title: Subgenomic analysis of microRNAs in polyploid wheat.
abstract: In this study, a survey of miRNAs using the next-generation sequencing data was performed at subgenomic level. After analyzing shotgun sequences from chromosome 4A of bread wheat (Triticum aestivum L.), a total of 68 different miRNAs were predicted in silico, of which 37 were identified in wheat for the first time. The long arm of the chromosome was found to harbor a higher variety (51) and representation (3,928) of miRNAs compared with the short arm (49; 2,226). Out of the 68 miRNAs, 32 were detected to be common to both arms, revealing the presence of separate miRNA clusters in the two chromosome arms. The differences in degree of representation of the different miRNAs were found to be highly variable, ranging 592-fold, which may have an effect on target regulation. Targets were retrieved for 62 (out of 68) of wheat-specific, newly identified miRNAs indicated that fundamental aspects of plant morphology such as height and flowering were predicted to be affected. In silico expression blast analysis indicated 24 (out of 68) were found to give hits to expressed sequences. This is the first report of species- and chromosome-specific miRNAs.
authors.affiliation: Biological Sciences and Bioengineering Program, Sabanci University, Tuzla, Istanbul, Turkey.
authors.forename: Melda
authors.initials: M
authors.lastname: Kantar
authors.forename: Bala Anı
authors.initials: BA
authors.lastname: Akpınar
authors.forename: Miroslav
authors.initials: M
authors.lastname: Valárik
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Lucas
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.forename: Pilar
authors.initials: P
authors.lastname: Hernández
authors.forename: Hikmet
authors.initials: H
authors.lastname: Budak
mesh_terms: D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D035264:Flowers / Q000235:genetics; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics; D009690:Nucleic Acid Conformation; D012275:Oryza / Q000235:genetics; D011123:Polyploidy; D018749:RNA, Plant / Q000032:analysis* / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods; D026801:Synteny; D014908:Triticum / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant