Abstract
BackgroundMicroRNAs (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).Methods/ResultsA 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.ConclusionsFunctional 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.
Highlights
MicroRNAs are small, endogenously transcribed, nonprotein-coding RNAs that play important roles in regulation of gene expression in animals and plants
Sequences suggested the pre-miR159 gene might be encoded at a single locus in Phalaenopsis species with the exception of P. sumatrana, P. lindenii, and P. gibbosa, which had distinct sequences in the hairpin region
To further validate sequences of the miRNA/ miRNA* duplexes for each Phalaenopsis species, five clones were randomly selected for amplification by inverse PCR and clone-based sequencing
Summary
MicroRNAs (miRNAs) are small, endogenously transcribed, nonprotein-coding RNAs that play important roles in regulation of gene expression in animals and plants. Selective constraints on the novel precursor microRNA159 (pre-miR159) gene were investigated in 42 Phalaenopsis species (Orchidaceae). Results demonstrated that the 59 and 39 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. Conclusions: Functional selective pressure might arise from the constraint of forming a hairpin structure and demonstrate co-evolution of sequences between the 59 and 39 fold-back regions of the novel pre-miR159 gene in Phalaenopsis species. MicroRNAs (miRNAs) are small, endogenously transcribed, non-protein-coding RNAs that regulate gene expression in animals and plants. The strand selected to produce the mature miRNA within RISC is biased towards the duplex strand with the weakest hydrogen bond at its 59 end. MiRNAs have been found in a wide range of eukaryotes, including fruit flies, nematodes, zebrafish, chicken, mice, humans, Arabidopsis, maize, and rice [1]
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