Bioinformatics prediction of miRNAs in the Prunus persica genome with validation of their precise sequences by miR-RACE
- Resource Type
- Article
- Authors
- Zhang, Yanping; Bai, Youhuang; Han, Jian; Chen, Ming; Kayesh, Emrul; Jiang, Weibing; Fang, Jinggui
- Source
- Journal of Plant Physiology. Jan2013, Vol. 170 Issue 1, p80-92. 13p.
- Subject
- *PRUNUS
*BIOINFORMATICS
*MICRORNA
*PLANT genomes
*GENE amplification
*REVERSE transcriptase polymerase chain reaction
*ANTISENSE DNA
*SEQUENCE alignment
- Language
- ISSN
- 0176-1617
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. [Copyright &y& Elsevier]