title: In-silico identification of miRNAs and their regulating target functions in Ocimum basilicum.
abstract: microRNA is known to play an important role in growth and development of the plants and also in environmental stress. Ocimum basilicum (Basil) is a well known herb for its medicinal properties. In this study, we used in-silico approaches to identify miRNAs and their targets regulating different functions in O. basilicum using EST approach. Additionally, functional annotation, gene ontology and pathway analysis of identified target transcripts were also done. Seven miRNA families were identified. Meaningful regulations of target transcript by identified miRNAs were computationally evaluated. Four miRNA families have been reported by us for the first time from the Lamiaceae. Our results further confirmed that uracil was the predominant base in the first positions of identified mature miRNA sequence, while adenine and uracil were predominant in pre-miRNA sequences. Phylogenetic analysis was carried out to determine the relation between O. basilicum and other plant pre-miRNAs. Thirteen potential targets were evaluated for 4 miRNA families. Majority of the identified target transcripts regulated by miRNAs showed response to stress. miRNA 5021 was also indicated for playing an important role in the amino acid metabolism and co-factor metabolism in this plant. To the best of our knowledge this is the first in silico study describing miRNAs and their regulation in different metabolic pathways of O. basilicum.
authors.affiliation: Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, UP, India. Electronic address: singh.rajpoot.noopur@gmail.com.
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: Ashok
authors.initials: A
authors.lastname: Sharma
mesh_terms: D003198:Computer Simulation; D035683:MicroRNAs / Q000235:genetics*; D018649:Ocimum basilicum / Q000235:genetics*; D010802:Phylogeny; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D018749:RNA, Plant
keywords: Ocimum basilicum; Plant development; Secondary metabolic pathway; Stress; miRNA; miRNA-targets