title: Identification and analysis of miRNAs and their targets in ginger using bioinformatics approach.
abstract: MicroRNAs (miRNAs) are a large family of endogenous small RNAs derived from the non-protein coding genes. miRNA regulates the gene expression at the post-transcriptional level and plays an important role in plant development. Zingiber officinale is an important medicinal plant having numerous therapeutic properties. Its bioactive compound gingerol and essential oil posses important pharmacological and physiological activities. In this study, we used a homology search based computational approach for identifying miRNAs in Z. officinale. A total of 16 potential miRNA families (miR167, miR407, miR414, miR5015, miR5021, miR5644, miR5645, miR5656, miR5658, miR5664, miR827, miR838, miR847, miR854, miR862 and miR864) were predicted in ginger. Phylogenetic and conserved analyses were performed for predicted miRNAs. Thirteen miRNA families were found to regulate 300 target transcripts and play an important role in cell signaling, reproduction, metabolic process and stress. To understand the miRNA mediated gene regulatory control and to validate miRNA target predictions, a biological network was also constructed. Gene ontology and pathway analyses were also done. miR5015 was observed to regulate the biosynthesis of gingerol by inhibiting phenyl ammonia lyase (PAL), a precursor enzyme in the biosynthesis of gingerol. Our results revealed that most of the predicted miRNAs were involved in the regulation of rhizome development. miR5021, miR854 and miR838 were identified to regulate the rhizome development and the essential oil biosynthesis in ginger.
authors.affiliation: Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 UP, India.
authors.forename: Noopur
authors.initials: N
authors.lastname: Singh
authors.affiliation: Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 UP, India.
authors.forename: Swati
authors.initials: S
authors.lastname: Srivastava
authors.affiliation: Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow, 226015 UP, India. Electronic address: ashoksharma@cimap.res.in.
authors.forename: Ashok
authors.initials: A
authors.lastname: Sharma
mesh_terms: D019295:Computational Biology / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D020939:Zingiber officinale / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D005810:Multigene Family; D010802:Phylogeny; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D027343:Rhizome / Q000235:genetics / Q000254:growth & development; D012689:Sequence Homology, Nucleic Acid
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Essential oil; Ginger; Gingerol; MiRNA; MiRNA-target