title: Evidence of purifying selection and co-evolution at the fold-back arm of the novel precursor microRNA159 gene in Phalaenopsis Species (Orchidaceae).
abstract: BACKGROUND
  MicroRNAs (miRNAs) are small, endogenously transcribed, non-protein-coding RNAs that play important roles in regulation of gene expression in animals and plants. Here, selective constraints on the novel precursor microRNA159 (pre-miR159) gene were investigated in 42 Phalaenopsis species (Orchidaceae).
  
  
  RESULTS
  A novel precursor microRNA159 gene was isolated from 42 Phalaenopsis species using a new microRNA-PCR (miR-PCR) approach. Sequencing of pre-miR159 genes revealed differences from the canonical pre-miR159 gene in Phalaenopsis species and other plants. Results demonstrated that the 5' and 3' fold-back arms and the terminal loop of the novel pre-miR159 gene have undergone purifying selection and selective constraint for stabilizing the secondary hairpin structure. Two conserved motifs within the 5' fold-back arm had the highest purifying selective pressure within the novel pre-miR159 gene. Evidence of sequence co-evolution between the 5' and 3' fold-back regions was observed.
  
  
  CONCLUSIONS
  Functional selective pressure might arise from the constraint of forming a hairpin structure and demonstrate co-evolution of sequences between the 5' and 3' fold-back regions of the novel pre-miR159 gene in Phalaenopsis species.
authors.affiliation: Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan; Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
authors.forename: Chi-Chu
authors.initials: CC
authors.lastname: Tsai
authors.affiliation: Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
authors.forename: Yu-Chung
authors.initials: YC
authors.lastname: Chiang
authors.affiliation: Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan.
authors.forename: I-Szu
authors.initials: IS
authors.lastname: Weng
authors.affiliation: Kaohsiung District Agricultural Research and Extension Station, Pingtung, 908, Taiwan.
authors.forename: Yu-Shium
authors.initials: YS
authors.lastname: Lin
authors.affiliation: Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan.
authors.forename: Chang-Hung
authors.initials: CH
authors.lastname: Chou
mesh_terms: D019143:Evolution, Molecular; D017343:Genes, Plant; D055029:Inverted Repeat Sequences; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D029595:Orchidaceae / Q000235:genetics*; D011110:Polymorphism, Genetic; D018749:RNA, Plant / Q000235:genetics*; D012641:Selection, Genetic
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant