Guo Wenhu, Grewe Felix, Mower Jeffrey P
Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, United States of America; School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, United States of America; ACGT, Inc., Wheeling, Illinois, United States of America.
Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska, United States of America; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska, United States of America.
PLoS One. 2015 Jan 8;10(1):e0117075. doi: 10.1371/journal.pone.0117075. eCollection 2015.
The distinct distribution and abundance of C-to-U and U-to-C RNA editing among land plants suggest that these two processes originated and evolve independently, but the paucity of information from several key lineages limits our understanding of their evolution. To examine the evolutionary diversity of RNA editing among ferns, we sequenced the plastid transcriptomes from two early diverging species, Ophioglossum californicum and Psilotum nudum. Using a relaxed automated approach to minimize false negatives combined with manual inspection to eliminate false positives, we identified 297 C-to-U and three U-to-C edit sites in the O. californicum plastid transcriptome but only 27 C-to-U and no U-to-C edit sites in the P. nudum plastid transcriptome. A broader comparison of editing content with the leptosporangiate fern Adiantum capillus-veneris and the hornwort Anthoceros formosae uncovered large variance in the abundance of plastid editing, indicating that the frequency and type of RNA editing is highly labile in ferns. Edit sites that increase protein conservation among species are more abundant and more efficiently edited than silent and non-conservative sites, suggesting that selection maintains functionally important editing. The absence of U-to-C editing from P. nudum plastid transcripts and other vascular plants demonstrates that U-to-C editing loss is a recurrent phenomenon in vascular plant evolution.
陆生植物中C到U和U到C的RNA编辑具有不同的分布和丰度，这表明这两个过程是独立起源和进化的，但来自几个关键谱系的信息匮乏限制了我们对其进化的理解。为了研究蕨类植物中RNA编辑的进化多样性，我们对两种早期分化物种加州瓶尔小草（Ophioglossum californicum）和松叶蕨（Psilotum nudum）的质体转录组进行了测序。我们采用一种宽松的自动化方法来尽量减少假阴性，并结合人工检查来消除假阳性，在加州瓶尔小草质体转录组中鉴定出297个C到U和3个U到C的编辑位点，而在松叶蕨质体转录组中仅鉴定出27个C到U的编辑位点，没有U到C的编辑位点。将编辑内容与薄囊蕨纲蕨类植物铁线蕨（Adiantum capillus-veneris）和角苔（Anthoceros formosae）进行更广泛的比较，发现质体编辑丰度存在很大差异，这表明蕨类植物中RNA编辑的频率和类型高度不稳定。与沉默和非保守位点相比，物种间增加蛋白质保守性的编辑位点更丰富且编辑效率更高，这表明选择维持了功能重要的编辑。松叶蕨质体转录本及其他维管植物中不存在U到C的编辑，这表明U到C编辑的缺失是维管植物进化中的一种反复出现的现象。
