Variable Frequency of Plastid RNA Editing among Ferns and Repeated Loss of Uridine-to-Cytidine Editing from Vascular Plants

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-to-U与U-to-C型RNA编辑（RNA editing）的分布模式与丰度存在显著差异，提示这两类编辑过程独立起源并演化，但多个关键类群的信息匮乏限制了我们对其演化历程的认知。为探究蕨类植物RNA编辑的演化多样性，我们对两个早期分化类群的质体转录组（plastid transcriptome）进行了测序：加利福尼亚瓶尔小草（Ophioglossum californicum）与裸蕨（Psilotum nudum）。我们采用宽松的自动化分析策略以最大限度降低假阴性结果，并结合人工校验剔除假阳性位点，最终在加利福尼亚瓶尔小草的质体转录组中鉴定出297个C-to-U编辑位点与3个U-to-C编辑位点，而在裸蕨的质体转录组中仅鉴定出27个C-to-U编辑位点，未发现U-to-C编辑位点。通过与薄囊蕨类植物铁线蕨（Adiantum capillus-veneris）以及角苔类植物台湾角苔（Anthoceros formosae）的编辑内容开展更广泛的比较，我们发现质体编辑的丰度存在巨大差异，这表明蕨类植物的RNA编辑频率与类型具有高度不稳定性。相较于沉默位点与非保守位点，能够提升物种间蛋白质保守性的编辑位点数量更多、编辑效率更高，这提示自然选择保留了具有功能重要性的RNA编辑事件。裸蕨与其他维管植物的质体转录组中均未发现U-to-C型RNA编辑，这表明U-to-C编辑的丢失是维管植物演化过程中反复出现的现象。