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DOI	10.1186/s12870-022-03577-x
	Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau
	Cao, Qian; Gao, Qingbo; Ma, Xiaolei; Zhang, Faqi; Xing, Rui; Chi, Xiaofeng; Chen, Shilong
通讯作者	Chen, SL (通讯作者)，Chinese Acad Sci, Key Lab Crop Mol Breeding Qinghai Prov, Northwest Inst Plateau Biol, Xining 810008, Peoples R China.
发表日期	2022
ISSN	1471-2229
卷号	22 期号:1
英文摘要	Background The genus Swertia is of great medicinal importance and one of the most taxonomically challenging taxa within Gentianaceae, largely due to the morphological similarities of species within this genus and with its closely related genera. Previous molecular studies confirmed its polyphyly but suffered from low phylogenetic resolutions because only limited sequence loci were used. Thus, we conducted the structural, gene evolutionary, and phylogenetic analyses of 11 newly obtained plastomes of Swertia. Our result greatly improved the phylogenetic resolutions in Swertia, shed new light on the plastome evolution and phylogenetic relationships of this genus. Results The 11 Swertia plastomes together with the published seven species proved highly similar in overall size, structure, gene order, and content, but revealed some structural variations caused by the expansion and contraction of the IRb region into the LSC region, due to the heterogeneous length of the psi ycf1. The gene rps16 was found to be in a state flux with pseudogenes or completely lost. Similar situation was also documented in other genera of Gentianaceae. This might imply loss of the gene in the common ancestor of Gentianaceae. The distribution plot of ENC vs. GC3 showed all these plastomes arranging very close in the Wright line with an expected ENC value (49-52%), suggesting the codon usage of Swertia was mainly constrained by a GC mutation bias. Most of the genes remained under the purifying selection, however, the cemA was identified under positive selection, possibly reflecting an adaptive response to low CO2 atmospheric conditions during the Late Miocene. Our phylogenomic analyses, based on 74 protein-coding genes (CDS), supported the polyphyly of Swertia with its close allies in the subtribe Swertiinae, presumably due to recent rapid radiation. The topology inferred from our phylogenetic analyses partly supported the current taxonomic treatment. Finally, several highly variable loci were identified, which can be used in future phylogenetic studies and accurate identification of medicinal genuineness of Swertia. Conclusions Our study confirmed the polyphyly of Swertia and demonstrated the power of plastome phylogenomics in improvement of phylogenetic resolution, thus contributing to a better understanding of the evolutionary history of Swertia.
关键词	COMPLETE CHLOROPLAST GENOME COMPLETE NUCLEOTIDE-SEQUENCE PHYLOGENETIC ANALYSIS MOLECULAR PHYLOGENY EFFECTIVE NUMBER ALPINE PLANTS CODON USAGE DNA SUBSTITUTION GENTIANEAE
英文关键词	Swertia; Plastome; Pseudogene; Positive selection; Polyphyly; Phylogenetic relationships; Rapid radiation
语种	英语
WOS研究方向	Plant Sciences
WOS类目	Plant Sciences
WOS记录号	WOS:000781972100002
来源期刊	BMC PLANT BIOLOGY
来源机构	中国科学院西北生态环境资源研究院
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/253854
作者单位	[Cao, Qian; Gao, Qingbo; Ma, Xiaolei; Zhang, Faqi; Xing, Rui; Chi, Xiaofeng; Chen, Shilong] Chinese Acad Sci, Key Lab Crop Mol Breeding Qinghai Prov, Northwest Inst Plateau Biol, Xining 810008, Peoples R China; [Cao, Qian; Ma, Xiaolei] Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Cao, Qian,Gao, Qingbo,Ma, Xiaolei,et al. Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau[J]. 中国科学院西北生态环境资源研究院,2022,22(1).
APA	Cao, Qian.,Gao, Qingbo.,Ma, Xiaolei.,Zhang, Faqi.,Xing, Rui.,...&Chen, Shilong.(2022).Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau.BMC PLANT BIOLOGY,22(1).
MLA	Cao, Qian,et al."Plastome structure, phylogenomics and evolution of plastid genes in Swertia (Gentianaceae) in the Qing-Tibetan Plateau".BMC PLANT BIOLOGY 22.1(2022).