Oryza sativa Indica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA310656 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3140960.fastq.gz | Fastqsanger.gz | |||
| SRR3140952.fastq.gz | Fastqsanger.gz | |||
| SRR3140953.fastq.gz | Fastqsanger.gz | |||
| SRR3140954.fastq.gz | Fastqsanger.gz | |||
| SRR3140955.fastq.gz | Fastqsanger.gz |
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Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced
2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5’ rapid amplification of cDNA ends (RLM 5’-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice.
2010-01-01 | GSE19050 | GEO
Project description:MicroRNAs (miRNAs) are 19-24 nucleotide (nt) noncoding RNAs that play important roles in abiotic stress responses in plants. High temperatures have been the subject of considerable attention due to their negative effects on plant growth and development. Heat-responsive miRNAs have been identified in some plants. However, there have been no reports on the global identification of miRNAs and their targets in tomato at high temperatures, especially at different elevated temperatures. Here, three small-RNA libraries and three degradome libraries were constructed from the leaves of the heat-tolerant tomato at normal, moderately and acutely elevated temperatures (26/18°C, 33/33°C and 40/40°C, respectively). Following high-throughput sequencing, 662 conserved and 97 novel miRNAs were identified. Of these miRNAs, 96 and 150 miRNAs were responsive to the moderately and acutely elevated temperature, respectively. Following degradome sequencing, 349 sequences were identified as targets of 138 conserved miRNAs, and 13 sequences were identified as targets of eight novel miRNAs. The expression levels of four miRNAs and five target genes obtained by quantitative real-time PCR (qRT-PCR) were largely consistent with the sequencing results. This study enriches the number of heat-responsive miRNAs and lays a foundation for the elucidation of the miRNA-mediated regulatory mechanism in tomatoes at elevated temperatures.
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Project description:In this study, we identified a set of heat stress-responsive miRNAs and verified their targets through degradome sequencing. Nine libraries (triplicate for 0 h, 12 h and 24 h heat treatment) were constructed and sequenced. Four hundred and nineteen conserved miRNAs and 77 novel miRNAs were identified, of which, 40 conserved and two novel miRNAs were expressed differentially. Quantitative PCR of three selected miRNAs and their targets confirmed that these loci were responsive to heat stress. A total of 1364 target transcripts were identified for 114 conserved miRNA and a total of 65 were identified for 22 novel miRNA families. Gene function and pathway analyses showed that these genes probably play vital roles in rice heat stress tolerance.
2017-12-21 | GSE77510 | GEO
Project description:Purpose: Circular RNAs (circRNAs) and microRNAs (miRNAs) play important roles in abiotic stress responses in plants. The aims of this study are to genome-widely identify the circRNAs, miRNAs and their targets in tomatoes at single heat, drought and their combination by high-throughput sequencing. Results: Following high-throughput sequencing, 765 miRNAs were identified in total with 335 conserved and 430 novel miRNAs in the 12 small-RNA libraries. Of these miRNAs, 32, 74 and 61 miRNAs were responsive to drought, heat and their combination, respectively. Following degradome sequencing, 50 sequences were identified as targets of 34 miRNAs in tomatoes at combined stress. Moreover, 467 circRNAs were identified in the 12 samples.
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Project description:Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica)
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Project description:High-throughput approaches for profiling the 5' ends of RNA degradation intermediates on a genome-wide scale are frequently applied in the validation of cleavage sites guided by microRNAs (miRNAs). However, the complexity of the RNA degradome beyond miRNA targets is currently largely unclear which limits the application of RNA degradome. Here, we provide multiple lines of evidence to show that the plant RNA degradome contains in vivo ribosome-protected mRNA fragments. We observed a 3-nt periodicity and a bias toward the translational frame in the global analysis of 5' truncated mRNA ends mapped to the coding sequence (CDS) of Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and soybean (Glycine max). In addition, predominant 5' termini of RNA degradation intermediates separated by a length equal to a ribosome-protected mRNA fragment were evident in some conserved peptide upstream open reading frames (uORFs) of Arabidopsis and rice. Through the analysis of RNA degradome data, we uncovered novel uORFs and CDS regions potentially associated with stacked ribosomes in Arabidopsis. Furthermore, the analysis of RNA degradome data suggested that the binding of Arabidopsis ARGONAUTE7 to a non-cleavable target site of miR390 might directly hinder ribosome movement. This work demonstrates an alternative use of RNA degradome data in the study of ribosome stalling.
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