Analysis of microRNAs in response to cycloastragenol treatment by small RNA sequencing in Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA718611 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14113941.fastq.gz | Fastqsanger.gz | |||
| SRR14113942.fastq.gz | Fastqsanger.gz |
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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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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.
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Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. arenosa), a natural allotetraploid (A. suecica), and two resynthesized allotetraploid lines (F1 and F7) derived from A. thaliana and A. arenosa. The siRNA populations present in A. thaliana were maintained in resynthesized allotetraploids and A. suecica. Although miRNA sequences were highly conserved, their expression patterns were highly variable between the allotetraploids and their progenitors. Significantly, many miRNAs were nonadditively expressed in the allotetraploids relative to the parents and preferentially degraded A. thaliana or A. arenosa targets. Stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to M-bM-^@M-^\genomic shockM-bM-^@M-^], whereas expression diversity of miRNAs and their target preference lead to interspecies variation in gene expression, growth, and development. NOTE: sff files unavailable for Samples AaL and F1L. 10 samples examined: Arabidopsis thaliana leaf, flower, Arabidopsis arenosa leaf and flower, F1 synthetic allopolyploid leaf and flower, F7 synthetic allopolyploid leaf and flower, Arabidopsis suecica leaf and flower. To determine small RNA profiles in Arabidopsis allotetraploids and their progenitors, we made 10 small RNA libraries from rosette leaves (L) and flower buds (F) in five lines, A. thaliana, A. arenosa, Allo(F1), Allo733(F7), and A. suecica. To examine expression of small RNAs among related species and their hybrids, we employed miRNA microarrays and compared small RNA levels.
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