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Method for quick DNA barcode reference library construction

文献类型：期刊论文

作者Liu, Yanlei3; Xu, Chao; Sun, Yuzhe3; Chen, Xun4; Dong, Wenpan1; Yang, Xueying5; Zhou, Shiliang3
刊名ECOLOGY AND EVOLUTION
出版日期2021
卷号11期号:17页码:11627-11638
关键词Cotu data processing method DNA barcode next-generation sequencing
ISSN号2045-7758
DOI10.1002/ece3.7788
文献子类Article
英文摘要DNA barcoding has become one of the most important techniques in plant species identification. Successful application of this technology is dependent on the availability of reference database of high species coverage. Unfortunately, there are experimental and data processing challenges to construct such a library within a short time. Here, we present our solutions to these challenges. We sequenced six conventional DNA barcode fragments (ITS1, ITS2, matK1, matK2, rbcL1, and rbcL2) of 380 flowering plants on next-generation sequencing (NGS) platforms (Illumina Hiseq 2500 and Ion Torrent S5) and the Sanger sequencing platform. After comparing the sequencing depths, read lengths, base qualities, and base accuracies, we conclude that Illumina Hiseq2500 PE250 run is suitable for conventional DNA barcoding. We developed a new Cotu method to create consensus sequences from NGS reads for longer output sequences and more reliable bases than the other three methods. Step-by-step instructions to our method are provided. By using high-throughput machines (PCR and NGS), labeling PCR, and the Cotu method, it is possible to significantly reduce the cost and labor investments for DNA barcoding. A regional or even global DNA barcoding reference library with high species coverage is likely to be constructed in a few years.
学科主题Ecology ; Evolutionary Biology
出版地HOBOKEN
WOS关键词SEQUENCING PLATFORMS ; ILLUMINA ; IDENTIFICATION ; PERFORMANCE ; SOFTWARE ; PLANTS ; DIET
WOS研究方向Science Citation Index Expanded (SCI-EXPANDED)
语种英语
WOS记录号WOS:000681085300001
出版者WILEY
资助机构National Key R&D Program of China [2017YFC0803803] ; open project of Institute of Forensic Science, Ministry of Public Security [2018FGKFKT04] ; Strategic Priority Research Program of the Chinese Academy of Sciences [XDA23080204, XDA19050303] ; National Natural Science Foundation of China [NSFC31872679] ; fundamental research fund of the Central Public Service Research Institute [2018JB001]
源URL[http://ir.ibcas.ac.cn/handle/2S10CLM1/26312]  
专题植物研究所_系统与进化植物学研究中心_系统与进化植物学研究中心_学位论文
作者单位1.Northeast Forestry Univ, Coll Landscape Architecture, Harbin, Peoples R China
2.Minist Publ Secur, Inst Forens Sci, Key Lab Forens Genet, Natl Engn Lab Forens Sci, Beijing 100038, Peoples R China
3.Chinese Acad Sci, Inst Bot, State Key Lab Systemat & Evolutionary Bot, Beijing 100093, Peoples R China
4.Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China
5.Beijing Forestry Univ, Sch Ecol & Nat Conservat, Lab Systemat Evolut & Biogeog Woody Plants, Beijing, Peoples R China
推荐引用方式
GB/T 7714		 Liu, Yanlei,Xu, Chao,Sun, Yuzhe,et al. Method for quick DNA barcode reference library construction[J]. ECOLOGY AND EVOLUTION,2021,11(17):11627-11638.
APA Liu, Yanlei.,Xu, Chao.,Sun, Yuzhe.,Chen, Xun.,Dong, Wenpan.,...&Zhou, Shiliang.(2021).Method for quick DNA barcode reference library construction.ECOLOGY AND EVOLUTION,11(17),11627-11638.
MLA Liu, Yanlei,et al."Method for quick DNA barcode reference library construction".ECOLOGY AND EVOLUTION 11.17(2021):11627-11638.

入库方式： OAI收割

来源：植物研究所

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