蕨类植物叶绿体RNA编辑及其适应性进化研究

RNA editing could recode the genetic information at post-transcriptional level to modify gene function and regulation. Our analyses have suggested that leptosporangiates have extremely higher levels of chloroplast RNA editing than that in basal fern lineages. Leptosporangiates are the largest monophyletic group within ferns. Recent studies have shown that the major diversity of living leptosporangiate ferns is mostly the result of a new radiation beginning in the Cretaceous, following the rise of angiosperms. Hence, it appears that leptosporangiates have successfully adapted and somehow been able to capitalize upon the angiosperm-dominated terrestrial ecosystems. The high levels of chloroplast RNA editing in leptosporangiates might play important roles in their rapid adaption and new radiation. In this study, we plan to carry out genome-wide identifications of chloroplast RNA editing sites in ferns by strand-specific RNA sequencing (RNA-Seq) tool, and then perform adaptive evolution analyses of RNA editing to verify its essential role in leptosporangiates’ adaption and diversity. The RNA editomes will be obtained from all the representatives from basal ferns to eupolypods, the major lineage resulting from the new radiation. Three specific issues will be investigated: 1) What are the differences of the type, frequency and genomic distribution of RNA editing between leptosporangiates and basal ferns? 2) Does the abundance of RNA editing correlate with the diversity of leptosporangiates? Was their diversification in fact linked to the large number of RNA editing sites? 3) Is there any advantageous or adaptive RNA editing in leptosporangiates related to the radiation? What are they? And what are their potential biological functions? This study firstly connects the RNA editing to a specific radiation event and provides new insights into the explanation of the radiation. The results will deepen our understanding of the evolution and importance of RNA editing.

RNA编辑通过在转录后水平对遗传信息重新编码来调控基因，进而影响植物的生长发育。薄囊蕨类是蕨类植物中最主要的单系群，它在被子植物兴起后，快速适应并发生了新的辐射分化。我们的前期研究发现，薄囊蕨类的RNA编辑量显著高于基部蕨类，提示高水平的RNA编辑可能在此辐射过程中发挥重要作用。基于此，本研究拟利用链特异性RNA-Seq技术，获取蕨类植物叶绿体全基因组RNA编辑信息，分析其进化式样，检验其在薄囊蕨类辐射分化中的作用。研究内容包括：1）选取从基部蕨类到真水龙骨类薄囊蕨的代表植物，明确其叶绿体RNA编辑的类型、频率和分布模式；2）阐明RNA编辑与薄囊蕨类多样性的相关性；3）开展RNA编辑的适应性进化分析，鉴定与薄囊蕨类辐射扩张相关的适应性编辑位点。本项目首次将RNA编辑与特定植物类群的辐射分化联系起来，以一个全新的角度探索薄囊蕨类适应性辐射的形成机制，将丰富和深化对RNA编辑进化意义的认识。

RNA编辑通过在转录后水平对遗传信息重新编码来调控基因，进而影响植物的生长发育。在种子植物中，RNA编辑一般仅有C-U一种形式；而蕨类植物则同时拥有C-U和U-C两种类型的RNA编辑。关于U-C型反向编辑的起源和功能，一直以来争议颇多。薄囊蕨类是蕨类植物中最繁盛的单系群，它在被子植物兴起后，快速适应并发生了新的辐射分化。我们的前期研究发现，薄囊蕨类的RNA编辑特征不同于基部蕨类，提示RNA编辑可能在此辐射过程中发挥重要作用。基于此，本项目选取从基部蕨类到真水龙骨类薄囊蕨的代表植物，利用链特异性RNA-Seq技术，获取蕨类植物叶绿体全基因组RNA编辑信息，检验了RNA编辑在薄囊蕨类辐射分化中的作用。本研究测定了12种蕨类植物的叶绿体基因组全序列，利用叶绿体系统发育基因组学方法，明确了蕨类植物各类群的系统发育关系。在此系统框架下，考察了蕨类植物叶绿体基因组的结构演化模式。对上述12种蕨类植物，利用链特异性RNA-seq数据，获取了它们全基因组的RNA编辑信息。分析发现：1）并不是所有的蕨类植物都有C-U和U-C两种类型的RNA编辑，其中U-C型反向编辑仅见于瓶尔小草类和除紫萁类以外的薄囊蕨类；2）U-C型编辑在薄囊蕨类和瓶尔小草类中的起源是相互独立的；3）U-C型编辑与编码区内部终止密码子的出现共进化，提示U-C型编辑可能是作为叶绿体基因组有害突变的修复机制而产生的；4）同时，不完全编辑的普遍存在，提示RNA编辑是后转录水平叶绿体基因表达调控的重要手段。本项目首次将RNA编辑与特定植物类群的辐射分化联系起来，以一个全新的角度探索薄囊蕨类适应性辐射的形成机制，丰富和深化了对RNA编辑进化意义的认识。