Xu Yingchun, Chu Lingling, Jin Qijiang, Wang Yanjie, Chen Xian, Zhao Hui, Xue Zeyun
College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P.R. China.
PLoS One. 2015 Apr 29;10(4):e0125462. doi: 10.1371/journal.pone.0125462. eCollection 2015.
MicroRNAs (miRNAs) play important roles in plant responses to environmental stress. In this work, we used high-throughput sequencing to analyze transcriptome and small RNAs (sRNAs) in Typha angustifolia under cadmium (Cd) stress. 57,608,230 raw reads were obtained from deep sequencing of a pooled cDNA library. Sequence assembly and analysis yielded 102,473 unigenes. We subsequently sequenced two sRNA libraries from T. angustifolia with or without Cd exposure respectively. Based on transcriptome data of T. angustifolia, we catalogued and analyzed the sRNAs, resulting in the identification of 114 conserved miRNAs and 41 novel candidate miRNAs in both small RNA libraries. In silico analysis revealed 764 targets for 89 conserved miRNAs and 21 novel miRNAs. Statistical analysis on sequencing reads abundance and experimental validation revealed that 4 conserved and 6 novel miRNAs showed specific expression. Combined with function of target genes, these results suggested that miRNAs might play a role in plant Cd stress response. This study provided the first transcriptome-based analysis of miRNAs and their targets responsive to Cd stress in T. angustifolia, which provide a framework for further analysis of miRNAs and their role in regulating plant responses to Cd stress.
微小RNA（miRNA）在植物对环境胁迫的响应中发挥着重要作用。在本研究中，我们利用高通量测序技术分析了狭叶香蒲在镉（Cd）胁迫下的转录组和小RNA（sRNA）。通过对混合cDNA文库的深度测序获得了57,608,230条原始 reads。序列组装和分析产生了102,473个单基因。随后，我们分别对暴露于Cd和未暴露于Cd的狭叶香蒲的两个sRNA文库进行了测序。基于狭叶香蒲的转录组数据，我们对sRNA进行了分类和分析，在两个小RNA文库中鉴定出114个保守miRNA和41个新的候选miRNA。计算机分析揭示了89个保守miRNA和21个新miRNA的764个靶标。对测序reads丰度的统计分析和实验验证表明，4个保守miRNA和6个新miRNA表现出特异性表达。结合靶基因的功能，这些结果表明miRNA可能在植物Cd胁迫响应中发挥作用。本研究首次基于转录组分析了狭叶香蒲中响应Cd胁迫的miRNA及其靶标，为进一步分析miRNA及其在调节植物对Cd胁迫响应中的作用提供了框架。
