Identification of Conserved and Novel miRNAs in Chlorophytum borivilianum Using Deep Sequencing of Small RNA

Chlorophytum borivilianum (Liliaceae family) had played a critical role in ayurvedic medicine for the treatment of various disease ailments. Root concentrate of C. borivilianum is utilized in the formulation of phyto-pharmaceuticals and nutraceutical drugs even in modern medicine. A number of studies have been performed through transcriptomic investigations and plant tissue culture focused to increase the amount of saponin, but any miRNA survey has not been conducted till now. Characteristic of plant miRNAs (20-24 nt) to serve as negative regulators of many metabolic processes, trigger to explore the miRNAs involved in secondary metabolism. In present study, our aim was to identify miRNAs involved in saponin biosynthesis and to scrutinize their targets. To execute this, in-silico identification of the conserved and novel miRNAs from C. borivilianum was carried out. An aggregate of 79,419,700 (of length =50bp) raw reads were created from small RNA library using Illumina MiSeq from C. borivilanum young leaves. About 95% of total data passed >= 30 phred score with an average base quality =37.41 and having 50.54% GC content. Total 251 conserved miRNAs belonging to 38 miRNA families and 6 novel miRNAs were determined. Five out of 6 novel miRNAs were found to potentially target the enzymes involved in saponin biosynthesis. Stem-loop RT-PCR and RT-PCR was performed to validate these miRNAs and their targets. Outcome of our study will provide a revolutionary approach to target the biosynthesis of secondary metabolites at miRNA level for their enhanced yield.