Discovery of barley miRNAs through deep sequencing of short reads.
Discovery of barley miRNAs through deep sequencing of short reads.
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通过对简短阅读的深度测序发现大麦miRNA。
DOI：
10.1186/1471-2164-12-129
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发表时间：
2011-02-25
期刊：
影响因子：
4.4
通讯作者：
Baumann U
中科院分区：
文献类型：
--
作者：
Schreiber AW;Shi BJ;Huang CY;Langridge P;Baumann U
微小RNA（MicroRNAs）是生物系统调控网络的重要组成部分，在动植物中已发现数千种。在拟南芥、水稻、杨树和短柄草等已测序基因组的物种中进行的系统研究，为了解这类小RNA在植物中的进化关系提供了见解。然而，大麦（最重要的谷类作物之一）的微小RNA仍然未知。
我们通过对从两个大麦品种叶片中提取的小RNA进行深度测序，对大麦微小RNA进行了大规模研究。通过将相关基因组中微小RNA前体序列的存在作为众多支持标准之一，我们在大麦中鉴定出多达100种微小RNA。其中只有56种在已知表达的小麦、水稻或短柄草中有直系同源物，而多达44种似乎在大麦中特异性表达。
我们的研究是对大麦小RNA的首次大规模调查，已鉴定出多达100种微小RNA。我们证明，在基因组尚未测序的物种中，通过深度测序可靠地鉴定微小RNA，需要比通常更仔细地分析测序错误。我们设计了一种读取过滤程序来处理错误。此外，我们发现使用近3500万条读取的大型数据集，可以将沿假定前体序列的读取丰度分布用作在来自其他非编码和编码RNA的大量读取背景下分离微小RNA的实用工具。因此，这项研究为在没有基因组序列可用的情况下发现新的微小RNA提供了一种通用方法。
MicroRNAs are important components of the regulatory network of biological systems and thousands have been discovered in both animals and plants. Systematic investigations performed in species with sequenced genomes such as Arabidopsis, rice, poplar and Brachypodium have provided insights into the evolutionary relationships of this class of small RNAs among plants. However, miRNAs from barley, one of the most important cereal crops, remain unknown. We performed a large scale study of barley miRNAs through deep sequencing of small RNAs extracted from leaves of two barley cultivars. By using the presence of miRNA precursor sequences in related genomes as one of a number of supporting criteria, we identified up to 100 miRNAs in barley. Of these only 56 have orthologs in wheat, rice or Brachypodium that are known to be expressed, while up to 44 appear to be specifically expressed in barley. Our study, the first large scale investigation of small RNAs in barley, has identified up to 100 miRNAs. We demonstrate that reliable identification of miRNAs via deep sequencing in a species whose genome has not been sequenced requires a more careful analysis of sequencing errors than is commonly performed. We devised a read filtering procedure for dealing with errors. In addition, we found that the use of a large dataset of almost 35 million reads permits the use of read abundance distributions along putative precursor sequences as a practical tool for isolating miRNAs in a large background of reads originating from other non-coding and coding RNAs. This study therefore provides a generic approach for discovering novel miRNAs where no genome sequence is available.
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