Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae)

doi:10.1038/srep42328

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	Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae)
	Wang, Hong-Juan ; Li, Wei-Tao ; Liu, Ya-Nan ; Yang, Fu-Sheng ; Wang, Xiao-Quan
刊名	MOLECULAR PHYLOGENETICS AND EVOLUTION
	2017
卷号	107 页码:345-355
关键词	Non-neutral gene Phylogenomics Phylogeny Recent radiation Selective pressure Transcriptome
ISSN号	1055-7903
DOI	10.1038/srep42328
文献子类	Article
英文摘要	Phylogenomics has shown great potential in resolving evolutionary relationships at different taxonomical levels. However, it remains controversial whether all orthologous genes under different selective pressures can be concatenated for phylogenomic reconstruction. Here we used sect. Cyathophora of Pedicularis, one of the most species-rich genera of angiosperms in the alpine and arctic regions of the Northern Hemisphere, as a model to investigate the efficiency of RNA-seq in resolving relationships of closely related congeneric species. Flower transcriptomes were sequenced for all species of sect. Cyathophora and two outgroup species. Forty-one highly conserved single-/low-copy nuclear genes and 1553 orthologous groups (OGs) were identified and concatenated into five datasets based on gene copy numbers and Ka/Ks values to reconstruct the phylogeny of section Cyathophora. We also tested how many genes minimally can resolve the interspecific relationships, and reconstructed the evolutionary history of some floral characters in sect. Cyathophora. The results showed that the five different datasets consistently resolved the interspecific relationships of sect. Cyathophora, and the interspecific relationships can be robustly reconstructed with maximal support when >= 20 single-/low-copy nuclear genes or 25 OGs are used. Our study suggests that all OGs under different selective pressures can be concatenated for phylogenomic reconstruction, and provides a successful and efficient use of RNA-seq in reconstructing interspecific relationships of a non-model plant group with recent radiations. (C) 2016 Elsevier Inc. All rights reserved.
学科主题	Science & Technology - Other Topics
电子版国际标准刊号	1095-9513
出版地	SAN DIEGO
WOS关键词	COPY NUCLEAR GENES ; PHYLOGENETIC ANALYSES ; TRANSCRIPTOME ANALYSIS ; FLORAL DIVERSITY ; SNP DISCOVERY ; GENOMIC DATA ; RADSEQ DATA ; RADIATION ; GENERATION ; ORIGIN
语种	英语
出版者	ACADEMIC PRESS INC ELSEVIER SCIENCE
WOS记录号	WOS:000393577900001
资助机构	National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31330008] ; Chinese Academy of Sciences (CAS/SAFEA International Partnership Program for Creative Research Teams)
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/22130]
专题	系统与进化植物学国家重点实验室
作者单位	1.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 2.Li, Wei-Tao 3.Liu, Ya-Nan 4.Yang, Fu-Sheng 5.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China 6.[Wang, Hong-Juan
推荐引用方式 GB/T 7714	Wang, Hong-Juan,Li, Wei-Tao,Liu, Ya-Nan,et al. Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae)[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2017,107:345-355.
APA	Wang, Hong-Juan,Li, Wei-Tao,Liu, Ya-Nan,Yang, Fu-Sheng,&Wang, Xiao-Quan.(2017).Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae).MOLECULAR PHYLOGENETICS AND EVOLUTION,107,345-355.
MLA	Wang, Hong-Juan,et al."Resolving interspecific relationships within evolutionarily young lineages using RNA-seq data: An example from Pedicularis section Cyathophora (Orobanchaceae)".MOLECULAR PHYLOGENETICS AND EVOLUTION 107(2017):345-355.