a combined approach of high-throughput sequencing and degradome analysis reveals tissue specific expression of micrornas and their targets in cucumber高通量测序和degradome分析揭示了一个综合的方法组织特定表达的小分子核糖核酸和黄瓜的目标.pdfVIP

A Combined Approach of High-Throughput Sequencing and Degradome Analysis Reveals Tissue Specific Expression of MicroRNAs and Their Targets in Cucumber 1,2 2 1 3 1 Weihua Mao , Zeyun Li , Xiaojian Xia , Yadan Li , Jingquan Yu * 1 Department of Horticulture, Zhejiang University, Hangzhou, China, 2 Center of Analysis and Measurement, Zhejiang University, Hangzhou, China, 3 Hunan Agricultural Bioengineering Research Institute, Hunan Agricultural University, Changsha, China Abstract MicroRNAs (miRNAs) are endogenous small RNAs playing an important regulatory function in plant development and stress responses. Among them, some are evolutionally conserved in plant and others are only expressed in certain species, tissue or developmental stages. Cucumber is among the most important greenhouse species in the world, but only a limited number of miRNAs from cucumber have been identified and the experimental validation of the related miRNA targets is still lacking. In this study, two independent small RNA libraries from cucumber leaves and roots were constructed, respectively, and sequenced with the high-throughput Illumina Solexa system. Based on sequence similarity and hairpin structure prediction, a total of 29 known miRNA families and 2 novel miRNA families containing a total of 64 miRNA were identified. QRT-PCR analysis revealed that some of the cucumber miRNAs were preferentially expressed in certain tissues. With the recently developed ‘high throughput degradome sequencing’ approach, 21 target mRNAs of known miRNAs were identified for the first time in cucumber. These targets were associated with development, reactive oxygen species scavenging, signaling transduction and transcriptional regulation. Our study provides an overview of