Plant noncoding RNA gene discovery by "single-genome comparative genomics"
Plant noncoding RNA gene discovery by "single-genome comparative genomics"
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通过“单基因组比较基因组学”发现植物非编码RNA基因
DOI：
10.1261/rna.2426511
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发表时间：
2011-03-01
期刊：
影响因子：
4.5
通讯作者：
Gautheret, Daniel
中科院分区：
文献类型：
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作者：
Chen, Chong-Jian;Zhou, Hui;Gautheret, Daniel
植物基因组经历了多轮复制，这对基因家族的发展做出了巨大贡献。由此产生的家族结构已经深入研究了蛋白质编码基因。然而，关于重复对非编码RNA（ncRNA）基因的影响知之甚少。在这里，我们对水稻基因组中的重复区域进行系统分析，以寻找此类ncRNA重复序列。我们观察到，就像它们的蛋白质对应物一样，大多数ncRNA基因经历了多次复制，留下了可见的序列保守足迹。植物中ncRNA基因复制的程度使得这些序列足迹可以被大规模地用于发现新的ncRNA基因家族。我们开发了一个SVM模型，能够在水稻基因组中的100，000多个重复家族中检索可能的ncRNA候选者，假阳性发现率相当低。在通过这种方法预测的近4000个ncRNA家族中，只有90个对应于推定的snoRNA或miRNA家族。剩下的家族中大约有一半被归类为结构化RNA。新的候选ncRNA特别富集在UTR和内含子区域。有趣的是，89%的推定ncRNA家族在将其序列与另一种草基因组（如玉米）进行比较时不会产生可检测的信号。我们的研究结果表明，大部分水稻ncRNA基因存在于多个拷贝，是物种特异性或最近的起源。基因组内比较是这一主要类别的ncRNA的计算注释的独特和有力的来源。
Plant genomes have undergone multiple rounds of duplications that contributed massively to the growth of gene families. The structure of resulting families has been studied in depth for protein-coding genes. However, little is known about the impact of duplications on noncoding RNA (ncRNA) genes. Here we perform a systematic analysis of duplicated regions in the rice genome in search of such ncRNA repeats. We observe that, just like their protein counterparts, most ncRNA genes have undergone multiple duplications that left visible sequence conservation footprints. The extent of ncRNA gene duplication in plants is such that these sequence footprints can be exploited for the discovery of novel ncRNA gene families on a large scale. We developed an SVM model that is able to retrieve likely ncRNA candidates among the 100,000+ repeat families in the rice genome, with a reasonably low false-positive discovery rate. Among the nearly 4000 ncRNA families predicted by this means, only 90 correspond to putative snoRNA or miRNA families. About half of the remaining families are classified as structured RNAs. New candidate ncRNAs are particularly enriched in UTR and intronic regions. Interestingly, 89% of the putative ncRNA families do not produce a detectable signal when their sequences are compared to another grass genome such as maize. Our results show that a large fraction of rice ncRNA genes are present in multiple copies and are species-specific or of recent origin. Intragenome comparison is a unique and potent source for the computational annotation of this major class of ncRNA.