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Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv

  • Bo Wei
  • Tao Cai
  • Rongzhi Zhang
  • Aili Li
  • Naxin Huo
  • Shan Li
  • Yong Q. Gu
  • John Vogel
  • Jizeng Jia
  • Yijun QiEmail author
  • Long MaoEmail author
Original Paper

Abstract

The small RNA transcriptomes of bread wheat and its emerging model Brachypodium distachyon were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNAs) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of expressed sequence tags, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5′ rapid amplification of complementary DNA ends experiments demonstrated their capability to cleave predicted target genes including three disease-resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in B. distachyon.

Keywords

Brachypodium Wheat Small RNA MicroRNA SiRNA 

Notes

Acknowledgements

We thank Dr. Charles Leseberg for critical reading of this manuscript. We are grateful to Professor Rudi Appels and Dr. Wujun Ma who provided constructive suggestions during the revision of the manuscript. This work was supported in part by the National HITECH Research and Development Program of China (“863” program, #2006AA10A104), Special Research Grant for Central Governmental Nonprofit Research Institutes (Yuan-Suo-Zhang-Ji-Jin), and National Basic Research Program (“973” program, #2004CB117200) of China.

Supplementary material

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Bo Wei
    • 1
  • Tao Cai
    • 2
  • Rongzhi Zhang
    • 1
  • Aili Li
    • 1
  • Naxin Huo
    • 3
  • Shan Li
    • 2
  • Yong Q. Gu
    • 3
  • John Vogel
    • 3
  • Jizeng Jia
    • 1
  • Yijun Qi
    • 2
    Email author
  • Long Mao
    • 1
    Email author
  1. 1.National Key Facility for Crop Gene Resources and Genetic Improvement and Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingPeople’s Republic of China
  2. 2.National Institute of Biological SciencesBeijingChina
  3. 3.Western Regional Research Center, Agricultural Research ServiceUS Department of AgricultureAlbanyUSA

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