National Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.
Plant Sci. 2013 Mar;201-202:108-14. doi: 10.1016/j.plantsci.2012.11.010. Epub 2012 Dec 3.
MicroRNAs (miRNAs) are endogenous, non-coding, small RNAs that play significant regulatory roles in plant growth, development, and biotic and abiotic stress responses. To date, a great number of conserved and species-specific miRNAs have been identified in many important plant species such as Arabidopsis, rice and poplar. However, little is known about identification of miRNAs and their target genes in radish (Raphanus sativus L.). In the present study, a small RNA library from radish root was constructed and sequenced using the high-throughput Solexa sequencing. Through sequence alignment and secondary structure prediction, a total of 545 conserved miRNA families as well as 15 novel (with their miRNA* strand) and 64 potentially novel miRNAs were identified. Quantitative real-time PCR (qRT-PCR) analysis confirmed that both conserved and novel miRNAs were expressed in radish, and some of them were preferentially expressed in certain tissues. A total of 196 potential target genes were predicted for 42 novel radish miRNAs. Gene ontology (GO) analysis showed that most of the targets were involved in plant growth, development, metabolism and stress responses. This study represents a first large-scale identification and characterization of radish miRNAs and their potential target genes. These results could lead to the further identification of radish miRNAs and enhance our understanding of radish miRNA regulatory mechanisms in diverse biological and metabolic processes.
MicroRNAs (miRNAs) 是内源性的、非编码的、小的 RNA，在植物的生长、发育以及生物和非生物胁迫反应中发挥重要的调控作用。迄今为止，在许多重要的植物物种如拟南芥、水稻和杨树中已经鉴定出了大量的保守和物种特异性的 miRNAs。然而，关于萝卜（Raphanus sativus L.）中 miRNAs 的鉴定及其靶基因的研究还很少。本研究利用高通量 Solexa 测序技术构建并测序了萝卜根的小 RNA 文库。通过序列比对和二级结构预测，共鉴定出 545 个保守的 miRNA 家族以及 15 个新的（及其 miRNA* 链）和 64 个潜在新的 miRNAs。定量实时 PCR（qRT-PCR）分析证实，保守和新的 miRNAs 都在萝卜中表达，其中一些在特定组织中优先表达。共预测到 42 个新的萝卜 miRNAs 的 196 个潜在靶基因。基因本体（GO）分析表明，大多数靶基因参与植物的生长、发育、代谢和应激反应。本研究代表了首次大规模鉴定和描述萝卜 miRNAs 及其潜在靶基因。这些结果可能会进一步鉴定萝卜 miRNAs，并增强我们对萝卜 miRNA 在不同生物和代谢过程中调控机制的理解。
