Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes
Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants...
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Veröffentlicht in: | Biomedical and environmental sciences 2014-10, Vol.27 (10), p.794-806 |
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description | Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Methods Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes (motK, rbcL, and ITS) were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment (PWG) distance, and Tree-Building were tested for discrimination power. Results The primer universality of all the three markers was high. Except in the case of ITS for Hemerocollis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method. |
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The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Methods Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes (motK, rbcL, and ITS) were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment (PWG) distance, and Tree-Building were tested for discrimination power. Results The primer universality of all the three markers was high. Except in the case of ITS for Hemerocollis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method.</description><identifier>ISSN: 0895-3988</identifier><identifier>EISSN: 2214-0190</identifier><identifier>DOI: 10.3967/bes2014.115</identifier><identifier>PMID: 25341815</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>China ; DNA ; DNA barcoding ; DNA Barcoding, Taxonomic - standards ; DNA Primers - genetics ; DNA, Intergenic - genetics ; ITS ; matK ; Plant Proteins - genetics ; Plants, Toxic - classification ; Plants, Toxic - genetics ; Poisonous plants ; PWG ; rbcL ; rbcL基因 ; Ribulose-Bisphosphate Carboxylase - genetics ; Sequence Analysis, DNA ; Species Specificity ; 中国 ; 有毒植物 ; 条形码 ; 距离和 ; 鉴定</subject><ispartof>Biomedical and environmental sciences, 2014-10, Vol.27 (10), p.794-806</ispartof><rights>2014 The Editorial Board of Biomedical and Environmental Sciences</rights><rights>Copyright © 2014 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.</rights><rights>Copyright © Wanfang Data Co. Ltd. All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://image.cqvip.com/vip1000/qk/84046X/84046X.jpg</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.3967/bes2014.115$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3549,27923,27924,45994</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25341815$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>XIE, Lei</creatorcontrib><creatorcontrib>WANG, Ying Wei</creatorcontrib><creatorcontrib>GUAN, Shan Yue</creatorcontrib><creatorcontrib>XIE, Li Jing</creatorcontrib><creatorcontrib>LONG, Xin</creatorcontrib><creatorcontrib>SUN, Cheng Ye</creatorcontrib><title>Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes</title><title>Biomedical and environmental sciences</title><addtitle>Biomedical and Environmental Sciences</addtitle><description>Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Methods Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes (motK, rbcL, and ITS) were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment (PWG) distance, and Tree-Building were tested for discrimination power. Results The primer universality of all the three markers was high. Except in the case of ITS for Hemerocollis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method.</description><subject>China</subject><subject>DNA</subject><subject>DNA barcoding</subject><subject>DNA Barcoding, Taxonomic - standards</subject><subject>DNA Primers - genetics</subject><subject>DNA, Intergenic - genetics</subject><subject>ITS</subject><subject>matK</subject><subject>Plant Proteins - genetics</subject><subject>Plants, Toxic - classification</subject><subject>Plants, Toxic - genetics</subject><subject>Poisonous plants</subject><subject>PWG</subject><subject>rbcL</subject><subject>rbcL基因</subject><subject>Ribulose-Bisphosphate Carboxylase - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Species Specificity</subject><subject>中国</subject><subject>有毒植物</subject><subject>条形码</subject><subject>距离和</subject><subject>鉴定</subject><issn>0895-3988</issn><issn>2214-0190</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNo9kU1vEzEQhi0EoqFw4o4sxIHLtjP2ftjHEr4qVSUHOHCyHO84dZXYqb0L6r_HJWlPlqXnHc_7mLG3CGdS98P5mooAbM8Qu2dsIQS2DaCG52wBSneN1EqdsFel3AK0qFv1kp2ITraosFuw36ucyp7cVLiNI6-39ZZ2hfuU-eVIcQo-ODuFFHnyfJVCSTHNha-2NtZMiHx5E6Llcwlxwz9fX_BPNrs0UnnNXni7LfTmeJ6yX1-__Fx-b65-fLtcXlw1TqKcGtWBtkIM5EcgcG7w1AstO_R1VSmUByUBrdAKCe2onRw63Vuk1g9kBy1P2YfD3L82ehs35jbNOdYXzVEMAkBfsY8HbJ_T3UxlMrtQHG1rD6qFDPYPQqDKqui7IzqvdzSafQ47m-_No7UKdAeAaq8_gbIpLlB0NIZcVZoxBYNgHn7ncQmD_3PvDzl3k-Lmrhp7mt33UrdCCSn_AfQDibA</recordid><startdate>20141001</startdate><enddate>20141001</enddate><creator>XIE, Lei</creator><creator>WANG, Ying Wei</creator><creator>GUAN, Shan Yue</creator><creator>XIE, Li Jing</creator><creator>LONG, Xin</creator><creator>SUN, Cheng Ye</creator><general>Elsevier B.V</general><general>College of Nature Conservation, Beijing Forestry University, Beijing 100083, China%Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China%School of Agricultural Forestry and Environmental Sciences Forest Resources, Clemson University, South Carolina 29634, USA%National Institute of 0ccupational Health and Poison Control, China Center for Disease Control and Prevention, Beijing 100050, China</general><scope>2RA</scope><scope>92L</scope><scope>CQIGP</scope><scope>W91</scope><scope>~WA</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>7X8</scope><scope>2B.</scope><scope>4A8</scope><scope>92I</scope><scope>93N</scope><scope>PSX</scope><scope>TCJ</scope></search><sort><creationdate>20141001</creationdate><title>Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes</title><author>XIE, Lei ; WANG, Ying Wei ; GUAN, Shan Yue ; XIE, Li Jing ; LONG, Xin ; SUN, Cheng Ye</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c313t-8509a227efd0e0cc7fe629351f948328f08301a2981e1ad9c37596a1e4f7ea793</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>China</topic><topic>DNA</topic><topic>DNA barcoding</topic><topic>DNA Barcoding, Taxonomic - standards</topic><topic>DNA Primers - genetics</topic><topic>DNA, Intergenic - genetics</topic><topic>ITS</topic><topic>matK</topic><topic>Plant Proteins - genetics</topic><topic>Plants, Toxic - classification</topic><topic>Plants, Toxic - genetics</topic><topic>Poisonous plants</topic><topic>PWG</topic><topic>rbcL</topic><topic>rbcL基因</topic><topic>Ribulose-Bisphosphate Carboxylase - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Species Specificity</topic><topic>中国</topic><topic>有毒植物</topic><topic>条形码</topic><topic>距离和</topic><topic>鉴定</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>XIE, Lei</creatorcontrib><creatorcontrib>WANG, Ying Wei</creatorcontrib><creatorcontrib>GUAN, Shan Yue</creatorcontrib><creatorcontrib>XIE, Li Jing</creatorcontrib><creatorcontrib>LONG, Xin</creatorcontrib><creatorcontrib>SUN, Cheng Ye</creatorcontrib><collection>中文科技期刊数据库</collection><collection>中文科技期刊数据库-CALIS站点</collection><collection>中文科技期刊数据库-7.0平台</collection><collection>中文科技期刊数据库-医药卫生</collection><collection>中文科技期刊数据库- 镜像站点</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>MEDLINE - Academic</collection><collection>Wanfang Data Journals - Hong Kong</collection><collection>WANFANG Data Centre</collection><collection>Wanfang Data Journals</collection><collection>万方数据期刊 - 香港版</collection><collection>China Online Journals (COJ)</collection><collection>China Online Journals (COJ)</collection><jtitle>Biomedical and environmental sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>XIE, Lei</au><au>WANG, Ying Wei</au><au>GUAN, Shan Yue</au><au>XIE, Li Jing</au><au>LONG, Xin</au><au>SUN, Cheng Ye</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes</atitle><jtitle>Biomedical and environmental sciences</jtitle><addtitle>Biomedical and Environmental Sciences</addtitle><date>2014-10-01</date><risdate>2014</risdate><volume>27</volume><issue>10</issue><spage>794</spage><epage>806</epage><pages>794-806</pages><issn>0895-3988</issn><eissn>2214-0190</eissn><abstract>Objective Poisonous plants are a deadly threat to public health in China. The traditional clinical diagnosis of the toxic plants is inefficient, fallible, and dependent upon experts. In this study, we tested the performance of DNA barcodes for identification of the most threatening poisonous plants in China. Methods Seventy-four accessions of 27 toxic plant species in 22 genera and 17 families were sampled and three DNA barcodes (motK, rbcL, and ITS) were amplified, sequenced and tested. Three methods, Blast, pairwise global alignment (PWG) distance, and Tree-Building were tested for discrimination power. Results The primer universality of all the three markers was high. Except in the case of ITS for Hemerocollis minor, the three barcodes were successfully generated from all the selected species. Among the three methods applied, Blast showed the lowest discrimination rate, whereas PWG Distance and Tree-Building methods were equally effective. The ITS barcode showed highest discrimination rates using the PWG Distance and Tree-Building methods. When the barcodes were combined, discrimination rates were increased for the Blast method.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>25341815</pmid><doi>10.3967/bes2014.115</doi><tpages>13</tpages></addata></record> |
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subjects | China DNA DNA barcoding DNA Barcoding, Taxonomic - standards DNA Primers - genetics DNA, Intergenic - genetics ITS matK Plant Proteins - genetics Plants, Toxic - classification Plants, Toxic - genetics Poisonous plants PWG rbcL rbcL基因 Ribulose-Bisphosphate Carboxylase - genetics Sequence Analysis, DNA Species Specificity 中国 有毒植物 条形码 距离和 鉴定 |
title | Prospects and Problems for Identification of Poisonous Plants in China using DNA Barcodes |
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