Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs

doi:10.1111/jse.12197

	Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs
	Zhang, Ting 1,2; Zeng, Chun-Xia 1; Yang, Jun-Bo 1; Li, Hong-Tao1 ; Li, De-Zhu1,2
	2016-05-01
发表期刊	JOURNAL OF SYSTEMATICS AND EVOLUTION
卷号	54 期号:3 页码:219-227
摘要	Chloroplast genome information helps improve the phylogenetic resolution and can act as organelle scale barcodes in recently radiated plant groups. Previously we reported that nine universal primer pairs could amplify angiosperm whole chloroplast genomes by long-range polymerase chain reaction and using next generation sequencing. Although these primers show high universality and efficiency for sequencing whole chloroplast genomes in angiosperms, they did not fully resolve the following two issues surrounding sequencing angiosperm chloroplast genomes: (i) approximately 3o% of angiosperms cannot be amplified successfully; and (ii) only fresh leaves can be applied. In this study, we designed another set of 15 universal primer pairs for amplifying angiosperm whole chloroplast genomes to complement the original nine primer pairs. Furthermore, we designed a primer pair for nuclear ribosomal DNAs (nrDNAs). To validate the functionality of the primers, we tested 44 species with silica gel-dried leaves and 15 species with fresh leaves that have been shown to not be amplified with the original nine primer pairs. The result showed that, in 65.9% and 88.6% of the 44 species with silica gel-dried leaves, the whole chloroplast genome and nrDNAs could be amplified, respectively. In addition, all 15 fresh leaf samples could have the whole chloroplast genome successfully amplified. The nrDNAs comprise partial sequences of 18S and 26S, along with the complete sequence of 5.8S and the internal transcribed spacers ITS1 and ITS2. The mean size of nrDNA was 58 oo bp. This study shows that the 15 universal primer set is an indispensable tool for amplifying whole chloroplast genomes in angiosperms, and these are an important supplement to the nine reported primer pairs.
关键词	Angiosperm Chloroplast Genomes Next-generation Sequencing Nuclear Ribosomal Dna Universal Primer Pairs
DOI	10.1111/jse.12197
收录类别	SCI
语种	英语
WOS记录号	WOS:000383770900004
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/33593
专题	中国西南野生生物种质资源库
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China 2.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Ting,Zeng, Chun-Xia,Yang, Jun-Bo,et al. Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs[J]. JOURNAL OF SYSTEMATICS AND EVOLUTION,2016,54(3):219-227.
APA	Zhang, Ting,Zeng, Chun-Xia,Yang, Jun-Bo,Li, Hong-Tao,&Li, De-Zhu.(2016).Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs.JOURNAL OF SYSTEMATICS AND EVOLUTION,54(3),219-227.
MLA	Zhang, Ting,et al."Fifteen novel universal primer pairs for sequencing whole chloroplast genomes and a primer pair for nuclear ribosomal DNAs".JOURNAL OF SYSTEMATICS AND EVOLUTION 54.3(2016):219-227.

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