title: Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE.
abstract: We predicted 262 potential MicroRNAs (miRNAs) belonging to 70 miRNA families from the peach (Prunus persica) genome and two specific 5' and 3' miRNA rapid amplification of cDNA ends (miR-RACE) PCR reactions and sequence-directed cloning were employed to accurately validate 61 unique P. persica miRNAs (Ppe-miRNAs) sequences belonging to 61 families comprising 97 Ppe-miRNAs. Validation of the termini nucleotides in particular can define the real sequences of the Ppe-miRNAs on peach genome. Comparison between predicted and validated Ppe-miRNAs through alignment revealed that 43 unique orthologous sequences were identical, while the remaining 18 exhibited some divergences at their termini nucleotides. Quantitative real-time polymerase chain reaction (qRT-PCR) was further employed to analyze the expression of all the 61 miRNAs and 10 putative targets of 8 randomly selected Ppe-miRNAs in peach leaves, flowers and fruits at different stages of development, where both the miRNAs and the putative target genes showed tissue-specific expression.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Zhang
authors.forename: Youhuang
authors.initials: Y
authors.lastname: Bai
authors.forename: Jian
authors.initials: J
authors.lastname: Han
authors.forename: Ming
authors.initials: M
authors.lastname: Chen
authors.forename: Emrul
authors.initials: E
authors.lastname: Kayesh
authors.forename: Weibing
authors.initials: W
authors.lastname: Jiang
authors.forename: Jinggui
authors.initials: J
authors.lastname: Fang
mesh_terms: D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics; D035264:Flowers / Q000235:genetics / Q000254:growth & development; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D035683:MicroRNAs / Q000235:genetics*; D009928:Organ Specificity; D018515:Plant Leaves / Q000235:genetics / Q000254:growth & development; D027861:Prunus / Q000235:genetics* / Q000254:growth & development; D018749:RNA, Plant / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D018076:DNA, Complementary; D035683:MicroRNAs; D018749:RNA, Plant