Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica)

文献类型： 外文期刊

第一作者： Han, Jun

作者： Han, Jun;Xie, Hao;Sun, Qingpeng;Lu, Min;Wang, Weixiang;Pan, Jinbao;Wang, Jun;Guo, Erhu

作者机构：

关键词： MicroRNA;Bioinformatic identification;Targets;qRT-PCR;Foxtail millet

期刊名称：GENE （ 影响因子：3.688； 五年影响因子：3.329 ）

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收录情况： SCI

摘要： MiRNAs are a novel group of non-coding small RNAs that negatively regulate gene expression. Many miRNAs have been identified and investigated extensively in plant species with sequenced genomes. However, few miRNAs have been identified in foxtail millet (Setaria italica), which is an ancient cereal crop of great importance for dry land agriculture. In this study, 271 foxtail millet miRNAs belonging to 44 families were identified using a bioinformatics approach. Twenty-three pairs of sense/antisense miRNAs belonging to 13 families, and 18 miRNA clusters containing members of 8 families were discovered in foxtail millet. We identified 432 potential targets for 38 miRNA families, most of which were predicted to be involved in plant development, signal transduction, metabolic pathways, disease resistance, and environmental stress responses. Gene ontology (GO) analysis revealed that 101, 56, and 23 target genes were involved in molecular functions, biological processes, and cellular components, respectively. We investigated the expression patterns of 43 selected miRNAs using qRT-PCR analysis. All of the miRNAs were expressed ubiquitously with many exhibiting different expression levels in different tissues. We validated five predicted targets of four miRNAs using the RNA ligase mediated rapid amplification of cDNA end (5'-RLM-RACE) method. (C) 2014 Elsevier B.V. All rights reserved.

分类号： R394

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