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Molecular Genetics and Genomics

, Volume 287, Issue 7, pp 555–563 | Cite as

High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

  • Fengde Wang
  • Libin Li
  • Lifeng Liu
  • Huayin Li
  • Yihui Zhang
  • Yingyin Yao
  • Zhongfu Ni
  • Jianwei GaoEmail author
Original Paper

Abstract

MicroRNAs (miRNAs) are a class of 21–24 nucleotide non-coding RNAs that down-regulate gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in a few model plant species such as Arabidopsis, rice and Populus, and partially investigated in other non-model plant species. However, only a few conserved miRNAs have been identified in Chinese cabbage, a common and economically important crop in Asia. To identify novel and conserved miRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis) we constructed a small RNA library. Using high-throughput Solexa sequencing to identify microRNAs we found 11,210 unique sequences belonging to 321 conserved miRNA families and 228 novel miRNAs. We ran a Blast search with these sequences against the Chinese cabbage mRNA database and found 2,308 and 736 potential target genes for 221 conserved and 125 novel miRNAs, respectively. The BlastX search against the Arabidopsis genome and GO analysis suggested most of the targets were involved in plant growth, metabolism, development and stress response. This study provides the first large scale-cloning and characterization of Chinese cabbage miRNAs and their potential targets. These miRNAs add to the growing database of new miRNAs, prompt further study on Chinese cabbage miRNA regulation mechanisms, and help toward a greater understanding of the important roles of miRNAs in Chinese cabbage.

Keywords

Chinese cabbage High-throughput sequencing MicroRNA Target gene 

Notes

Acknowledgments

This work was supported by the Prospect of Shandong Seed Project, China (2011lzgcshucaizy); National Nature Science Foundation of China (31101553); Modern Agricultural Industrial Technology System Funding of Shandong Province, China (2010sdxdcyjstxshucai) and the Promotive Research Fund for Excellent Young and Middle-aged Scientists of Shandong Province, China (BS2010SW027).

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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Fengde Wang
    • 1
  • Libin Li
    • 1
  • Lifeng Liu
    • 1
  • Huayin Li
    • 1
  • Yihui Zhang
    • 1
  • Yingyin Yao
    • 2
  • Zhongfu Ni
    • 2
  • Jianwei Gao
    • 1
    Email author
  1. 1.Institute of Vegetables, Shandong Academy of Agricultural Sciences Shandong, Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement CenterJinanChina
  2. 2.State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Genomics and Genetic Improvement (MOA)China Agricultural UniversityBeijingChina

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