Extreme plastid RNA editing may confound phylogenetic reconstruction:A case study of Selaginella(lycophytes)

作     者：Xin-Yu Du Jin-Mei Lu De-Zhu Li Xin-Yu Du;Jin-Mei Lu;De-Zhu Li

作者机构：Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of Sciences132 Lanhei RoadKunmingYunnan 650201China Kunming College of Life ScienceUniversity of Chinese Academy of Sciences19 Qingsong RoadKunmingYunnan 650201China 

出 版 物：《Plant Diversity》 (植物多样性（英文版）)

年 卷 期：2020年第42卷第5期

页      面：356-361页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 09[农学] 071007[理学-遗传学] 0901[农学-作物学] 090102[农学-作物遗传育种] 

基　　金：We thank Dr.Peng-Fei Ma for improving the manuscript.We also thank the two anonymous reviewers for their constructive comments and suggestions.The study was supported by the Strategic Priority Research Program,Chinese Academy of Sciences,China(XDB 31000000) the National Natural Science Foundation of China(31970232) the Large-scale Scientific Facilities of the Chinese Academy of Sciences,China(2017-LSF-GBOWS-02) the technological leading talent project of Yunnan,China(2017HA014) 

主　　题：GC content Land plants Organellar genome Phylogenomics RNA editing 

摘      要：Cytidine-to-uridine(C-to-U)RNA editing is common in coding regions of organellar genomes throughout land *** most cases RNA editing alters translated amino acids or creates new start codons,potentially confounds phylogenetic *** this study,we used the spike moss genus Selaginella(lycophytes),which has the highest frequency of RNA editing,as a model to test the effects of extreme RNA editing on phylogenetic *** predicted the C-to-U RNA editing sites in coding regions of 18 Selaginella plastomes,and reconstructed the phylogenetic relationships within Selaginella based on three data set pairs consisted of plastome or RNA-edited coding sequences,first and second codon positions,and translated amino acid sequences,*** predicted between 400 and 3100 RNA editing sites of 18 Selaginella *** numbers of RNA editing sites in plastomes were highly correlated with the GC content of first and second codon positions,but not correlated with the GC content of plastomes as a *** phylogenetic analyses showed that there were substantial differences(e.g.,the placement of clade B in Selaginella)between the phylogenies generated by the plastome and RNA-edited data *** empirical study provides evidence that extreme C-to-U RNA editing in the coding regions of organellar genomes alters the sequences used for phylogenetic reconstruction,and might even confound phylogenetic ***,RNA editing sites should be corrected when plastid or mitochondrial genes are used for phylogenetic studies,particularly in those lineages with abundant organellar RNA editing sites,such as hornworts,quillworts,spike mosses,and some seed plants.