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

Mengxing Wang,Lingqiao Ge,Guangwei Xing,Meng Wang,Xiaojun Nie,Song Weining,Hui Liu

doi:10.3390/genes8010013

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.

Highlights

RNA editing is a post-transcriptional process for converting cytidine (C) to uridine (U), or U to C, at specific sites within RNA molecules to alter the identity of nucleotides between RNA and genomic
Since the first editing event of the land plant plastome was found in the mRNA transcript of the rpl2 gene in the maize chloroplast genome in 1991 [6], extensive RNA editing sites have been detected in a variety of higher plants, such as tobacco [7,8], Arabidopsis [9], pea [10], and tomato [11], and some of them have been validated by experiments [12]
30 out of 34 (88.24%) editing events were observed in the second position of the codon and the rest were in the first position

Summary

Introduction

DNA, serving as a mechanism to correct missense mutations of genes at the RNA level, and to enrich genetic information [1,2]. It can act upon transcripts in the cell nucleus, cytoplasm, mitochondria, and chloroplast (cp), which has been widely documented in various organisms, including eukaryotes, prokaryotes, archaebacteria, viruses, etc. Since the first editing event of the land plant plastome was found in the mRNA transcript of the rpl gene in the maize chloroplast genome in 1991 [6], extensive RNA editing sites have been detected in a variety of higher plants, such as tobacco [7,8], Arabidopsis [9], pea [10], and tomato [11], and some of them have been validated by experiments [12]. In other land plant clades, editing frequencies vary widely, with no editing in marchantiid liverworts [16].

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Conclusion