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

Virginie Gébelin,Worrawat Engchuan,Pascal Montoro,Julie Leclercq,Bertrand Pitollat,Xavier Argout,Cuifang Duan

doi:10.1186/1471-2229-12-18

Abstract

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.

Highlights

Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs
Classification of small RNAs A total of 4,223,792 raw reads was generated by Solexa sequencing from the small RNA library prepared from pooled juvenile and mature plant materials subjected to various types of abiotic stress (Table 1 and Table 2)
Annotation of the Hevea small RNAs was attempted by BLASTN on the Arabidopsis genome

Summary

Introduction

Plants respond to external stimuli through fine regulation of gene expression partially ensured by small RNAs. Of these, microRNAs (miRNAs) play a crucial role. South-East Asian countries supplied 92% of the 10 million tons of natural rubber produced in 2010, but ever-growing worldwide demand calls for enhanced tree productivity. This goal is increasingly becoming a crucial challenge for the corresponding research activities in a context of global climate change and redistribution. Tapping Panel Dryness (TPD) is a physiological disease that causes 10-40% annual rubber production losses over the 30 years of a rubber cultivation cycle This physiological disorder, triggered by oxidative stress, is partially induced by excessive environmental and harvesting stresses [3]. Biotic and abiotic stress, such as drought, salinity, strong light, temperature, heavy metals, UV radiation, atmospheric contamination, mechanical wounding, nutrient starvation and pathogen attacks are major sources of ROS in plants [9]

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