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Bioinformatic Identification and Expression Analysis of Nelumbo nucifera MicroRNA and Their Targets

Pan, Lei, Wang, Xiaolei, Jin, Jing, Yu, Xiaolu, Hu, Jihong
Applications in plant sciences 2015 v.3 no.9
Nelumbo nucifera, bioinformatics, flowers, genes, herbaceous plants, leaves, microRNA, plant development, quantitative polymerase chain reaction, reverse transcriptase polymerase chain reaction, stems, tissues, transcriptome
Premise of the study: Sacred lotus (Nelumbo nucifera) is a perennial aquatic herbaceous plant of ecological, ornamental, and economic importance. MicroRNAs (miRNAs) play an important role in plant development. However, reports of miRNAs and their role in sacred lotus have been limited.Methods: Using the homology search of known miRNAs with genome and transcriptome contig sequences, we employed a pipeline to identify miRNAs in N. nucifera. We also predicted the targets of these miRNAs.Results: We found 106 conserved miRNAs in N. nucifera, and 456 of their miRNA targets were annotated. Quantitative real-time PCR (qRT-PCR) analysis revealed the different expression levels of the 10 selected conserved miRNAs in tissues of young leaves, stems, and flowers of N. nucifera. Negative correlation of expression level between five miRNAs and their target genes was also revealed.Discussion: Combining bioinformatics and experiment analysis, we identified the miRNAs in N. nucifera. The results can be used as a workbench for further investigation of the roles of miRNAs in N. nucifera.