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Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing


MicroRNAs (miRNAs) play important roles in response of plants to biotic and abiotic stresses. Aluminum (Al) toxicity is a major factor limiting plant growth in acidic soils. However, there has been limited report on the involvement of miRNAs in response of plants to toxic Al3+. To identify Al3+-responsive miRNAs at whole-genome level, high-throughput sequencing technology was used to sequence libraries constructed from root apices of the model legume plant Medicago truncatula treated with and without Al3+. High-throughput sequencing of the control and two Al3+-treated libraries led to generation of 17.1, 14.1 and 17.4 M primary reads, respectively. We identified 326 known miRNAs and 21 new miRNAs. Among the miRNAs, expression of 23 miRNAs was responsive to Al3+, and the majority of Al3+-responsive mRNAs was down-regulated. We further classified the Al3+-responsive miRNAs into three groups based on their expression patterns: rapid-responsive, late-responsive and sustained-responsive miRNAs. The majority of Al3+-responsive miRNAs belonged to the ‘rapid-responsive’ category, i.e. they were responsive to short-term, but not long-term Al3+ treatment. The Al3+-responsive miRNAs were also verified by quantitative real-time PCR. The potential targets of the 21 new miRNAs were predicted to be involved in diverse cellular processes in plants, and their potential roles in Al3+-induced inhibition of root growth were discussed. These findings provide valuable information for functional characterization of miRNAs in Al3+ toxicity and tolerance.

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MicroRNA precursor


MicroRNA primary transcript


MicroRNA star


Quantitative real-time PCR


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This work was supported by Natural Science Foundation of China (90817011, 30788003 and 30800706) and the State Key Basic Research Development Program of China (2007CB106800) and State Key Laboratory of Vegetation and Environmental Chang.

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Correspondence to Wen-Hao Zhang.

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Chen, L., Wang, T., Zhao, M. et al. Identification of aluminum-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. Planta 235, 375–386 (2012).

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  • Aluminum toxicity
  • High-throughput sequencing
  • Medicago
  • MicroRNA