Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus
Liu, Jie1,2; Provan, Jim3; Gao, Lian-Ming1; Li, De-Zhu1,2
2012-07-01
发表期刊INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
ISSN1661-6596 ; 1661-6596
卷号13期号:7页码:8740-8751
摘要Although DNA barcoding has become a useful tool for species identification and biodiversity surveys in plant sciences, there remains little consensus concerning appropriate sampling strategies and the treatment of indels. To address these two issues, we sampled 39 populations for nine Taxus species across their entire ranges, with two to three individuals per population randomly sampled. We sequenced one core DNA barcode (matK) and three supplementary regions (trnH-psbA, trnL-trnF and ITS) for all samples to test the effects of sampling design and the utility of indels. Our results suggested that increasing sampling within-population did not change the clustering of individuals, and that meant within-population P-distances were zero for most populations in all regions. Based on the markers tested here, comparison of methods either including or excluding indels indicated that discrimination and nodal support of monophyletic groups were significantly increased when indels were included. Thus we concluded that one individual per population was adequate to represent the within-population variation in these species for DNA barcoding, and that intra-specific sampling was best focused on representing the entire ranges of certain taxa. We also found that indels occurring in the chloroplast trnL-trnF and trnH-psbA regions were informative to differentiate among for closely related taxa barcoding, and we proposed that indel-coding methods should be considered for use in future for closed related plant species DNA barcoding projects on or below generic level.
关键词Dna Barcoding Indel (Gap) Coding Sampling Strategy Noncoding Chloroplast Regions Taxus
资助信息Chinese Academy of Sciences [2009-LSF-GBOWS-01, 9223111W1]; National Natural Science Foundation of China [30700042]; talent project of Yunnan province [2008YP064]; Chinese Academy of Sciences [2009-LSF-GBOWS-01, 9223111W1]; National Natural Science Foundation of China [30700042]; talent project of Yunnan province [2008YP064]
DOI10.3390/ijms13078740
收录类别SCI
语种英语
WOS研究方向Chemistry
WOS类目Chemistry, Multidisciplinary
WOS记录号WOS:000306760000008
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被引频次:19[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/15780
专题中国科学院东亚植物多样性与生物地理学重点实验室
作者单位1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming 650201, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Plant Germplasm & Genom Ctr, Kunming 650201, Peoples R China
3.Queens Univ Belfast, Sch Biol Sci, Belfast BT9 7BL, Antrim, North Ireland
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Liu, Jie,Provan, Jim,Gao, Lian-Ming,et al. Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2012,13(7):8740-8751.
APA Liu, Jie,Provan, Jim,Gao, Lian-Ming,&Li, De-Zhu.(2012).Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,13(7),8740-8751.
MLA Liu, Jie,et al."Sampling Strategy and Potential Utility of Indels for DNA Barcoding of Closely Related Plant Species: A Case Study in Taxus".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 13.7(2012):8740-8751.
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