Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity

doi:10.1111/1755-0998.12438

	Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity
	Cheng, Tao ; Xu, Chao ; Lei, Li 1; Li, Changhao ; Zhang, Yu 2; Zhou, Shiliang
	2016
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
卷号	16 期号:1 页码:138-149
摘要	The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding.
关键词	barcoding internal transcribed spacer PCR plant-specific primer
学科领域	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
DOI	10.1111/1755-0998.12438
收录类别	SCI
语种	英语
WOS关键词	INTERNAL TRANSCRIBED SPACER ; DNA BARCODE ; RIBOSOMAL DNA ; ITS2 REGION ; IDENTIFICATION ; PHYLOGENY ; AUTHENTICATION ; DIVERSITY ; MARKERS ; DESIGN
WOS研究方向	Science Citation Index Expanded (SCI-EXPANDED)
WOS记录号	WOS:000369141000015
出版者	WILEY
文献子类	Article
出版地	HOBOKEN
EISSN	1755-0998
资助机构	Ministry of Science and Technology of ChinaMinistry of Science and Technology, China [2011FY120200, 2012AA021602, 2012BAC01B05] ; NSFCNational Natural Science Foundation of China (NSFC) [31270239]
作者邮箱	slzhou@ibcas.ac.cn
引用统计	被引频次：239[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/2S10CLM1/25075
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 100093, Peoples R China 2.Kansas State Univ, Dept Plant Pathol, Throckmorton Hall, Manhattan, KS 66506 USA 3.Beijing Bot Gardens, Beijing 100093, Peoples R China
推荐引用方式 GB/T 7714	Cheng, Tao,Xu, Chao,Lei, Li,et al. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity[J]. MOLECULAR ECOLOGY RESOURCES,2016,16(1):138-149.
APA	Cheng, Tao,Xu, Chao,Lei, Li,Li, Changhao,Zhang, Yu,&Zhou, Shiliang.(2016).Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity.MOLECULAR ECOLOGY RESOURCES,16(1),138-149.
MLA	Cheng, Tao,et al."Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity".MOLECULAR ECOLOGY RESOURCES 16.1(2016):138-149.

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