Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.
Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.
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作者：
Wang M;Liu H;Ge L;Xing G;Wang M;Weining S;Nie X
RNA编辑是高等植物叶绿体中在转录后水平将胞苷（C）在RNA分子内的特定位点转化为尿苷（U）的重要途径。虽然在许多植物中已经进行了系统的研究，但对小麦D基因组供体节节麦中的RNA编辑知之甚少。本文研究了Ae. tauschii，并将其与其他小麦近缘种进行比较，以追溯小麦的进化。通过生物信息学预测，共鉴定出34个C-to-U编辑位点，其中17个经RT-PCR产物测序验证。此外，通过RNA-Seq读段作图方法发现了60个位点，其中24个与预测一致，6个经过实验验证。这些编辑位点偏向于tCn或nCa三核苷酸和5′-嘧啶，与其它种子植物的编辑位点侧翼碱基一致。此外，RNA编辑事件还可能导致相应蛋白质的二级结构和拓扑结构发生改变，提示RNA编辑可能影响靶基因的功能。最后，通过比较分析发现了小麦中一些进化上保守的编辑位点，并获得了两个物种特异性位点。本研究首次报道了节节麦中RNA编辑的研究，不仅从RNA编辑的角度揭示了小麦的进化，也为进一步研究C-to-U变异的机制奠定了基础。
RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing. Furthermore, 60 sites were found by the RNA-Seq read mapping approach, 24 of which agreed with the prediction and six were validated experimentally. The editing sites were biased toward tCn or nCa trinucleotides and 5′-pyrimidines, which were consistent with the flanking bases of editing sites of other seed plants. Furthermore, the editing events could result in the alteration of the secondary structures and topologies of the corresponding proteins, suggesting that RNA editing might impact the function of target genes. Finally, comparative analysis found some evolutionarily conserved editing sites in wheat and two species-specific sites were also obtained. This study is the first to report on RNA editing in Aegilops tauschii L, which not only sheds light on the evolution of wheat from the point of view of RNA editing, but also lays a foundation for further studies to identify the mechanisms of C-to-U alterations.