Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales

doi:10.1093/gbe/evt063

	Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales
	Dong, Wenpan ; Xu, Chao 1; Cheng, Tao 1; Lin, Kui 2; Zhou, Shiliang
	2013
发表期刊	GENOME BIOLOGY AND EVOLUTION
ISSN	1759-6653
卷号	5 期号:5 页码:989-997
摘要	Plastid genomes are an invaluable resource for plant biological studies. However, the number of completely sequenced plant plastid genomes is still small compared with the vast number of species. To provide an alternative generalized approach, we designed a set of 138 pairs of universal primers for amplifying (termed short-range PCR) and sequencing the entire genomes of the angiosperm plastid genomes. The universality of the primers was tested by using species from the basal to asterid angiosperms. The polymerase chain reaction (PCR) success rate was higher than 96%. We sequenced the complete chloroplast genome of Liquidambar formosana as an example using this method and compared it to the genomes independently determined by long-range PCR (from 6.3 kb to 13.3 kb) and next-generation sequencing methods. The three genomes showed that they were completely identical. To test the phylogenetic efficiency of this method, we amplified and sequenced 18 chloroplast regions of 19 Saxifragales and Saxifragales related taxa, as a case study, to reconstruct the phylogeny of all families of the order. Phylograms based on a combination of our data, together with those from GenBank, clearly indicate three family groups and three single families within the order. This set of universal primers is expected to accelerate the accumulation of angiosperm plastid genomes and to make faster mass data collection of plastid genomes for molecular systematics.
关键词	plastid genome universal primers Saxifragales
学科领域	Evolutionary Biology ; Genetics & Heredity
DOI	10.1093/gbe/evt063
收录类别	SCI
语种	英语
WOS关键词	COMPLETE CHLOROPLAST GENOME ; COMPLETE NUCLEOTIDE-SEQUENCE ; INVERTED REPEAT ; EVOLUTION ; INSIGHTS ; PINACEAE ; GENES ; DIVERSIFICATION ; IDENTIFICATION ; REARRANGEMENTS
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000324593500019
出版者	OXFORD UNIV PRESS
文献子类	Article
出版地	OXFORD
资助机构	National Natural Science Foundation of China(National Natural Science Foundation of China (NSFC)) ; Ministry of Science and Technology(Ministry of Science, ICT & Future Planning, Republic of Korea)
作者邮箱	Lin, Kui/P-4492-2015 ; Dong, Wenpan/C-8167-2013 ; 董, 文攀/D-1297-2015
作品OA属性	Green Submitted, gold, Green Published, Green Accepted
引用统计	被引频次：176[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/2S10CLM1/27880
专题	系统与进化植物学国家重点实验室
作者单位	1.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Beijing Normal Univ, Coll Life Sci, Beijing 100875, Peoples R China
推荐引用方式 GB/T 7714	Dong, Wenpan,Xu, Chao,Cheng, Tao,et al. Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales[J]. GENOME BIOLOGY AND EVOLUTION,2013,5(5):989-997.
APA	Dong, Wenpan,Xu, Chao,Cheng, Tao,Lin, Kui,&Zhou, Shiliang.(2013).Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales.GENOME BIOLOGY AND EVOLUTION,5(5),989-997.
MLA	Dong, Wenpan,et al."Sequencing Angiosperm Plastid Genomes Made Easy: A Complete Set of Universal Primers and a Case Study on the Phylogeny of Saxifragales".GENOME BIOLOGY AND EVOLUTION 5.5(2013):989-997.

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