title: Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets.
abstract: OBJECTIVE
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Pan
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.
authors.forename: Jing
authors.initials: J
authors.lastname: Jin
authors.affiliation: Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People's Republic of China.
authors.forename: Xiaolu
authors.initials: X
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.
authors.forename: Jihong
authors.initials: J
authors.lastname: Hu
keywords: Nelumbo nucifera; expressed sequence tag (EST); miRNA; qRT-PCR; target genes