Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA257964 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1542700_1.fastq.gz | Fastqsanger.gz | |||
| SRR1542700_2.fastq.gz | Fastqsanger.gz | |||
| SRR1542701_1.fastq.gz | Fastqsanger.gz | |||
| SRR1542701_2.fastq.gz | Fastqsanger.gz | |||
| SRR1542702_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
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Project description:The advent of next generation sequencing (NGS) has greatly enriched the database of miRNAs. For plants so far 8455 miRNAs sequences from 73 species and 15401 miRNAs sequences from 150 species have been deposited in miRBase 21.0 and Plant Non-coding RNA Database, respectively. The occurrence of miRNAs in such a huge number, which is still increasing, is because of the fact that the profile of miRNAs expression differs greatly from species to species, both quantitatively and qualitatively. Besides, even within a species it is expected that the miRNA expression profile would differ from cultivar to cultivar depending on the trait with regard to which the two cultivars differ, and on the same logic it is also expected that their expression profile would differ considerably in the plant under contrasting environmental conditions. However, report on comparative study of expression profile of miRNAs in rice cultivars, or in any crop cultivars, contrast for salt tolerance, or tolerance to any abiotic stress is scant. Therefore, the current study was planned to see the expression profile of miRNAs in a salt-tolerant rice (Oryza sativa L. ssp indica) cultivar (cv.) Pokkali in presence and absence of NaCl and to check the response pattern of a few important salt-responsive miRNAs in a salt-sensitive rice cultivar Badami in order to identify the miRNAs and their targets that could be involved in the salt tolerance process
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2013-08-21 | E-MTAB-4392 | biostudies-arrayexpress
Project description:Abiotic environmental stresses cause serious economic losses in agriculture. These stresses include temperature extremes, high salinity and drought. To isolate drought-responsive novel coding and noncoding genes, we used the next generation sequencing method from three rice cultivars (wild type nipponbare, nipponbare AP2 transgenic plants, wild type vandana). 36 NGS data of mRNA-seq, small RNA-seq, riboZero-seq were analyzed. For the analyses of these data we constructed a TF-TG (Transcription Factor-Target Gene) network and an ap2 rooted cascading tree. Using these networks and tress we isolated lincRNAs, differentially expressed miRNAs and their targets. We identified several drought stress-related novel/function unknown coding transcripts (transcription factors and functional genes) and non-coding transcripts (small noncoding transcripts such as microRNA and long noncoding transcripts) from these database analyses and have constructed databases of drought stress-related coding and noncoding transcripts Identification of drought-responsive Regulatory Coding and Non-coding Transcripts from rice by deep RNA sequencing
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Project description:Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments. Our results suggest time course and As(III)-dosing treatments were devised. Cluster analyses show that root and shoot samples were differentially grouped. For roots, sub-clusters were more distinct in the dosage course whereas for shoots they were most recognizable for the time course treatments. Other than the significantly regulated gene expression in the heavy metal-responsive sulfur and glutathione metabolism pathways, the expression of genes related to heavy metal transportation, jasmonate biosynthesis and signaling pathways, lipid metabolism and gene transcription were sharply regulated, indicating that rice allocates energy and resources from growth to stress response under As(III) stress. In addition to the detection of previously identified stress-related miRNAs, we further discovered 36 new As(III)-responsive miRNAs. These results expand our understanding of As(III) stress mechanism to the As(III)-responsive mRNA and miRNA transcriptomes, which provide a foundation for subsequent functional research.
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Project description:Rice (Oryza staiva) is staple food for the human consumption and model plants for genetic and molecular studies. Only few studies have been conducted on ultraviolet-B (UV-B) stress on rice. UV-B stress effects different morphological and physiological changes in plants. However, underlying mechanisms governing these integrated responses are unknown. In this study, we conducted proteomic response of rice leaves to UV-B stress using two-dimensional gel electrophoresis and identified the selected proteins by mass spectrometry analysis. To identify changes in protein accumulation in response to UV-B stress, two cultivars, i.e., IR6 and REX were irradiated by artificial UV-B radiation. Four 4 levels of daily biologically effective UV-B radiation intensities, 0 (control), 5, 10, and 15 kJ m-2 d-1 were imposed. We conducted this experiment in Sunlit Soil-Plant-Atmosphere-Research (SPAR) chambers to mimic the natural environment.
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