Background: RNA editing is a post-transcriptional modification that complement variation at the DNA level. Until now, different RNA editing systems were found in the major eukaryotic lineages. However, the evolution trajectory in plant chloroplast remains unclear. To gain a better understanding of RNA editing in plant chloroplast, in this study, based on publicly available RNA-seq data across three plant lineages (fern, gymnosperm, and angiosperm), we provided a detailed analysis of RNA editing events in plant chloroplasts and discussed the evolution of RNA editing in land plants. Results: There were a total of 5,389 editing sites located in leaf chloroplast identified across 21 plants after rigorous screening. We found that the cluster of RNA editing sites across 21 plants complied with the phylogenetic tree based on linked protein sequences approximately, and majority (~ 95%) of the editing events resulted in non-synonymous codon changes, RNA editing occurred in second codon position was mainly the largest. Additionally, RNA editing caused an overall increase in hydrophobicity of the resulting proteins. The analyses also revealed that there is an uneven distribution of editing sites among species, genes, and codon positions, the average RNA editing extent varied among different plant species as well as genes. Finally, we found that the loss of editing sites along angiosperm evolution is mainly occurring by reduce of cytosines content, fern plants has the highest cytosine content, with the evolution of plants, cytosine were lost in RNA edited genes. Conclusions: Many of the identified sites in our study have not been previously reported and represent a valuable data set for future research community. Our findings provide valuable information for evolution of RNA editing in plants.

中文翻译：

---

通过执行广谱RNA序列分析获得对叶绿体RNA编辑的全面生物学见解

背景：RNA编辑是一种转录后修饰，可补充DNA水平的变异。到目前为止，在主要的真核生物谱系中发现了不同的RNA编辑系统。但是，植物叶绿体的进化轨迹仍然不清楚。为了更好地了解植物叶绿体中的RNA编辑，在这项研究中，基于三个植物谱系（蕨类，裸子植物和被子植物）的RNA序列数据，我们提供了植物叶绿体和植物中RNA编辑事件的详细分析。讨论了陆地植物中RNA编辑的演变。结果：经过严格筛选后，在21株植物的叶绿体中共有5389个编辑位点。我们发现，跨21个植物的RNA编辑位点簇与基于连锁蛋白序列的系统进化树相符，并且大多数（〜95％）编辑事件导致非同义密码子变化，RNA编辑发生在第二个密码子位置主要是最大的。另外，RNA编辑导致所得蛋白质的疏水性整体增加。分析还显示，物种，基因和密码子位置之间的编辑位点分布不均，不同植物物种和基因之间的平均RNA编辑程度也不同。最后，我们发现被子植物进化过程中编辑位点的丢失主要是由于胞嘧啶含量的降低，蕨类植物的胞嘧啶含量最高，随着植物的进化，RNA编辑基因中的胞嘧啶丢失。结论：我们的研究中许多鉴定出的位点以前未曾报道过，它们代表了未来研究界的宝贵数据集。我们的发现为植物中RNA编辑的进化提供了有价值的信息。