food additive and flavoring agent. In the present study, using Ion Proton next generation sequencing technology we performed the small RNA sequencing, conserved and novel miRNA predictions of a wild and five cultivar genotypes of cardamom. Small RNA sequencing generated a total of 5,451,328 and 2,756,250 raw reads for wild and cultivar cardamom respectively. The raw data was submitted to SRA database of NCBI under the accession numbers and SRX2273863 (wild) and SRX2273862 (cultivars). The raw reads were quality filtered and predicted conserved and novel miRNAs for wild and cultivar cardamom. The predicted miRNAs, miRNA-targets and functional annotations might provide valuable insights into differences between wild progenitor and cultivated cardamom.
| S-EPMC5604955 | biostudies-literature
Project description:Black tea is consumed worldwide and is believed to play a role in cancer prevention. Xerophilic aflatoxigenic fungi are highly hazardous contaminants of tea since they are associated with tea quality impairment and human health risk. The present study reports isolation of such xerophilic and aflatoxigenic fungi associated with marketed tea. Twenty different tea samples collected from the local markets of Tamilnadu, India were investigated for fungal contamination. The results indicated contamination by 0.38% Aspergillus flavus. Other common contaminant fungi including Penicillium spp. (0.30%), Pacelomyces spp. (0.14%), and Mucor spp. (0.19%) were also isolated. Amongst the fungi isolated Aspergillus niger ML01 and A. flavus ML02 were found to be xerophilic aflatoxigenic mycoflora. Phylogenetic analysis based on 28S rRNA revealed their close ancestry. The chloroform and acetone extracts of spices Elettaria cardamomum and Syzygium aromaticum exhibited antifungal inhibitory activity on growth and toxin elaboration of both these xerophilic tea contaminants A. niger ML01 and A. flavus ML02. The results advocate the use of these spices plant or their extracts as novel antimicrobials which may add preservation and flavour in marketed tea.
| S-EPMC3730779 | biostudies-literature
Project description:BackgroundCardamom (Elettaria cardamomum) is a spice and exhibits potent antioxidant and biological activities through distinct molecular mechanisms. However, the anticancer effect of cardamom was not explored yet in Ehrlich solid tumor (EST)-bearing mice.ObjectivesThis investigation was aimed to evaluate the anti-cancer effects of green cardamom (GCar) alone or combined with the anti-cancer drug cyclophosphamide in an in vivo model to explore its mechanistic role in tumor cell death in EST-bearing mice.MethodsEhrlich ascites tumor cells were injected in the mice and 5 days later the animals treated with GCar and/or cyclophosphamide for 10 days. Twenty-four hours from the last treatment, animals were sacrificed for the different measurements.ResultsData recorded for tumor size, percentage of tumor growth inhibition, tumor growth delay and mean survival time of EST-bearing mice demonstrated the effective role of GCar alone or combined with CPO as a promising anti-cancer agent because it reduced tumor size. GCar elevated the mean survival time of EST-bearing mice compared to that of untreated EST and EST + CPO groups. Analysis of qPCR mRNA gene and protein expression revealed that GCar alone or combined with CPO were promising anticancer agents. After the treatment of EST with GCar, the apoptotic-related genes and proteins were significantly modulated. GCar induced markedly significant decreases in oxidative stress biomarkers and a significant increment in glutathione levels and that of antioxidant enzymes. With a marked diminish in liver and kidney function biomarkers.ConclusionThe results revealed that GCar could serve as an apoptotic stimulator agent, presenting a novel and potentially curative approach for cancer treatment, inducing fewer side effects than those of the commercially used anti-cancer drugs, such as CPO.
| S-EPMC8086365 | biostudies-literature
Project description:Microsatellite markers in small cardamom (Elettaria cardamomum Maton) were developed using the selective hybridization enrichment method. A total of 140 microsatellite repeats were identified from 270 clones. Primers were designed for 58 microsatellites and 44 primer pairs amplified products of expected size in cardamom. These markers were used for studying the diversity of 20 important small cardamom genotypes, and six markers were found to be polymorphic. The number of alleles ranged from 2 to 7 with an average of 3.6 per locus. Polymorphic information content values ranged from 0.14 to 0.38 based on dominant scoring. The two markers ECM 47a and ECMG 28 generated specific banding patterns for the genotypes MCC7 (Pink tiller) and APG434 (MA18) respectively. Dendrogram illustrated the genetic similarity between different genotypes of Kerala and Karnataka regions. It differentiated the closely related genotypes and released varieties into separate groups. Principal coordinate analysis revealed PV1 and ICRI 1 as the most divergent genotypes. The study demonstrated that these markers are informative and can be further utilized for generating reliable molecular data for assisting the crop improvement of small cardamom. Cross generic transferability (71.4 %) of the developed primers proved that they are useful for phylogenetic studies in the family Zingiberaceae. This is the first report of de novo isolation, characterisation and utilization of microsatellite markers for the genetic diversity analysis of small cardamom.
| S-EPMC4938822 | biostudies-literature
Project description:Spanish marjoram (Thymus mastichina) and cardamom (Elettaria cardamomum) are traditional aromatic plants with which several pharmacological properties have been associated. In this study, the volatile composition, antioxidative and antimigratory effects on human breast cancer (MDA-MB-468 cell line), antimicrobial activity, and antibiofilm effect were evaluated. Results obtained via treatment of human breast cancer cells generally indicated an inhibitory effect of both essential oils (EOs) on cell viability (after long-term treatment) and antioxidative potential, as well as the reduction of nitric oxide levels. Antimigratory effects were revealed, suggesting that these EOs could possess significant antimetastatic properties and stop tumor progression and growth. The antimicrobial activities of both EOs were determined using the disc diffusion method and minimal inhibition concentration, while antibiofilm activity was evaluated by means of mass spectrometry. The best antimicrobial effects of T. mastichina EO were found against the yeast Candida glabrata and the G+ bacterium Listeria monocytogenes using the disc diffusion and minimal inhibitory concentration methods. E. cardamomum EO was found to be most effective against Pseudomas fluorescens biofilm using both methods. Similarly, better effects of this oil were observed on G- compared to G+ bacterial strains. Our study confirms that T. mastichina and E. cardamomum EOs act to change the protein structure of older P. fluorescens biofilms. The results underline the potential use of these EOs in manufactured products, such as foodstuffs, cosmetics, and pharmaceuticals.
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