title: Computational identification of microRNAs in apple expressed sequence tags and validation of their precise sequences by miR-RACE.
abstract: Thirty-one potential miRNAs that belong to 16 miRNA families were discovered from more than 324 000 EST sequences of apple (Malus domestica). In addition, precise sequences, especially terminal nucleotides of the 16 apple miRNAs (mdo-miRNAs) in 16 families were validated by miR-RACE, a newly developed method for the determination of the potential miRNAs predicted computationally. The expression of these 16 microRNAs could be detected in apple young leaf, old leaf, young stem, flower bud, flower and developing fruits by quantitative RT-PCR (qRT-PCR) and some of them showed tissue-specific expression. Fifty-six potential targets were identified for the 16 apple miRNAs, most of which were transcription factors that play important roles in apple development. Twelve target genes were experimentally verified by qRT-PCR, with some exhibiting different expression trends from their corresponding microRNAs, indicating the cleavage mode of miRNAs on their target genes.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Huaping
authors.initials: H
authors.lastname: Yu
authors.forename: Changnian
authors.initials: C
authors.lastname: Song
authors.forename: Qidong
authors.initials: Q
authors.lastname: Jia
authors.forename: Chen
authors.initials: C
authors.lastname: Wang
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.forename: Korir Kibet
authors.initials: KK
authors.lastname: Nicholas
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Zhang
authors.forename: Jinggui
authors.initials: J
authors.lastname: Fang
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics; D027845:Malus / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs