Jin Qijiang, Xue Zeyun, Dong Chunlan, Wang Yanjie, Chu Lingling, Xu Yingchun
College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
PLoS One. 2015 Feb 6;10(2):e0117584. doi: 10.1371/journal.pone.0117584. eCollection 2015.
MicroRNAs (miRNAs) are a class of non-coding, small RNAs recognized as important regulators of gene expression. Although plant miRNAs have been extensively studied in model systems, less is known in other plants with limited genome sequence data, including Paeonia ostii. In this work, we used high-throughput sequencing to identify conserved and nonconserved miRNAs and other short RNAs in Paeonia ostii under control and copper stressed condition. 102 previously known plant miRNAs were identified and classified into 89 families according to their gene sequence identity. Some miRNAs were highly conserved in the plant kingdom suggesting that these miRNA play important and conserved roles. Combined our transcriptome sequencing data of Paeonia ostii under same conditions, 34 novel potential miRNAs were identified. The potential targets of the identified known and novel miRNAs were also predicted based on sequence homology search. Comparing the two libraries, it was observed that 12 conserved miRNAs and 18 novel miRNAs showed significantly changes in response to copper stress. Some of the new identified potential miRNAs might be involved in Paeonia ostii-specific regulating mechanisms under copper stress. These results provide a framework for further analysis of miRNAs and their role in regulating Paeonia ostii response to copper stress.
微小RNA（miRNA）是一类非编码小RNA，被认为是基因表达的重要调节因子。尽管植物miRNA已在模式系统中得到广泛研究，但在包括芍药在内的基因组序列数据有限的其他植物中，人们对其了解较少。在这项研究中，我们利用高通量测序技术，在对照和铜胁迫条件下鉴定芍药中的保守和非保守miRNA以及其他短RNA。共鉴定出102个先前已知的植物miRNA，并根据其基因序列同一性将它们分为89个家族。一些miRNA在植物界高度保守，表明这些miRNA发挥着重要且保守的作用。结合相同条件下芍药的转录组测序数据，鉴定出34个新的潜在miRNA。还基于序列同源性搜索预测了已鉴定的已知和新miRNA的潜在靶标。比较两个文库，发现12个保守miRNA和18个新miRNA在响应铜胁迫时表现出显著变化。一些新鉴定的潜在miRNA可能参与了芍药在铜胁迫下的特异性调节机制。这些结果为进一步分析miRNA及其在调节芍药对铜胁迫响应中的作用提供了框架。
