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

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.

Transcriptome-Wide Identification and Characterization of MicroRNAs from Castor Bean (Ricinus communis L.)

“…Further, we found that all homologs of 27 conserved miRNA families of castor bean in rubber tree, but we did not find any homolog of the 72 novel miRNAs identified from castor bean in other members of Euphorbiaceae including rubber tree [43], [44], Jatropha curcas [45] and Manihot esculenta [46], implying that the 72 novel miRNAs detected might represent castor bean species-specific miRNAs. Compared to the target genes identified in other plants, rco-miR167, rco-miR172 and rco-miR482 exhibited similar targets to their homologs in Arabidopsis [47] and maize [25].…”

Sequence and Expression Analyses of Ethylene Response Factors Highly Expressed in Latex Cells from Hevea brasiliensis

“…More recently, several high-throughput analyses have led to the identification of microRNAs [56], [57], transcriptomes [11], [58]–[60], and genomes [61] using NGS technologies. All the transcriptome analyses have provided a partial overview of the Hevea transcriptome, as RNAs from only a few specific tissues were sequenced, such as shoot apex [58] and leaf [61] from clone RRIM 600, along with leaf and latex from CATAS 7-33-97 [59].…”

Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development?

“…miR828 is the trigger for production of TAS4 siRNAs, and was originally thought to be unique to Arabidopsis , but has subsequently been found in grape [55], poplar ( Populus trichocarpa ) [56], cotton ( Gossypium hirsutum ) [57], cabbage ( Brassica rapa ) [58], flax ( Linum usitatissimum ) [59], soybean ( Glycine max ) [21], common bean ( Phaseolus vulgaris ) [60], clary sage ( Salvia sclarea ) [61], melon ( Cucumis melo ) [62], rose ( Rosa multiflora ) [63], tomato ( Solanum lycopersicum ) [64], tobacco ( Nicotiana tabacum and N. attenuata ) [65, 66], cocoa ( Theobroma cacao ) [67], Chinese apricot ( Prunus mume ) [68, 69], peach ( Prunus persica ) [70, 71], citrus ( Citrus sinensis ) [72], apple ( Malus domestica ) [73], hickory ( Carya cathayensis ) [74], cassava ( Manihot esculenta ) [75], Brazilian cherry ( Eugenia uniflora ) [76], Chinese tulip tree ( Liriodendron chinense ) [77], and Red Sea mangrove ( Avicennia marina ) [78]. Figure 1 shows a phylogram of the evolutionary relationships for eudicot species which have evidence of TAS4 in their genomes.…”