Identification of miRNAs from Eugenia uniflora by high-throughput sequencing and bioinformatics analysis [mRNA-seq]. Eugenia uniflora

miRNAs are small non-coding regulatory RNAs that play important functions in the regulation of gene expression at the post-transcriptional level by targeting mRNAs for degradation or by inhibiting protein translation. Eugenia uniflora is a plant native to tropical America with pharmacological and ecological importance without previous studies about its gene expression and regulation. To date, there is not miRNAs reported in species of Myrtaceae. A small RNA library was constructed to identify miRNAs in Eugenia uniflora. Solexa technology was used to perform high throughput sequencing of the library and the data obtained was analysed using bioinformatics tools. From 14,489,131 clean reads, we obtained 1,852,722 small RNAs representing 45 known miRNA families that have been identified in other plant species. Further analysis using contigs assembled from Illumina mRNA sequencing of leaves from the same individual allowed the prediction of secondary structures of 25 known and 17 novel miRNAs. Potential targets were predicted for the most abundant mature miRNAs in the identified pre-miRNAs based on sequence homology. This study provide the first large scale identification of miRNAs and their potential targets of a species from Myrtaceae without previous genomic sequence resources. Our study provides more information about the evolutionary conservation of the regulatory network of miRNAs in plants and highlights the miRNAs species-specific. Overall design: mRNA profiles in 1 leaf library of Eugenia uniflora by deep sequencing (Illumina HiSeq2000)

微小RNA（microRNAs，miRNAs）是一类小型非编码调控RNA，通过靶向信使RNA（mRNA）使其降解或抑制蛋白质翻译，在转录后水平的基因表达调控中发挥关键功能。红果仔（Eugenia uniflora）是一种原产于热带美洲的植物，兼具药理学与生态学价值，但此前尚无关于其基因表达与调控的相关研究。截至目前，桃金娘科（Myrtaceae）物种中尚未见miRNAs的相关报道。本研究构建小型RNA文库以鉴定红果仔中的miRNAs，采用Solexa测序技术对该文库进行高通量测序，并借助生物信息学工具对所得数据进行分析。从14,489,131条洁净读段（clean reads）中，共获得1,852,722条小型RNA序列，其中包含45个已在其他植物物种中鉴定到的保守miRNA家族。基于同一植株叶片的Illumina mRNA测序数据组装得到的重叠群（contigs），本研究进一步预测得到25个已知miRNAs及17个全新miRNAs的二级结构。基于序列同源性，本研究对鉴定得到的前体miRNAs（pre-miRNAs）中丰度最高的成熟miRNAs预测了潜在靶标基因。本研究首次在缺乏前期基因组序列资源的情况下，实现了桃金娘科物种miRNAs及其潜在靶标的大规模鉴定。本研究为解析植物miRNAs调控网络的进化保守性提供了更多数据支撑，并凸显了miRNAs的物种特异性。实验设计概要：利用Illumina HiSeq2000高通量测序技术，对红果仔的1个叶片文库进行mRNA表达谱分析。