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Nucleic Acids Research Advance Access published online on November 26, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp1035
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

RNA

Conservation and divergence of microRNAs and their functions in Euphorbiaceous plants

Changying Zeng1,2, Wenquan Wang1, Yun Zheng3, Xin Chen1, Weiping Bo1,2, Shun Song1,2, Weixiong Zhang1,3,4,* and Ming Peng1,*

1The Institute of Tropical Bioscience and Biotechnology (ITBB), Chinese Academy of Tropical Agricultural Sciences (CATAS), 2Hainan University, Haikou, P. R. China, 3Department of Computer Science and Engineering, Washington University in St. Louis and 4Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA

*To whom correspondence should be addressed. Tel: +1 314 935 8788; Fax: +1 314 935 7302; Email: weixiong.zhang{at}wustl.edu

Correspondence may also be addressed to Ming Peng. Tel: +86 0898 66963138; Fax: +86 0898 66988081; Email: mmpeng_2000{at}yahoo.com

Received July 17, 2009. Revised October 20, 2009. Accepted October 21, 2009.

MicroRNAs (miRNAs) are ~21 nt non-coding RNAs which regulate post-transcriptional gene expression. miRNAs are key regulators of nearly all essential biological processes. Aiming at understanding miRNA’s functions in Euphorbiaceae, a large flowering plant family, we performed a genome-scale systematic study of miRNAs in Euphorbiaceae, by combining computational prediction and experimental analysis to overcome the difficulty of lack of genomes for most Euphorbiaceous species. Specifically, we predicted 85 conserved miRNAs in 23 families in the Castor bean (Ricinus communis), and experimentally verified and characterized 58 (68.2%) of the 85 miRNAs in at least one of four Euphorbiaceous species, the Castor bean, the Cassava (Manihot esculenta), the Rubber tree (Hevea brasiliensis) and the Jatropha (Jatropha curcas) during normal seedling development. To elucidate their function in stress response, we verified and profiled 48 (56.5%) of the 85 miRNAs under cold and drought stresses as well as during the processes of stress recovery. The results revealed some species- and condition-specific miRNA expression patterns. Finally, we predicted 258 miRNA:target partners, and identified the cleavage sites of six out of ten miRNA targets by a modified 5' RACE. This study produced the first collection of miRNAs and their targets in Euphorbiaceae. Our results revealed wide conservation of many miRNAs and diverse functions in Euphorbiaceous plants during seedling growth and in response to abiotic stresses.

The authors wish it to be known that, in their opinion, the first three authors and the seventh author should be regarded as joint First Authors.

Present address: Yun Zheng, Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai, China.


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