title: Identification of micro-RNAs in cotton.
abstract: The plant genome has conserved small non-coding microRNAs (miRNAs) genes about 20-24 nucleotides long. They play a vital role in the gene regulation at various stages of plant life. Their conserved nature among the various organisms not only suggests their early evolution in eukaryotes but also makes them a good source of new miRNA discovery by homology search using bioinformatics tools. A systematic search approach was used for interspecies orthologues of miRNA precursors, from known sequences of Gossypium in GenBank. The study resulted in 22 miRNAs belonging to 13 families. We found 7 miRNA families (miR160, 164, 827, 829, 836, 845 and 865) for the first time in cotton. All 22 miRNA precursors form stable minimum free energy (mfe) stem loop structure as their orthologues form in Arabidopsis and the mature miRNAs reside in the stem portion of the stem loop structure. Fifteen miRNAs belong to the world's most commercial fiber producing upland cotton (Gossypium hirsutum), five are from Gossypium raimondii and one each is from Gossypium herbaceum and Gossypium arboreum. Their targets consist of transcription factors, cell division regulating proteins and virus response gene. The discovery of 22 miRNAs will be helpful in future for detection of precise function of each miRNA at a particular stage in life cycle of cotton.
authors.affiliation: Botany Department, University of Baluchistan, Quetta, Pakistan. barozaikhan@gmail.com
authors.forename: Muhammad Younas
authors.initials: MY
authors.lastname: Khan Barozai
authors.forename: Muhammad
authors.initials: M
authors.lastname: Irfan
authors.forename: Rizwan
authors.initials: R
authors.lastname: Yousaf
authors.forename: Imran
authors.initials: I
authors.lastname: Ali
authors.forename: Uzma
authors.initials: U
authors.lastname: Qaisar
authors.forename: Asma
authors.initials: A
authors.lastname: Maqbool
authors.forename: Muzna
authors.initials: M
authors.lastname: Zahoor
authors.forename: Bushra
authors.initials: B
authors.lastname: Rashid
authors.forename: Tayyab
authors.initials: T
authors.lastname: Hussnain
authors.forename: Sheikh
authors.initials: S
authors.lastname: Riazuddin
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D018745:Genome, Plant; D003368:Gossypium / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018749:RNA, Plant / Q000235:genetics*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant