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Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE

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Abstract

Twenty-two potential miRNAs from seven miRNA families were first predicted from more than 80,857 EST sequences of peach (Prunus persica). Using two specific 5′ and 3′ miRNA RACE (miR-RACE) PCR reactions and sequence-directed cloning, we accurately determined the precise sequences, especially both ends, of eight candidate miRNAs. The sequencing results demonstrated that the ppe-miRNAs were conserved to those that were predicted computationally except ppe-miR171b. We validated the existence of two members (ppe-miR171a and miR171b) of the miR171 family in peach that belonged to different precursors. qRT-PCR was further employed in analyzing expression of the eight miRNAs in peach leaves, flowers, and fruits at different developing stages, where some of the miRNAs showed tissue-specific expression.

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Acknowledgments

This research was supported by grants from the Fundamental Research Funds for the Central Universities (No. KYJ200909), a Program of NCET (No. NCET-08-0796), and the Science and Technology Key Project of Ministry of Education of China (No. 109084).

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Authors and Affiliations

  1. College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China

    Yanping Zhang, Huaping Yu, Jian Han, Changnian Song & Jinggui Fang

  2. Institute of Horticulture, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People’s Republic of China

    Mingliang Yu & Ruijuan Ma

Authors
  1. Yanping Zhang
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  2. Mingliang Yu
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  3. Huaping Yu
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  4. Jian Han
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  5. Changnian Song
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  6. Ruijuan Ma
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  7. Jinggui Fang
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Corresponding author

Correspondence to Jinggui Fang.

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Yanping Zhang and Mingliang Yu contributed equally to this work.

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Zhang, Y., Yu, M., Yu, H. et al. Computational identification of microRNAs in peach expressed sequence tags and validation of their precise sequences by miR-RACE. Mol Biol Rep 39, 1975–1987 (2012). https://doi.org/10.1007/s11033-011-0944-6

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  • DOI: https://doi.org/10.1007/s11033-011-0944-6

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