smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways.This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to understand their roles in key stevia traits.MicroRNAs (miRNAs) constitute a class of single stranded 19–24 nucleotide long non-coding RNAs that mediate endogenous gene silencing by binding to their target genes. miRNAs binds either to the open reading frame (ORF) or untranslated regions (UTRs) of target mRNAs and silencing occurs either by target cleavage or by inhibiting mRNA translation [1,2] through perfect or partial complementarity respectively [3]. miRNA feature to regulate gene expression is exemplified by their indispensable roles in critical biological and cellular events in plants including lateral root formation, leaf morphology and polarity, hormonal control, flowering time [4], cell death and apoptosis [5]. These are also involved in plant adaptation to vast array of biotic and abiotic stresses such as cold, drought, salinity, nutrient deficiency [4,6] and oxidative stress [7]. Majority of the targets of plant miRNAs were found to be transcription factors such as Squamosa-promoter Binding Protei