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Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress

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142 miRNAs were identified and 38 miRNA targets were predicted, 4 of which were validated, in C. intermedia . The expression of 12 miRNAs in salt-stressed leaves was assessed by qRT-PCR.

Abstract

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 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 and analysis of transcriptome data were 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. Furthermore, 36 potential target genes of 17 known miRNA families and 2 potential target genes of 1 novel miRNA were predicted; 4 of these were validated by 5′ RACE. The expression of 12 miRNAs was validated in different tissues, and these and five target mRNAs were assessed by qRT-PCR after salt treatment. The expression levels of seven miRNAs (cin-miR157a, cin-miR159a, cin-miR165a, cin-miR167b, cin-miR172b, cin-miR390a and cin-miR396a) were upregulated, while cin-miR398a expression was downregulated after salt treatment. The targets of cin-miR157a, cin-miR165a, cin-miR172b and cin-miR396a were downregulated and showed an approximately negative correlation with their corresponding miRNAs under salt treatment. These results would help further understanding of miRNA regulation in response to abiotic stress in C. intermedia.

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Acknowledgments

This work was supported by the National Basic Research Program of China (2009CB119100), the National High Technology Research and Development Program of China (2011AA100203) and the National Natural Science Foundation of China (30830086).

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Authors and Affiliations

  1. Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, People’s Republic of China

    Jianfeng Zhu, Wanfeng Li, Wenhua Yang & Liwang Qi

  2. Key Laboratory of Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, 100091, People’s Republic of China

    Suying Han

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  1. Jianfeng Zhu
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  2. Wanfeng Li
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  3. Wenhua Yang
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  4. Liwang Qi
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  5. Suying Han
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Correspondence to Suying Han.

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Communicated by H. Judelson.

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Zhu, J., Li, W., Yang, W. et al. Identification of microRNAs in Caragana intermedia by high-throughput sequencing and expression analysis of 12 microRNAs and their targets under salt stress. Plant Cell Rep 32, 1339–1349 (2013). https://doi.org/10.1007/s00299-013-1446-x

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  • DOI: https://doi.org/10.1007/s00299-013-1446-x

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