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Open Access Highly Accessed Research article

Identification of novel microRNAs in Hevea brasiliensis and computational prediction of their targets

Virginie Gébelin1, Xavier Argout1, Worrawat Engchuan12, Bertrand Pitollat1, Cuifang Duan13, Pascal Montoro1* and Julie Leclercq1

Author Affiliations

1 CIRAD, UMR AGAP, F-34398 Montpellier, France

2 King Mongkut's University of Technology, Thonburi, Thailand

3 CATAS, RRI, Danzhou, 571737 Hainan, China

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BMC Plant Biology 2012, 12:18  doi:10.1186/1471-2229-12-18

Published: 13 February 2012

Abstract

Background

Plants 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.

Results

Deep 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.

Conclusions

Deep 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.

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