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

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.

Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

“…In addition, we compared the RNA editing sites patterns in these plastids, and 15 sites in nine genes were found to be shared by these six Panicoideae cp genomes ( Table 5). It has been proven that the RNA editing was evolutionarily conserved and that species having a closer relationship generally shared more editing sites [45]. In this study, broomcorn millet was found to share 29 editing sites with switchgrass, which was more overlap than for the other four species.…”

“…RNA editing is an important way to regulate gene expression at a post-transcriptional level, which generally changes original genetic information by insertion, deletion, and base substitution of nucleotides within mRNA molecules [44]. Various studies in the chloroplasts of higher plants have suggested that identification of RNA editing sites could be very useful for enriching the genetic information, which makes it easier for organisms to adapt to the environment and also uncover the evolutionary patterns of RNA editing [18,45]. Here, a total of 175 editing sites were predicted in these six Panicoideae cp genomes, and further analysis found that all of these sites were C to U conversions, which was consistent with a previous study of RNA editing in cp genomes in N. tabacum [46].…”

Intraspecific Variation within the Utricularia amethystina Species Morphotypes Based on Chloroplast Genomes

“…Both lead to protein variations ( Table 2, Tables S8-S10), whereas amino acid changes from Alanine to Valine, Histidine to Tyrosine, Leucine to Phenylalanine, Proline to Phenylalanine, Proline to Leucine, Proline to Serine, Arginine to Tryptophan, Threonine to Isoleucine, and Threonine to Methionine result in no physicochemical properties changes in protein. In addition, the Arginine to Cysteine, Serine to Leucine, and Serine to Phenylalanine mutations can modify protein formation due to hydrophilic (Serine and Arginine) to hydrophobic (Leucine, Phenylalanine, and Cysteine) molecule changes [52,53]. Moreover, PREPACT3 has predicted that the genes rps2 and rpl32 can be edited from Glutamine into a Stop codon, and despite they could be polycistronic genes as in other plants [54], these genes are still transcribed according to RNA-Seq data.…”

Comparative Analysis of the Transcriptional Response of Tolerant and Sensitive Wheat Genotypes to Drought Stress in Field Conditions

“…RNA editing is a process that occurs in the RNA molecular base change or modification when transcribed, which is one of most important mechanisms regulating gene expression and enriching genetic information at the post-transcription level [50]. A larger number of studies have reported that RNA editing not only controls plant organ formation, growth, and development, but also plays an indispensable role in the response to diverse stresses [51,52]. The RNA-seq data provides a resource to identify the RNA editing sites at the whole transcriptome level.…”