title: Identification of conserved and novel microRNAs in Catharanthus roseus by deep sequencing and computational prediction of their potential targets.
abstract: MicroRNAs are small endogenous non-coding RNAs of ~19-24 nucleotides and perform regulatory roles in many plant processes. To identify miRNAs involved in regulatory networks controlling diverse biological processes including secondary metabolism in Catharanthus roseus, an important medicinal plant, we employed deep sequencing of small RNA from leaf tissue. A total of 88 potential miRNAs comprising of 81 conserved miRNAs belonging to 35 families and seven novel miRNAs were identified. Precursors for 16 conserved and seven novel cro-miRNAs were identified, and their stem-loop hairpin structures were predicted. Selected cro-miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in different vegetative tissues of C. roseus. Targets were predicted for conserved and novel cro-miRNAs, which were found to be involved in diverse biological role(s) including secondary metabolism. Our study enriches available resources and information regarding miRNAs and their potential targets for better understanding of miRNA-mediated gene regulation in plants.
authors.affiliation: Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India.
authors.forename: Pravin
authors.initials: P
authors.lastname: Prakash
authors.affiliation: Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India.
authors.forename: Dolly
authors.initials: D
authors.lastname: Ghosliya
authors.affiliation: Biotechnology Division, CSIR - Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, India. Electronic address: vikrant.gupta@gmail.com.
authors.forename: Vikrant
authors.initials: V
authors.lastname: Gupta
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D030008:Catharanthus / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D017124:Conserved Sequence; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D010940:Plant Proteins / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics* / Q000378:metabolism; D064210:Secondary Metabolism; D017423:Sequence Analysis, RNA; D013045:Species Specificity
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant
keywords: Catharanthus roseus; Deep sequencing; MicroRNA; Real-time PCR