Microarray identification of conserved microRNAs in Pinellia pedatisecta
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ABSTRACT:
ORGANISM(S): Pinellia pedatisecta synthetic construct
PROVIDER: GSE33915 | GEO | 2014/01/01
SECONDARY ACCESSION(S): PRJNA148241
REPOSITORIES: GEO
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Project description:miRNA expression profiling of Pinellia pedatisecta leaves comparing Pinellia ternata leaves in the same condition. Then we compared the accumulation of known miRNA families using microarray signals to identify further the differential miRNA expression between Pinellia pedatisecta and Pinellia ternata.
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Project description:miRNA expression profiling of Pinellia pedatisecta leaves comparing Pinellia ternata leaves in the same condition. Then we compared the accumulation of known miRNA families using microarray signals to identify further the differential miRNA expression between Pinellia pedatisecta and Pinellia ternata. Pinellia pedatisecta vs Pinellia ternata, independently grown and harvested. Each sample are mixed. One replicate per array.
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Project description:In plants, non-coding small RNAs play a vital role for plant development and stress responses. To explore the possible role of non-coding small RNAs in the regulation of the jasmonate (JA) pathway, we compared the non-coding small RNAs between the JA-deficient aos mutant and the JA-treated wild type Arabidopsis via high-throughput sequencing. 30 new miRNAs and 27 new miRNA candidates were identified through a bioinformatics approach. 49 known miRNAs (belonging to 24 families), 15 new miRNAs and new miRNA candidates (belonging to 11 families) and 3 tasiRNA families were induced by JA, whereas 1 new miRNA, 1 tasiRNA family and 22 known miRNAs (belonging to 9 families) were repressed by JA. 2 samples were examined: wild type treated with JA, and the JA-deficient aos mutant.
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Project description:MicroRNAs (miRNAs) are endogenous small RNAs that play important roles in various biological and metabolic processes in plants. Caragana intermedia is an important ecological and economic tree species that is prominent in the desert environment of west and northwest China. To date, no investigation into C. intermedia miRNAs has been reported. In this study, high-throughput sequencing of small RNAs was performed to identify both conserved and novel miRNAs, and also their target mRNA genes in C. intermedia. Based on sequence similarity and hairpin structure prediction, 132 putative conserved miRNAs (12 of which were confirmed to form hairpin precursors) belonging to 31 known miRNA families were identified. Ten novel miRNAs (including the miRNA* sequences of three novel miRNAs) were also discovered. The expression of 12 miRNAs was validated in different tissues, and the 12 miRNAs were further assessed by qRT-PCR after salt treatment. Furthermore, 36 potential target genes of 17 known miRNA families and two potential target genes of one novel miRNA were predicted, and some target genes were also assessed by qRT-PCR after salt treatment. Our study provides a basic catalog of miRNAs and their targets, which will promote further understanding of the important roles of miRNAs in C. intermedia and in other species of the leguminous genus, Caragana.
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