Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)

doi:10.1016/j.ympev.2023.107912

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	Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)
	Zhang,Qiong; Folk,Ryan A.; Mo,Zhi-Qiong; Ye,Hang; Zhang,Zhao-Yuan; Peng,Hua; Zhao,Jian-Li; Yang,Shi-Xiong; Yu,Xiang-Qin
	2023
发表期刊	MOLECULAR PHYLOGENETICS AND EVOLUTION
ISSN	1095-9513
卷号	188 页码:107912
摘要	Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of se-lection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discor-dance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.
关键词	Camellia Gene tree discordance Transcriptome Rapid diversification Selective pressure RNA-SEQ DATA PHYLOGENETIC ANALYSIS NUCLEAR GENES SEQUENCE EVOLUTION RESOLUTION HISTORY INFERENCE ALGORITHM SELECTION
DOI	10.1016/j.ympev.2023.107912
收录类别	SCI
WOS记录号	WOS:001097311500001
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75495
专题	中国科学院昆明植物研究所
推荐引用方式 GB/T 7714	Zhang,Qiong,Folk,Ryan A.,Mo,Zhi-Qiong,et al. Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)[J]. MOLECULAR PHYLOGENETICS AND EVOLUTION,2023,188:107912.
APA	Zhang,Qiong.,Folk,Ryan A..,Mo,Zhi-Qiong.,Ye,Hang.,Zhang,Zhao-Yuan.,...&Yu,Xiang-Qin.(2023).Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae).MOLECULAR PHYLOGENETICS AND EVOLUTION,188,107912.
MLA	Zhang,Qiong,et al."Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae)".MOLECULAR PHYLOGENETICS AND EVOLUTION 188(2023):107912.

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