莲微小RNA及其靶标的生物信息学鉴定与表达分析
Bioinformatic identification and expression analysis of Nelumbo nucifera microRNA and their targets.
作者信息
Pan Lei, Wang Xiaolei, Jin Jing, Yu Xiaolu, Hu Jihong
机构信息
Hubei Province Engineering Research Center of Legume Plants, School of Life Sciences, Jianghan University, Wuhan 430056, People's Republic of China.
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.
出版信息
Appl Plant Sci. 2015 Sep 16;3(9). doi: 10.3732/apps.1500046. eCollection 2015 Sep.
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.
研究前提
荷花（莲）是一种具有生态、观赏和经济价值的多年生水生草本植物。微小RNA（miRNA）在植物发育中起重要作用。然而，关于荷花中miRNA及其作用的报道有限。
方法
通过将已知miRNA与基因组和转录组重叠群序列进行同源性搜索，我们采用一套流程来鉴定荷花中的miRNA。我们还预测了这些miRNA的靶标。
结果
我们在荷花中发现了106个保守的miRNA，并注释了其中456个miRNA靶标。实时定量PCR（qRT-PCR）分析揭示了所选择的10个保守miRNA在荷花幼叶、茎和花组织中的不同表达水平。还揭示了5个miRNA与其靶基因之间表达水平的负相关。
讨论
结合生物信息学和实验分析，我们鉴定了荷花中的miRNA。这些结果可作为进一步研究miRNA在荷花中作用的平台。
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