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Transcriptomic Analysis reveals responses to Cycloastragenol in Arabidopsis thaliana

ABSTRACT: Transcriptomic Analysis reveals responses to Cycloastragenol in Arabidopsis thaliana

PROVIDER: PRJNA665188 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12697039.fastq.gz	Fastqsanger.gz
	SRR12697040.fastq.gz	Fastqsanger.gz

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Transcriptomic Analysis reveals responses to Cycloastragenol in Arabidopsis thaliana

Project description:Purpose: we aimed to demonstrate the effects of Cycloastragenol on the different plant signaling mechanisms and analyze genome-wide transcriptional responses in order to demonstrate its potential as a new key molecule to help plants overcome different environmental stresses. Methods: RNA-seq was employed to assess transcriptional profiles in treated and non-treated A. thaliana calli. We sequenced two cDNA libraries developed from A. thaliana (wild type Col-0) calli treated with 1µM Cycloatragenol and without. The sequence reads that was filtered, were mapped, aligned and then compared to the reference annotation (the known genes of A. thaliana genome) using Cufflinks tools. Clean data was analyzed using CPC software and results were validated by qRT-PCR using TaqMan and SYBER green assays. Results: We mapped around 63 and 70 million sequence reads from, respectively, control and CAG-treated samples. After filtration and mapping about 21 thousands genes corresponding to an average of 34 thousands transcripts, for each sample were identified. 1045 genes showed differential expression between control and treated sample with a p value < 0.05. Seven genes, which have been chosen randomly, were validated with qRT-PCR. RNA-seq data had a linear relationship with qRT-PCR for a goodness of fit (R2) of 0.959.

2020-11-24 | GSE158409 | GEO

Transcriptomic analysis reveals responses to Cycloastragenol in Arabidopsis thaliana.

Project description:Cycloastragenol (CAG), a molecule isolated from 'Astragalus membranaceus', stimulates the telomerase activity and cell proliferation significantly. It has been proven that CAG has the ability to prevent some diseases in humans. In this study, we aimed to figure out the CAG effects on the different signaling mechanisms in plants and to broadly analyze the genome-wide transcriptional responses in order to demonstrate CAG as a new key molecule that can potentially help plants to overcome different environmental stresses. RNA-seq strategy was employed to assess the transcriptional profiles in A. thaliana calli. Our work primarily focused on an overall study on the transcriptomic responses of A. thaliana to CAG. A total of 22593 unigenes have been detected, among which 1045 unigenes associated with 213 GO terms were differentially expressed and were assigned to 118 KEGG pathways. The up-regulated genes are principally involved in cellular and metabolic processes in addition to the response to a stimulus. The data analysis revealed genes associated with defense signaling pathways such as cytochrome P450s transporter, antioxidant system genes, and stress-responsive protein families were significantly upregulated. The obtained results can potentially help in better understanding biotic and/or abiotic tolerance mechanisms in response to CAG.

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Project description:Purpose:we aimed to demonstrate the effects of cycloastragenol on the different plant signaling mechanisms and analyze microRNAomic responses in order to demonstrate its potential as a new key molecule to help plants overcome different environmental stresses. Methods: smallRNA-seq was employed to give a quantitative profile of microRNA expression and to identify new micro RNAs and in treated and non-treated A. thaliana calli. We sequenced two cDNA libraries developed from A. thaliana (wild type Col-0) calli, one non-treated and the other is treated with 1µM cycloatragenol. Reads were filtered, mapped, aligned and then compared to the reference annotation (miRBase database). Clean data was analyzed using different software in order to identify differentilly expressed miRNAs and their target genes. Results were validated by qRT-PCR using TaqMan and SYBER green assays. Results: We mapped more than 31 and 30 million tags from, respectively, control and CAG-treated samples. After filtration and mapping, a total of 273 known micro RNAs, 298 novels expressed miRNAs and 6160 target genes were identified, among which a total of 119 miRNAs and 961 target genes showed differential expression between control and treated sample with a p value < 0.05. Nine miRNAs, which have been chosen randomly, were validated with qRT-PCR. SmallRNA-seq data had a linear relationship with qRT-PCR for a goodness of fit (R2) of 0.938.

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