Genome-wide lncRNAs identification and meta-analysis for cold-responsive genes at the booting stage in rice (Oryza sativa L)
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ABSTRACT:
PROVIDER: PRJNA510141 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8324520_1.fastq.gz | Fastqsanger.gz | |||
| SRR8324520_2.fastq.gz | Fastqsanger.gz | |||
| SRR8324521_1.fastq.gz | Fastqsanger.gz | |||
| SRR8324521_2.fastq.gz | Fastqsanger.gz | |||
| SRR8324522_1.fastq.gz | Fastqsanger.gz |
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Project description:Long non-coding RNAs (lncRNAs) are essential regulators of a broad range of biological processes in plants. Spectacular progress in next-generation sequencing technologies has enabled genome-wide identification of lncRNAs in multiple plant species. In this study, genome-wide lncRNA sequencing technology was used to identify cold-responsive lncRNAs at the booting stage in rice by comparison of a tolerant variety, Kongyu131 (KY131), and a sensitive variety, Dongnong422 (DN422). GO and KEGG enrichment analysis were performed, focusing on the cis- and trans- target genes of differential lncRNAs. To identify cold-responsive genes, a meta-analysis was used to integrate cold-tolerant QTLs at the booting stage. In total, 13 cold-responsive target genes were obtained by KEGG enrichment analysis combined with meta-analysis, as confirmed by qRT-PCR. Finally, three of these genes were identified in response to cold stress. These results sought to provide new insight into cold-resistance research for rice.
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Project description:The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains.
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Project description:We sequenced the total RNA from a tissues mixed sample (inflorescences, rosette leaves, cauline leaves and stems) of Arabidopsis thaliana. After total RNA extraction, the same amount of tissue RNA were mixed. Ribosomal RNAs were deleted from the mixed tissue total RNAs using RiboMinus™ Plant Kit repeated three times. We also sequenced 9 poly(A)- RNAs from seedlings treated with different stress conditions at different times. The poly(A)- RNAs were collected by removing poly(A)+ RNAs four times . Then rRNAs were removed from poly(A)- RNAs three times. Sequencing of total RNAs from the mixed tissues sample is taken as an example of collecting novel transcripts from high-throughput data, which could be clarified by noncoding scores derived from our integrative models. Sequencing of nonpolyA RNAs are used for identifing stress-responsive nonpolyA lncRNAs and for validation of predicted lncRNAs.
2014-09-18 | E-GEOD-49325 | biostudies-arrayexpress
Project description:The genome-wide transcriptome analyses using microarray probes containing genes and repeat sequences have been performed to examine response to the low-temperature in rice. We have particularly focused on the rice anther at the booting stage, since the low-temperature at this stage resulted in pollen abortion. The results demonstrated that the low-temperature stress caused genome-wide changes of transcriptional activities not only in genes, but also in repeat sequences of the rice anther. The degrees of the temperature responsive changes varied among the rice strains. The five rice strains exposed to the low temperature at 12°C for four days, were used for the microarray analyses. RNA was extracted from the anthers one day (C1), three days (C3) and five days (C5: this is one day after completion of the cool treatment) after the cool treatment and non-treated anthers (C0) with three biological replicates.
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Project description:Cytokinins are N6-substituted adenine derivatives that play diverse roles in plant growth and development. We sought to define a robust set of genes regulated by cytokinin, as well as to query the response of genes not represented on microarrays. To this end, we performed a meta- analysis of microarray data from a variety of cytokinin-treated samples and used RNA-seq to examine cytokinin-regulated gene expression in Arabidopsis thaliana. Microarray meta-analysis using thirteen microarray experiments combined with empirically-defined filtering criteria identified a set of 226 genes differentially regulated by cytokinin, a subset of which have previously been validated by other methods. RNA-seq validated about 73% of the up-regulated genes identified by this meta-analysis. In silico promoter analysis indicated an over- representation of type-B ARR binding elements, consistent with the role of type-B ARRs as primary mediators of cytokinin-responsive gene expression. RNA-seq analysis identified 73 cytokinin-regulated genes that were not represented on the ATH1 microarray. Representative genes were verified using qRT-PCR and NanoString analysis. Analysis of the genes identified reveals a substantial effect of cytokinin on genes encoding proteins involved in secondary metabolism, particularly those acting in flavonoid and phenylpropanoid biosynthesis, as well as in the regulation of redox state of the cell, particularly a set of glutaredoxin genes. Novel splicing events were found in members of some gene families that are known to play a role in cytokinin signaling or metabolism. The genes identified in this analysis represent a robust set of cytokinin- responsive genes that are useful in the analysis of cytokinin function in plants.
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Project description:The DEGs, lncRNAs and cirRNAs in responsive to the CGMMV infection in watermelon leaves were obtained through deep sequencing.
2019-04-24 | GSE130223 | GEO
Project description:Background: Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new glyphosate-tolerant varieties is a research focus of seed companies and researchers. The glyphosate stress-responsive genes were used for the development of genetically modified crops, while only the EPSPS gene has been used currently in the study on glyphosate-tolerance in rice. Therefore, it is essential and crucial to intensify the exploration of glyphosate stress-responsive genes, to not only acquire otherglyphosate stress-responsive genes with clean intellectual property rights but also obtain non-transgenic glyphosate-tolerant rice varieties. This study is expected to elucidate the responses of miRNAs, lncRNAs, and mRNAs to glyphosate applications and the potential regulatory mechanisms in response to glyphosate stress in rice. Results: Leaves of the non-transgenic glyphosate-tolerant germplasm CA21 sprayed with 2 mg•ml-1 glyphosate (GLY) and CA21 plants with no spray (CK) were collected for high-throughput sequencing analysis. A total of 1197 DEGs, 131 DELs, and 52 DEMs were identified in the GLY samples in relation to CK samples. Genes were significantly enriched for various biological processes involved in detoxification of plant response to stress. A total of 385 known miRNAs from 59 miRNA families and 94 novel miRNAs were identified. Degradome analysis led to the identification of 32 target genes, of which, the squamosa promoter-binding-like protein 12 (SPL12) was identified as a target of osa-miR156a_L+1. The lncRNA-miRNA-mRNA regulatory network consisted of osa-miR156a_L+1, two transcripts of SPL12 (LOC_Os06g49010.3 and LOC_Os06g49010.5), and 13 lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1). Conclusion: Large-scale expression changes in coding and noncoding RNA were observed in rice mainly due to its response to glyphosate. SPL12, osa-miR156, and lncRNAs (e.g., MSTRG.244.1 and MSTRG.16577.1) could be a novel ceRNA mechanism in response to glyphosate stress in rice.
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