Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing

doi:10.1016/j.ympev.2022.107507

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	Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing
	Zhang, Meng-Hua ; Xiang, Qiao-Ping ; Zhang, Xian-Chun
刊名	MOLECULAR PHYLOGENETICS AND EVOLUTION
	2022
卷号	173
关键词	Alternative topologies Gene-tree conflict Plastome Phylogenetic signal Selaginella sanguinolenta group Species trees
ISSN号	1055-7903
DOI	10.1016/j.ympev.2022.107507
文献子类	Article
英文摘要	Different from the generally conserved plastomes (plastid genomes) of most land plants, the Selaginellaceae plastomes exhibit dynamic structure, high GC content and high substitution rates. Previous plastome analyses identified strong conflict on several clades in Selaginella, however the factors causing the conflictions and the impact on the phylogenetic inference have not been sufficiently investigated. Here, we dissect the distribution of phylogenetic signals and conflicts in Selaginella sanguinolenta group, the plastome of which is DR (direct repeats) structure and with genome-wide RNA editing. We analyzed the data sets including 22 plastomes representing all species of the S. sanguinolenta group, covering the entire geographical distribution from the Himalayas to Siberia and the Russian Far East regions. We recovered four different topologies by applying multispecies coalescent (ASTRAL) and concatenation methods (IQ-TREE and RAxML) on four data sets of PC (protein-coding genes), NC (non-coding sequences), PCN (the concatenated PC and NC), and RC (predicted RNA editing sites C were corrected by T ), respectively. Six monophyletic clades, S. nummularifolia clade, S. rossii clade, S. sajanensis clade, S. sanguinolenta I clade, S. sanguinolenta II clade, and S. sanguinolenta III clade, were consistently resolved and supported by the characteristics of GC content, RNA editing frequency, and gene content. However, the relationships among these clades varied across the four topologies. To explore the underlying causes of the uncertainty, we compared the phylogenetic signals of the four topologies. We identified that the sequence types (coding versus non-coding), outlier genes (genes with extremely high \|delta GLS\| values), and C-to-U RNA editing frequency in the protein-coding genes were responsible for the unstable phylogenomic relationship. We further revealed a significant positive correlation between the \|delta GLS\| values and the variation coefficient of the RNA editing number. Our results demonstrated that the coalescent method performed better than the concatenation method in overcoming the problems caused by outlier genes and extreme RNA editing events. Our study particularly focused on the importance of exploring the plastid phylogenomic conflicts and suggested conducting concatenated analyses cautiously when adopting organelle genome data.
学科主题	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
电子版国际标准刊号	1095-9513
出版地	SAN DIEGO
WOS关键词	CHLOROPLAST DNA ; SPECIES TREE ; GENOMES ; COMPLEX ; CLASSIFICATION ; IDENTIFICATION ; ORGANIZATION ; CHROMOSOMES ; INFERENCE ; PLATFORM
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号	WOS:000806808000005
资助机构	National Natural Science Foundation of China [32170233]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/28995]
专题	系统与进化植物学国家重点实验室
作者单位	1.[Zhang, Meng-Hua 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Xiang, Qiao-Ping 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Meng-Hua,Xiang, Qiao-Ping,Zhang, Xian-Chun. Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2022,173.
APA	Zhang, Meng-Hua,Xiang, Qiao-Ping,&Zhang, Xian-Chun.(2022).Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing.MOLECULAR PHYLOGENETICS AND EVOLUTION,173.
MLA	Zhang, Meng-Hua,et al."Plastid phylogenomic analyses of the Selaginella sanguinolenta group (Selaginellaceae) reveal conflict signatures resulting from sequence types, outlier genes, and pervasive RNA editing".MOLECULAR PHYLOGENETICS AND EVOLUTION 173(2022).