Identification of novel microRNAs in Hevea brasiliensisand computational prediction of their targets

BMC Plant Biology

Research Article

Bertrand Pitollat¹  Virginie Gébelin¹  Xavier Argout¹  Pascal Montoro¹  Julie Leclercq¹  Cuifang Duan²  Worrawat Engchuan³ 

[1] CIRAD, UMR AGAP, F-34398, Montpellier, France;CIRAD, UMR AGAP, F-34398, Montpellier, France;CATAS, RRI, Danzhou, 571737, Hainan, China;CIRAD, UMR AGAP, F-34398, Montpellier, France;King Mongkut's University of Technology, Thonburi, Thailand;

关键词: Gene expression;    miRNA;    MIR;    Next-generation sequencing;    Rubber tree;    Transcription;    Transcriptome;    Abiotic stress;    miRNA editing;   

DOI  :  10.1186/1471-2229-12-18

 received in 2011-10-05, accepted in 2012-02-13,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundPlants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. They negatively regulate gene expression by targeting the cleavage or translational inhibition of target messenger RNAs (mRNAs). In Hevea brasiliensis, environmental and harvesting stresses are known to affect natural rubber production. This study set out to identify abiotic stress-related miRNAs in Hevea using next-generation sequencing and bioinformatic analysis.ResultsDeep sequencing of small RNAs was carried out on plantlets subjected to severe abiotic stress using the Solexa technique. By combining the LeARN pipeline, data from the Plant microRNA database (PMRD) and Hevea EST sequences, we identified 48 conserved miRNA families already characterized in other plant species, and 10 putatively novel miRNA families. The results showed the most abundant size for miRNAs to be 24 nucleotides, except for seven families. Several MIR genes produced both 20-22 nucleotides and 23-27 nucleotides. The two miRNA class sizes were detected for both conserved and putative novel miRNA families, suggesting their functional duality. The EST databases were scanned with conserved and novel miRNA sequences. MiRNA targets were computationally predicted and analysed. The predicted targets involved in "responses to stimuli" and to "antioxidant" and "transcription activities" are presented.ConclusionsDeep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs when the complete genome is not yet available. Our study provided additional information for evolutionary studies and revealed potentially specific regulation of the control of redox status in Hevea.

【 授权许可】

Unknown   
© Gébelin et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/2.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.