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 

机构地区：[1]Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences,132 Lanhei Road,Kunming,Yunnan 650201,China [2]Kunming College of Life Science,University of Chinese Academy of Sciences,19 Qingsong Road,Kunming,Yunnan 650201,China

出　　处：《Plant Diversity》2020年第5期356-361,共6页植物多样性（英文版）

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).

摘　　要：Cytidine-to-uridine(C-to-U)RNA editing is common in coding regions of organellar genomes throughout land plants.In most cases RNA editing alters translated amino acids or creates new start codons,potentially confounds phylogenetic reconstructions.In 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 reconstruction.We 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,respectively.We predicted between 400 and 3100 RNA editing sites of 18 Selaginella plastomes.The 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 whole.Contrast 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 sets.This 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 reconstruction.Therefore,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.

关 键 词：GC content Land plants Organellar genome PHYLOGENOMICS RNA editing 

分 类 号：Q943.2[生物学—植物学]