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. 2015 Sep 16;3(9):apps.1500046.
doi: 10.3732/apps.1500046. eCollection 2015 Sep.

Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets

Lei Pan  1 , Xiaolei Wang  2 , Jing Jin  2 , Xiaolu Yu  1 , Jihong Hu  2
Affiliations

Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets

Lei Pan et al. Appl Plant Sci. .

Abstract

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.

Keywords: Nelumbo nucifera; expressed sequence tag (EST); miRNA; qRT-PCR; target genes.

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Figures

Fig. 1.
Fig. 1.
Workflow for identifying potential miRNAs in Nelumbo nucifera.
Fig. 2.
Fig. 2.
Distribution of Nelumbo nucifera mature miRNA lengths (A) and pre-miRNA lengths (B).
Fig. 3.
Fig. 3.
Several miRNA-5p/miRNA-3p secondary structures in Nelumbo nucifera. (A) Nnu-miR156c-5p/3p; (B) Nnu-miR169c-5p/3p; (C) Nnu-miR390a-5p/3p; (D) Nnu-miR396b-5p/3p.
Fig. 4.
Fig. 4.
Sense and antisense miRNAs and their secondary structures in Nelumbo nucifera.
Fig. 5.
Fig. 5.
The relative expression levels of five miRNAs and target genes in young leaves, stems, and flowers of Nelumbo nucifera. (A) The relative expression levels of five miRNAs in N. nucifera. (B) The relative expression levels of five corresponding target genes in N. nucifera. Significant differences of the differential expression among different tissues in N. nucifera were evaluated by Student’s t test (*P < 0.05; **P < 0.01).
Fig. 6.
Fig. 6.
The relative expression levels of five miRNAs in young leaves, stems, and flowers of Nelumbo nucifera. Significant differences of the differential expression among different tissues in N. nucifera were evaluated by Student’s t test (*P < 0.05; **P < 0.01).
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