Assessment of candidate plant DNA barcodes using the Rutaceae family
DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention. Here, seven regions ( psbA-trnH, matK, ycf5, rpoC1, rbcL , ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the f...
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| Veröffentlicht in: | Science China. Life sciences 2010-06, Vol.53 (6), p.701-708 |
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| container_title | Science China. Life sciences |
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| creator | Luo, Kun Chen, ShiLin Chen, KeLi Song, JingYuan Yao, Hui Ma, Xinye Zhu, YingJie Pang, XiaoHui Yu, Hua Li, XiWen Liu, Zhen |
| description | DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention. Here, seven regions (
psbA-trnH, matK, ycf5, rpoC1, rbcL
, ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae. To evaluate each barcode’s utility for species authentication, PCR amplification efficiency, genetic divergence, and barcoding gaps were assessed. We found that the ITS2 region exhibited the highest inter-specific divergence, and that this was significantly higher than the intra-specific variation in the “DNA barcoding gap” assessment and Wilcoxon two-sample tests. The ITS2 locus had the highest identification efficiency among all tested regions. In a previous study, we found that ITS2 was able to discriminate a wide range of plant taxa, and here we confirmed that ITS2 was also able to discriminate a number of closely related species. Therefore, we propose that ITS2 is a promising candidate barcode for plant species identification. |
| doi_str_mv | 10.1007/s11427-010-4009-1 |
| format | Article |
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psbA-trnH, matK, ycf5, rpoC1, rbcL
, ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae. To evaluate each barcode’s utility for species authentication, PCR amplification efficiency, genetic divergence, and barcoding gaps were assessed. We found that the ITS2 region exhibited the highest inter-specific divergence, and that this was significantly higher than the intra-specific variation in the “DNA barcoding gap” assessment and Wilcoxon two-sample tests. The ITS2 locus had the highest identification efficiency among all tested regions. In a previous study, we found that ITS2 was able to discriminate a wide range of plant taxa, and here we confirmed that ITS2 was also able to discriminate a number of closely related species. Therefore, we propose that ITS2 is a promising candidate barcode for plant species identification.</description><identifier>ISSN: 1674-7305</identifier><identifier>EISSN: 1869-1889</identifier><identifier>DOI: 10.1007/s11427-010-4009-1</identifier><identifier>PMID: 20602273</identifier><language>eng</language><publisher>Beijing: Science China Press</publisher><subject>Base Sequence ; Biomedical and Life Sciences ; DNA Primers ; DNA, Plant - genetics ; Genes, Plant ; Genetic Variation ; Life Sciences ; Polymerase Chain Reaction ; Research Papers ; Rutaceae ; Rutaceae - genetics</subject><ispartof>Science China. Life sciences, 2010-06, Vol.53 (6), p.701-708</ispartof><rights>Science China Press and Springer-Verlag Berlin Heidelberg 2010</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c402t-341a27d9b18baa367751ab08e8d04c316178fdc73716271f5cd4ff14056f51153</citedby><cites>FETCH-LOGICAL-c402t-341a27d9b18baa367751ab08e8d04c316178fdc73716271f5cd4ff14056f51153</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11427-010-4009-1$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11427-010-4009-1$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20602273$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Luo, Kun</creatorcontrib><creatorcontrib>Chen, ShiLin</creatorcontrib><creatorcontrib>Chen, KeLi</creatorcontrib><creatorcontrib>Song, JingYuan</creatorcontrib><creatorcontrib>Yao, Hui</creatorcontrib><creatorcontrib>Ma, Xinye</creatorcontrib><creatorcontrib>Zhu, YingJie</creatorcontrib><creatorcontrib>Pang, XiaoHui</creatorcontrib><creatorcontrib>Yu, Hua</creatorcontrib><creatorcontrib>Li, XiWen</creatorcontrib><creatorcontrib>Liu, Zhen</creatorcontrib><title>Assessment of candidate plant DNA barcodes using the Rutaceae family</title><title>Science China. Life sciences</title><addtitle>Sci. China Life Sci</addtitle><addtitle>Sci China Life Sci</addtitle><description>DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention. Here, seven regions (
psbA-trnH, matK, ycf5, rpoC1, rbcL
, ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae. To evaluate each barcode’s utility for species authentication, PCR amplification efficiency, genetic divergence, and barcoding gaps were assessed. We found that the ITS2 region exhibited the highest inter-specific divergence, and that this was significantly higher than the intra-specific variation in the “DNA barcoding gap” assessment and Wilcoxon two-sample tests. The ITS2 locus had the highest identification efficiency among all tested regions. In a previous study, we found that ITS2 was able to discriminate a wide range of plant taxa, and here we confirmed that ITS2 was also able to discriminate a number of closely related species. Therefore, we propose that ITS2 is a promising candidate barcode for plant species identification.</description><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>DNA Primers</subject><subject>DNA, Plant - genetics</subject><subject>Genes, Plant</subject><subject>Genetic Variation</subject><subject>Life Sciences</subject><subject>Polymerase Chain Reaction</subject><subject>Research Papers</subject><subject>Rutaceae</subject><subject>Rutaceae - genetics</subject><issn>1674-7305</issn><issn>1869-1889</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqFkU1LxDAQhoMorqg_wIsUL56qM0maaY_L-gmLgug5pGmiXbbt2rSH_fdmWT9AEOeSYfLMO8m8jJ0gXCAAXQZEySkFhFQCFCnusAPMVUzyvNiNuSKZkoBswo5DWEAMIYAT7bMJBwWckzhgV9MQXAiNa4ek84k1bVVXZnDJamli6ephmpSmt13lQjKGun1NhjeXPI2Dsc64xJumXq6P2J43y-COP89D9nJz_Ty7S-ePt_ez6Ty1EviQComGU1WUmJfGCEWUoSkhd3kF0gpUSLmvLAlCxQl9ZivpPUrIlM8QM3HIzre6q757H10YdFMH65bxqa4bgybFuSqI6H9SCCUQVR7Js1_kohv7Nn5DK1CFzFBsINxCtu9C6J3Xq75uTL_WCHrjht66oaMbeuOGxthz-ik8lo2rvju-dh8BvgVCvGpfXf8z-W_VDwpAkVU</recordid><startdate>20100601</startdate><enddate>20100601</enddate><creator>Luo, Kun</creator><creator>Chen, ShiLin</creator><creator>Chen, KeLi</creator><creator>Song, JingYuan</creator><creator>Yao, Hui</creator><creator>Ma, Xinye</creator><creator>Zhu, YingJie</creator><creator>Pang, XiaoHui</creator><creator>Yu, Hua</creator><creator>Li, XiWen</creator><creator>Liu, Zhen</creator><general>Science China Press</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QP</scope><scope>7TK</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>7X8</scope><scope>7TM</scope></search><sort><creationdate>20100601</creationdate><title>Assessment of candidate plant DNA barcodes using the Rutaceae family</title><author>Luo, Kun ; 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Life sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Luo, Kun</au><au>Chen, ShiLin</au><au>Chen, KeLi</au><au>Song, JingYuan</au><au>Yao, Hui</au><au>Ma, Xinye</au><au>Zhu, YingJie</au><au>Pang, XiaoHui</au><au>Yu, Hua</au><au>Li, XiWen</au><au>Liu, Zhen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Assessment of candidate plant DNA barcodes using the Rutaceae family</atitle><jtitle>Science China. Life sciences</jtitle><stitle>Sci. China Life Sci</stitle><addtitle>Sci China Life Sci</addtitle><date>2010-06-01</date><risdate>2010</risdate><volume>53</volume><issue>6</issue><spage>701</spage><epage>708</epage><pages>701-708</pages><issn>1674-7305</issn><eissn>1869-1889</eissn><abstract>DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention. Here, seven regions (
psbA-trnH, matK, ycf5, rpoC1, rbcL
, ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae. To evaluate each barcode’s utility for species authentication, PCR amplification efficiency, genetic divergence, and barcoding gaps were assessed. We found that the ITS2 region exhibited the highest inter-specific divergence, and that this was significantly higher than the intra-specific variation in the “DNA barcoding gap” assessment and Wilcoxon two-sample tests. The ITS2 locus had the highest identification efficiency among all tested regions. In a previous study, we found that ITS2 was able to discriminate a wide range of plant taxa, and here we confirmed that ITS2 was also able to discriminate a number of closely related species. Therefore, we propose that ITS2 is a promising candidate barcode for plant species identification.</abstract><cop>Beijing</cop><pub>Science China Press</pub><pmid>20602273</pmid><doi>10.1007/s11427-010-4009-1</doi><tpages>8</tpages></addata></record> |
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| ispartof | Science China. Life sciences, 2010-06, Vol.53 (6), p.701-708 |
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| source | MEDLINE; Alma/SFX Local Collection; SpringerLink Journals - AutoHoldings |
| subjects | Base Sequence Biomedical and Life Sciences DNA Primers DNA, Plant - genetics Genes, Plant Genetic Variation Life Sciences Polymerase Chain Reaction Research Papers Rutaceae Rutaceae - genetics |
| title | Assessment of candidate plant DNA barcodes using the Rutaceae family |
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