A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources.
A contig-based strategy for the genome-wide discovery of microRNAs without complete genome resources.
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在没有完整基因组资源的情况下，基于重叠群的 MicroRNA 全基因组发现策略
DOI：
10.1371/journal.pone.0088179
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Qu LH
中科院分区：
文献类型：
--
作者：
Wen JZ;Liao JY;Zheng LL;Xu H;Yang JH;Guan DG;Zhang SM;Zhou H;Qu LH
microRNA（miRNAs）是许多细胞过程的重要调控因子，广泛存在于真核生物中。高通量测序是一种主流的miRNA鉴定方法，通过该方法可以获得生物体的完整小RNA谱。目前，大多数鉴定miRNA的方法依赖于参考基因组来预测发夹结构。然而，许多具有经济和系统发育重要性的物种是没有完整基因组序列的非模式生物，这限制了miRNA的发现。为了克服这一局限性，我们开发了一种基于重叠群的miRNA鉴定策略。我们将该方法应用于三倍体食用香蕉（GCTCV-119，Musa spp.）AAA组），共鉴定出180个pre-miRNAs和314个成熟miRNAs，比现有的基于EST+GSS的方法预测的数量多3倍。基于最近发表的尖叶芭蕉的miRNA数据集，我们的策略的召回率和准确率估计分别为70.6%和92.2%，明显优于基于EST+ GSS的策略（分别为10.2%和50.0%）。我们的新的，有效的和具有成本效益的策略，促进了研究的功能和进化作用的miRNA，以及基于miRNA的分子育种，在非模式物种的经济或进化的利益。
MicroRNAs (miRNAs) are important regulators of many cellular processes and exist in a wide range of eukaryotes. High-throughput sequencing is a mainstream method of miRNA identification through which it is possible to obtain the complete small RNA profile of an organism. Currently, most approaches to miRNA identification rely on a reference genome for the prediction of hairpin structures. However, many species of economic and phylogenetic importance are non-model organisms without complete genome sequences, and this limits miRNA discovery. Here, to overcome this limitation, we have developed a contig-based miRNA identification strategy. We applied this method to a triploid species of edible banana (GCTCV-119, Musa spp. AAA group) and identified 180 pre-miRNAs and 314 mature miRNAs, which is three times more than those were predicted by the available dataset-based methods (represented by EST+GSS). Based on the recently published miRNA data set of Musa acuminate, the recall rate and precision of our strategy are estimated to be 70.6% and 92.2%, respectively, significantly better than those of EST+GSS-based strategy (10.2% and 50.0%, respectively). Our novel, efficient and cost-effective strategy facilitates the study of the functional and evolutionary role of miRNAs, as well as miRNA-based molecular breeding, in non-model species of economic or evolutionary interest.
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