State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
BMC Plant Biol. 2013 Dec 13;13:212. doi: 10.1186/1471-2229-13-212.
MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood.
In this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing.
We predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.
microRNAs（miRNAs）是一类短的非编码内源性 RNA，在动植物的许多生物过程中发挥着关键作用。虽然在大量生物中已经鉴定出许多 miRNAs，但直到现在，对谷子（Setaria italica）中的 miRNAs 了解甚少。
本研究对谷子幼穗的两个重复小 RNA 文库进行了测序，共产生了 4000 万个代表超过 1000 万个独特序列的读段。我们在谷子中鉴定出了 43 个已知 miRNAs、172 个新 miRNAs 和 2 个 mirtron 前体候选物。还检测到了一些已知和新 miRNAs 的 miRNA*。此外，通过茎环 RT-PCR 验证了 8 个新 miRNAs。根据我们严格的标准预测了谷子 miRNAs 的潜在靶基因。在预测的靶基因中，79%（351 个）在 InterPro 和 GO 分析中有功能注释，表明这些 miRNA 的靶基因参与了广泛的调节功能和一些特定的生物学过程。在谷子和高粱之间发现了总共 69 对保守的 miRNA 前体。此外，通过茎环 RT-PCR 确认了深度测序确定的 4 种组织中一些 miRNAs 的组织特异性表达。
我们首次在全基因组水平上预测了谷子中的 215 个 miRNAs 和 447 个 miRNA 靶基因。对鉴定出的 miRNA 前体、表达水平、miRNA*序列、靶基因功能、保守性和进化进行了研究。一些新的谷子 miRNAs 和 miRNA 靶基因通过实验得到了验证。
