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Genomics. 2014 Apr;103(4):298-307. doi: 10.1016/j.ygeno.2014.03.002. Epub 2014 Mar 22.

Identification and characterization of a subset of microRNAs in wheat (Triticum aestivum L.).

Author information

1
Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
2
Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
3
Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China.
4
Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China. Electronic address: cp_zhao@vip.sohu.com.
5
Engineering and Technique Research Center of Hybrid Wheat, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China; Department of Biology, University of Virginia, Charlottesville, VA 22904, USA. Electronic address: ll4jn@virginia.edu.

Abstract

MicroRNAs (miRNAs) represent a class of endogenous regulator for post-transcriptionally modulating gene expression. Elucidating complete miRNA repertoires for individual species is a long-desired goal in miRNA research. So far only 42 have been annotated for common wheat (Triticum aestivum) due to its large genome. Here, we employed miRDeep-P, a program developed previously for retrieving miRNAs from deep sequencing data in plants, to parse 14 sequenced small RNA libraries of wheat using expression sequence tags (ESTs) as the reference in lieu of a complete genome sequence. This effort identified 145 miRNAs along with the corresponding stem-looped precursors with many differentially expressed in development and associated with powdery mildew infection. Examination of the phylogenetic distribution of these miRNAs and their target genes revealed that many are conserved in monocots. The set of miRNAs identified in this study is thus useful to further miRNA research in wheat and other important cereal crop species.

KEYWORDS:

Deep sequencing; EST; MicroRNA; Triticum aestivum; Wheat; miRDeep-P

PMID:
24667243
DOI:
10.1016/j.ygeno.2014.03.002
[Indexed for MEDLINE]
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