Identification of conserved MicroRNAs and their targets in Phalaenopsis orchid

Abstract

The microRNAs (miRNAs) are a new type of tiny, noncoding, single-stranded endogenous RNA molecules performing their function of regulating gene expression by targeting mRNAs for degradation or restraining protein translation. Thousands of miRNAs have been identified in many plant species to date, whereas only limited number of miRNAs have been identified in Phalaenopsis orchid. By using an exact computational analysis, 30 potential miRNAs were found from all known sequences (205 823 nt, 5505 GSS, and 8066 EST) in this study. These 30 miRNAs belong to 26 miRNA families and show significant variation in size. According to the previously established systemic method, 193 Phalaenopsis orchid genes were predicted as potential target genes of 20 miRNAs. The majority of these potential target genes in Phalaenopsis orchid encode hypothetical proteins, which functions are either indefinite or unknown. The rest miRNA target genes encode transcription factors that function in stress response, signal transduction, and a variety of other metabolic processes. To validate the predicted miRNAs and the mutual relationship between miRNAs and their target genes, qRT-PCR was applied to detect the tissue-specific expression levels of four putative miRNAs and their target genes in Phalaenopsis leaves, flowers, and roots. This study provided for some important information about Phalaenopsis pre-miRNAs, mature miRNAs, and miRNA target genes and will be helpful for future research of miRNA functions in Phalaenopsis.