Abstract:MicroRNAs (miRNA) are ∼21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of la… Show more
“…The expression of target genes should be negatively correlated with miRNA expression, since miRNA triggers degradation of target mRNA (Zhang et al 2010). The result of GO analysis shows that miRNA-targeted genes induced in V592-infected plants were involved in extensive pathways (Figure 4(a), Table S4), which is consistent with the complicated role of miRNAs in plant developments and responses to biotic or abiotic stimulation.10.1080/21501203.2018.1426062-F0004Figure 4.The function and expression of altered miRNAs targeted genes.…”
Section: Resultsmentioning
confidence: 99%
“…Perl scripts were used to search these miRNA sequences from our sRNA libraries. The targets of miRNA in Arabidopsis were downloaded from Plant MicroRNA Database (Zhang et al 2010). The function of these targets was annotated by AgriGO (Du et al 2010).…”
Small RNAs (sRNAs, including small interfering RNAs [siRNAs] and micro RNAs [miRNAs]) are key mediators of RNA silencing (or RNA interference), which play important roles in plant development and response to biotic and abiotic stimulation. Verticillium wilt is a plant vascular disease caused by the soil-borne fungal pathogens, such as Verticillium dahliae. We previously reported that V. dahliae infection increased two plant endogenous miRNAs that were exported to fungal cell to silence virulence genes. To investigate plant sRNAs in genome-wide response to V. dahliae infection, in this study, we constructed two sRNA libraries from Arabidopsis roots with and without V. dahliae infection, respectively. In total, 31 conserved miRNAs were found to be differentially expressed during the early stage of infection with V. dahliae using sRNA sequencing. Among these, the expression levels of miR160, miR164, miR166, miR167, miR390 and miR156h were confirmed by northern blot. Reverse transcription quantitative real time polymerase chain reaction results showed that the induction of miRNAs (miR160, miR164, miR166 and miR167) upon V. dahliae infection downregulated the expression of their targeted genes (ARF10, NAC1, PHV and ARF6), respectively. In addition, we identified specific phased siRNAs generated from distinct regions of two libraries. Profiling of these miRNAs and sRNAs lay the foundation for further understanding and utilising the host-induced gene silencing strategy to control plant vascular pathogens.
“…The expression of target genes should be negatively correlated with miRNA expression, since miRNA triggers degradation of target mRNA (Zhang et al 2010). The result of GO analysis shows that miRNA-targeted genes induced in V592-infected plants were involved in extensive pathways (Figure 4(a), Table S4), which is consistent with the complicated role of miRNAs in plant developments and responses to biotic or abiotic stimulation.10.1080/21501203.2018.1426062-F0004Figure 4.The function and expression of altered miRNAs targeted genes.…”
Section: Resultsmentioning
confidence: 99%
“…Perl scripts were used to search these miRNA sequences from our sRNA libraries. The targets of miRNA in Arabidopsis were downloaded from Plant MicroRNA Database (Zhang et al 2010). The function of these targets was annotated by AgriGO (Du et al 2010).…”
Small RNAs (sRNAs, including small interfering RNAs [siRNAs] and micro RNAs [miRNAs]) are key mediators of RNA silencing (or RNA interference), which play important roles in plant development and response to biotic and abiotic stimulation. Verticillium wilt is a plant vascular disease caused by the soil-borne fungal pathogens, such as Verticillium dahliae. We previously reported that V. dahliae infection increased two plant endogenous miRNAs that were exported to fungal cell to silence virulence genes. To investigate plant sRNAs in genome-wide response to V. dahliae infection, in this study, we constructed two sRNA libraries from Arabidopsis roots with and without V. dahliae infection, respectively. In total, 31 conserved miRNAs were found to be differentially expressed during the early stage of infection with V. dahliae using sRNA sequencing. Among these, the expression levels of miR160, miR164, miR166, miR167, miR390 and miR156h were confirmed by northern blot. Reverse transcription quantitative real time polymerase chain reaction results showed that the induction of miRNAs (miR160, miR164, miR166 and miR167) upon V. dahliae infection downregulated the expression of their targeted genes (ARF10, NAC1, PHV and ARF6), respectively. In addition, we identified specific phased siRNAs generated from distinct regions of two libraries. Profiling of these miRNAs and sRNAs lay the foundation for further understanding and utilising the host-induced gene silencing strategy to control plant vascular pathogens.
“…We utilized MiRPI for internal research to test the sample data which were downloaded from public databases such as National Centre for Biotechnology Information (NCBI) and plant miRNA database (PMRD) (Zhang et al, 2010). The output retrieves required information and frames into columns as follows, the gene id, their length, matching miRNA id, start and end position, strand, and conserved mature miRNA sequence.…”
Section: Fig 3 Formulas Used For Calculating Adjusted Minimum Foldimentioning
confidence: 99%
“…Targets were checked with plant mRNA sequences which were downloaded from NCBI GenBank (www.ncbi.nlm. nih.gov/genbank) database and miRNAs from PMR database (Zhang et al, 2010). Identified target results were outlined into seven columns, and organized as follows miRNA id, target gene id, target, start and end position of mature miRNA, strand, and compliment mature miRNA sequences which binds to identified miRNA.…”
Section: Fig 3 Formulas Used For Calculating Adjusted Minimum Foldimentioning
confidence: 99%
“…Efficiency of the tool was evaluated with standard example sets of data which were downloaded from the NCBI database and plant miRNA database (Zhang et al, 2010). Overlapping miRNAs were removed by in home developed scripts and resulted 1191 non-repeated mature miRNAs.…”
Section: Fig 3 Formulas Used For Calculating Adjusted Minimum Foldimentioning
MicroRNAs (miRNAs) are recently discovered small RNA molecules usually resulting in translational repression and gene silencing. Despite the fact that specific cloning of small RNA's is a method in practice, computational identification of miRNA's has been a major focus recent days, since is a rapid process following AB initio and sequence alignment methods. Here we developed new software called MiRPI that aims to identify the highly conserved miRNAs without any mismatches from given fasta formatted gene sequences by using non-repeated miRNA dataset of the user's interest. The new window embedded with the software is used to identify the targets for inputted mature miRNAs in the mRNA sequences. Also MiRPI is designed to measure the precursor miRNA statistics, majorly focusing the Adjusted Minimum Folding free Energy (AMFE) and Minimum Folding free Energy Index (MFEI), the most important parameters in miRNA confirmation. MiRPI is developed by PERL (Practical Extraction and Report Language) and Tk (Tool kit widgets) scripting languages. It is user friendly, portable offline software that works in all windows OS, sized to 3 MB.
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