Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs
Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs
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DOI：
10.1038/ncomms4722
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发表时间：
2014-04-01
影响因子：
16.6
通讯作者：
de Folter, Stefan
中科院分区：
文献类型：
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作者：
Chavez Montes, Ricardo A.;de Fatima Rosas-Cardenas, Flor;de Folter, Stefan
小RNA是真核生物（包括植物）中基因表达的关键调节因子，指导转录和转录后沉默机制。在这里，我们报告了一个全面的sRNA和miRNA图谱，从3种藻类和31个代表性物种的维管植物，包括非模式植物。我们对来自99种不同组织或治疗的sRNA进行测序和定量，产生了超过1.32亿个不同序列的数据集。使用miRBase成熟序列作为参考，我们鉴定了这些文库中存在的miRNA序列。我们应用不同的分析方法来研究关键的sRNA和miRNA特征，如大小分布，组织特异性调节和物种之间的序列保守性，以及预测推定的新的miRNA序列。我们还开发数据库资源，计算分析工具和一个专门的网站，http://smallrna.udel.edu/。本研究为植物sRNAs和miRNAs的研究提供了新的视角，为今后的研究奠定了基础。
Small RNAs are pivotal regulators of gene expression that guide transcriptional and post-transcriptional silencing mechanisms in eukaryotes, including plants. Here we report a comprehensive atlas of sRNA and miRNA from 3 species of algae and 31 representative species across vascular plants, including non-model plants. We sequence and quantify sRNAs from 99 different tissues or treatments across species, resulting in a data set of over 132 million distinct sequences. Using miRBase mature sequences as a reference, we identify the miRNA sequences present in these libraries. We apply diverse profiling methods to examine critical sRNA and miRNA features, such as size distribution, tissue-specific regulation and sequence conservation between species, as well as to predict putative new miRNA sequences. We also develop database resources, computational analysis tools and a dedicated website, http://smallrna.udel.edu/. This study provides new insights on plant sRNAs and miRNAs, and a foundation for future studies.