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Analysis of microRNAs in response to cycloastragenol treatment by small RNA sequencing in Arabidopsis thaliana

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE171193 | GEO | 2022/12/30

REPOSITORIES: GEO

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Project description:MicroRNAs (miRNAs) are endogenous, noncoding, smallRNAs that regulate gene expression at the post-transcriptional level during plant development, growth and seed germination. Among all medicinal plants, Moringa oleifera is one of the most useful trees for which, despite its diffusion, no information about its miRNAs and their respective target genes is available. In this research, we report results obtained from a high-throughput sequencing analysis performed with the Illumina platform. A total of 31,290,964 raw reads were produced from M. oleifera seed smallRNA library. First, we found 99 conserved miRNAs and 43 novel ones that we partially validated by qRT- PCR. Second, by comparing their expression abundances with those of other common plants, we identified 20 conserved M. oleifera miRNAs. For both these results an in silico analysis allowed us to predict some of their targets which in turn allowed us to link them to a wide range of physiological processes. Based on qRT-PCR expression analyses, we reported the expression profile of some selected conserved miRNAs in different M. oleifera tissues (roots, stems and leafs). We compared the most conserved miRNAs found in Moringa with those of other edible plants, such as Olea europaea and Brassica rapa. Furthermore, by taking advantage of a recently developed web- application based on an algorithm that compares plants and mammalian miRNAs, we identify a few possible plant miRNAs with functional homologies with mammalian ones. We used the 20 most abundant M. oleifera miRNAs to conduct a preliminary analysis to investigate potential cross-kingdom gene regulation. To our knowledge, this is the first report of M. oleifera miRNAs that uses high-throughput sequencing analysis. Our analysis increases the amount of information about plant miRNAs currently available and it can help us understanding the molecular mechanism of this medical plant. microRNA profile of M. oleifera seed, germinated on paper soaked in sterile water.

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Analysis of microRNAs in response to cycloastragenol treatment by small RNA sequencing in Arabidopsis thaliana

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