Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation

doi:10.1186/s12862-019-1384-5

	Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation
	Li, Zhang-Hai ; Ma, Xiao ; Wang, De-Yi ; Li, Yun-Xia ; Wang, Cheng-Wang ; Jin, Xiao-Hua
	2019
发表期刊	BMC EVOLUTIONARY BIOLOGY
ISSN	1471-2148
卷号	19
摘要	BackgroundThe plastid is a semiautonomous organelle with its own genome. Plastid genomes have been widely used as models for studying phylogeny, speciation and adaptive evolution. However, most studies focus on comparisons of plastid genome evolution at high taxonomic levels, and comparative studies of the process of plastome evolution at the infrageneric or intraspecific level remain elusive. Holcoglossum is a small genus of Orchidaceae, consisting of approximately 20 species of recent radiation. This made it an ideal group to explore the plastome mutation mode at the infrageneric or intraspecific level.ResultsIn this paper, we reported 15 complete plastid genomes from 12 species of Holcoglossum and 1 species of Vanda. The plastid genomes of Holcoglossum have a total length range between 145kb and 148kb, encoding a set of 102 genes. The whole set of ndh-gene families in Holcoglossum have been truncated or pseudogenized. Hairpin inversion in the coding region of the plastid gene ycf2 has been found.ConclusionsUsing a comprehensive comparative plastome analysis, we found that all the indels between different individuals of the same species resulted from the copy number variation of the short repeat sequence, which may be caused by replication slippage. Annotation of tandem repeats shows that the variation introduced by tandem repeats is widespread in plastid genomes. The hairpin inversion found in the plastid gene ycf2 occurred randomly in the Orchidaceae.
关键词	Holcoglossum Plastid genome NDH complex Divergence hotspot Intraspecific variation Tandem repeat Hairpin inversion
学科领域	Evolutionary Biology ; Genetics & Heredity
DOI	10.1186/s12862-019-1384-5
收录类别	SCI
语种	英语
WOS关键词	CYCLIC ELECTRON FLOW ; MULTIPLE SEQUENCE ALIGNMENT ; PHYLOGENETIC ANALYSIS ; CHLOROPLAST GENOMES ; PROVIDES INSIGHTS ; PHOTOSYSTEM-I ; GENES ; ADAPTATION ; PLASTOMES ; AERIDINAE
WOS研究方向	Evolutionary Biology ; Genetics & Heredity
WOS记录号	WOS:000459864500003
出版者	BMC
文献子类	Article
出版地	LONDON
资助机构	Strategic Priority Research Program, Chinese Academy of Sciences [XDA19050201] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31670194, 31470299, 41672018] ; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences [Y4ZK111B01]
作者邮箱	zhanghailee@ibcas.ac.cn ; xiaohuajin@ibcas.ac.cn
作品OA属性	Green Published, gold
引用统计	被引频次：44[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/19694
专题	系统与进化植物学国家重点实验室
作者单位	1.[Li, Zhang-Hai 2.Ma, Xiao 3.Wang, De-Yi 4.Chinese Acad Sci, State Key Lab Systemat & Evolutionary Bot, Inst Bot, Beijing, Peoples R China 5.Chinese Acad Sci CAS SEABRI, Southeast Asia Biodivers Res Inst, Nay Pyi Taw, Myanmar 6.Univ Chinese Acad Sci, Beijing, Peoples R China 7.Fujian Agr & Forest Univ, Shanxiadian Rd 15, Fuzhou 350002, Fujian, Peoples R China 8.Nanchang Univ, Xuefu Rd 999, Nanchang, Jiangxi, Peoples R China
推荐引用方式 GB/T 7714	Li, Zhang-Hai,Ma, Xiao,Wang, De-Yi,et al. Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation[J]. BMC EVOLUTIONARY BIOLOGY,2019,19.
APA	Li, Zhang-Hai,Ma, Xiao,Wang, De-Yi,Li, Yun-Xia,Wang, Cheng-Wang,&Jin, Xiao-Hua.(2019).Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation.BMC EVOLUTIONARY BIOLOGY,19.
MLA	Li, Zhang-Hai,et al."Evolution of plastid genomes of Holcoglossum (Orchidaceae) with recent radiation".BMC EVOLUTIONARY BIOLOGY 19(2019).

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