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Genes 2017, 8(1), 13; doi:10.3390/genes8010013

Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.

State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest Agriculture and Forestry University, Yangling 712100, Xianyang, China
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Academic Editor: H. Ulrich Göringer
Received: 23 September 2016 / Revised: 9 December 2016 / Accepted: 20 December 2016 / Published: 30 December 2016
(This article belongs to the Special Issue RNA Editing)
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Abstract

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. View Full-Text
Keywords: Aegilops tauschii; chloroplast; RNA editing; Triticum Aegilops tauschii; chloroplast; RNA editing; Triticum
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Wang, M.; Liu, H.; Ge, L.; Xing, G.; Wang, M.; Weining, S.; Nie, X. Identification and Analysis of RNA Editing Sites in the Chloroplast Transcripts of Aegilops tauschii L.. Genes 2017, 8, 13.

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