Phylogenomic analyses based on the plastid genome and concatenated nrDNA sequence data reveal cytonuclear discordance in genus Atractylodes (Asteraceae: Carduoideae)

doi:10.3389/fpls.2022.1045423

CORC > 植物研究所 > 中国科学院植物研究所 > 系统与进化植物学国家重点实验室

	Phylogenomic analyses based on the plastid genome and concatenated nrDNA sequence data reveal cytonuclear discordance in genus Atractylodes (Asteraceae: Carduoideae)
	Liu, Jinxin ; Shi, Mengmeng 3; Zhang, Zhaolei 3; Xie, Hongbo 3; Kong, Weijun 2; Wang, Qiuling ; Zhao, Xinlei ; Zhao, Chunying 3; Lin, Yulin ; Zhang, Xiaoxia 1
刊名	FRONTIERS IN PLANT SCIENCE
	2022
卷号	13
关键词	Atractylodes plastid genome nrDNA concatenated sequence phylogeny cyto-nuclear discordance
ISSN号	1664-462X
DOI	10.3389/fpls.2022.1045423
文献子类	Article
英文摘要	Atractylodes species are widely distributed across East Asia and are cultivated as medicinal herbs in China, Japan, and Korea. Their unclear morphological characteristics and low levels of genetic divergence obscure the taxonomic relationships among these species. In this study, 24 plant samples were collected representing five species of Atractylodes located in China; of these, 23 belonged to members of the A. lancea complex. High-throughput sequencing was used to obtain the concatenated nrDNA sequences (18S-ITS1-5.8S-ITS2-28S) and plastid genomes. The concatenated nrDNA sequence lengths for all the Atractylodes species were 5,849 bp, and the GC content was 55%. The lengths of the whole plastid genome sequences ranged from 152,138 bp (A. chinensis) to 153,268 bp (A. lancea), while their insertion/deletion sites were mainly distributed in the intergenic regions. Furthermore, 33, 34, 36, 31, and 32 tandem repeat sequences, as well as 30, 30, 29, 30, and 30 SSR loci, were detected in A. chinensis, A. koreana, A. lancea, A. japonica, and A. macrocephala, respectively. In addition to these findings, a considerable number of heteroplasmic variations were detected in the plastid genomes, implying a complicated phylogenetic history for Atractylodes. The results of the phylogenetic analysis involving concatenated nrDNA sequences showed that A. lancea and A. japonica formed two separate clades, with A. chinensis and A. koreana constituting their sister clade, while A. lancea, A. koreana, A. chinensis, and A. japonica were found based on plastid datasets to represent a mixed clade on the phylogenetic tree. Phylogenetic network analysis suggested that A. lancea may have hybridized with the common ancestor of A. chinensis and A. japonica, while ABBA-BABA tests of SNPs in the plastid genomes showed that A. chinensis was more closely related to A. japonica than to A. lancea. This study reveals the extensive discordance and complexity of the relationships across the members of the A. lancea complex (A. lancea, A. chinensis, A. koreana, and A. japonica) according to cytonuclear genomic data; this may be caused by interspecific hybridization or gene introgression.
学科主题	Plant Sciences
出版地	LAUSANNE
WOS关键词	ALIGNMENT ; TOOL
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
语种	英语
出版者	FRONTIERS MEDIA SA
WOS记录号	WOS:000897206400001
资助机构	National Key R&D Program: Intergovernmental Cooperation in International Science and Technology Innovation ; China Postdoctoral Science Foundation ; Beijing Municipal Natural Science Foundation ; National Natural Science Foundation of China ; Guangxi Science and Technology base and talent project ; [2022YFE0119300] ; [2022M720504] ; [7202136] ; [81703659] ; [AD22080012]
内容类型	期刊论文
源URL	[http://ir.ibcas.ac.cn/handle/2S10CLM1/28949]
专题	系统与进化植物学国家重点实验室
作者单位	1.Capital Med Univ, Sch Tradit Chinese Med, Beijing, Peoples R China 2.Chengde Med Univ, Hebei Key Lab Study & Exploitat Chinese Med, Chengde, Peoples R China 3.Chinese Acad Med Sci & Peking Union Med Coll, Inst Med Plant Dev, Engn Res Ctr Chinese Med Resource, Minist Educ,Key Lab Chinese Med Resources Conserva, Beijing, Peoples R China 4.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Liu, Jinxin,Shi, Mengmeng,Zhang, Zhaolei,et al. Phylogenomic analyses based on the plastid genome and concatenated nrDNA sequence data reveal cytonuclear discordance in genus Atractylodes (Asteraceae: Carduoideae)[J]. FRONTIERS IN PLANT SCIENCE,2022,13.
APA	Liu, Jinxin.,Shi, Mengmeng.,Zhang, Zhaolei.,Xie, Hongbo.,Kong, Weijun.,...&Shi, Linchun.(2022).Phylogenomic analyses based on the plastid genome and concatenated nrDNA sequence data reveal cytonuclear discordance in genus Atractylodes (Asteraceae: Carduoideae).FRONTIERS IN PLANT SCIENCE,13.
MLA	Liu, Jinxin,et al."Phylogenomic analyses based on the plastid genome and concatenated nrDNA sequence data reveal cytonuclear discordance in genus Atractylodes (Asteraceae: Carduoideae)".FRONTIERS IN PLANT SCIENCE 13(2022).