Potential DNA barcodes for Melilotus species based on five single loci and their combinations
Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candid...
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| creator | Wu, Fan Ma, Jinxing Meng, Yuqin Zhang, Daiyu Pascal Muvunyi, Blaise Luo, Kai Di, Hongyan Guo, Wenli Wang, Yanrong Feng, Baochang Zhang, Jiyu |
| description | Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI) had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production. |
| doi_str_mv | 10.1371/journal.pone.0182693 |
| format | Article |
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As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI) had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0182693</identifier><identifier>PMID: 28910286</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Bar codes ; Biology and life sciences ; Breeding of animals ; Chloroplasts - genetics ; Computer and information sciences ; Deoxyribonucleic acid ; Divergence ; DNA ; DNA Barcoding, Taxonomic - methods ; DNA sequencing ; DNA, Chloroplast - genetics ; DNA, Intergenic ; DNA, Plant - genetics ; Ecosystems ; Flowers & plants ; Gene sequencing ; Genetic aspects ; Genetic Loci ; Genetic Variation ; Grasslands ; Herbal medicine ; Laboratories ; Loci ; Melilotus - classification ; Melilotus - genetics ; Mutation ; Phylogenetics ; Phylogeny ; Quality control ; Research and Analysis Methods ; Sequence Analysis, DNA - methods ; Spacer ; Species ; Studies ; Sweet clover</subject><ispartof>PloS one, 2017-09, Vol.12 (9), p.e0182693-e0182693</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Wu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2017 Wu et al 2017 Wu et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-ef5da64e2dda40d2f46ad13999509017da76b6aea035a9861fcdae64a85087743</citedby><cites>FETCH-LOGICAL-c692t-ef5da64e2dda40d2f46ad13999509017da76b6aea035a9861fcdae64a85087743</cites><orcidid>0000-0002-3230-8996</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5598934/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5598934/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28910286$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wu, Fan</creatorcontrib><creatorcontrib>Ma, Jinxing</creatorcontrib><creatorcontrib>Meng, Yuqin</creatorcontrib><creatorcontrib>Zhang, Daiyu</creatorcontrib><creatorcontrib>Pascal Muvunyi, Blaise</creatorcontrib><creatorcontrib>Luo, Kai</creatorcontrib><creatorcontrib>Di, Hongyan</creatorcontrib><creatorcontrib>Guo, Wenli</creatorcontrib><creatorcontrib>Wang, Yanrong</creatorcontrib><creatorcontrib>Feng, Baochang</creatorcontrib><creatorcontrib>Zhang, Jiyu</creatorcontrib><title>Potential DNA barcodes for Melilotus species based on five single loci and their combinations</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI) had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production.</description><subject>Analysis</subject><subject>Bar codes</subject><subject>Biology and life sciences</subject><subject>Breeding of animals</subject><subject>Chloroplasts - genetics</subject><subject>Computer and information sciences</subject><subject>Deoxyribonucleic acid</subject><subject>Divergence</subject><subject>DNA</subject><subject>DNA Barcoding, Taxonomic - methods</subject><subject>DNA sequencing</subject><subject>DNA, Chloroplast - genetics</subject><subject>DNA, Intergenic</subject><subject>DNA, Plant - genetics</subject><subject>Ecosystems</subject><subject>Flowers & plants</subject><subject>Gene sequencing</subject><subject>Genetic aspects</subject><subject>Genetic Loci</subject><subject>Genetic Variation</subject><subject>Grasslands</subject><subject>Herbal medicine</subject><subject>Laboratories</subject><subject>Loci</subject><subject>Melilotus - classification</subject><subject>Melilotus - genetics</subject><subject>Mutation</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Quality control</subject><subject>Research and Analysis Methods</subject><subject>Sequence Analysis, DNA - methods</subject><subject>Spacer</subject><subject>Species</subject><subject>Studies</subject><subject>Sweet clover</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk01v1DAQhiMEoqXwDxBEQkJw2MWOHce-IK3K10qFIr5uyJrYk12vvPESJxX8e5xuWnVRD8gHW-Nn3vGMZ7LsMSVzyir6ahOGrgU_34UW54TKQih2JzumihUzURB298b5KHsQ44aQkkkh7mdHhVSUFFIcZz8_hx7b3oHP33xa5DV0JliMeRO6_CN650M_xDzu0LhkrSGizUObN-4C8-jalcfcB-NyaG3er9F1uQnb2rXQu9DGh9m9BnzER9N-kn1_9_bb6YfZ2fn75enibGaEKvoZNqUFwbGwFjixRcMFWMqUUiVRhFYWKlELQCCsBCUFbYwFFBxkSWRVcXaSPd3r7nyIeqpM1Cl_KYuqkCOx3BM2wEbvOreF7o8O4PSlIXQrDV3vjEdNOBJagwVWCl5XlSLEWC55bQsjCoNJ6_UUbai3aE2qXwf-QPTwpnVrvQoXuiyVVGx8zItJoAu_Boy93rpo0HtoMQzjuzkTNGUmEvrsH_T27CZqBSkB1zYhxTWjqF6UhJclq5hK1PwWKi2LW2dSGzUu2Q8cXh44JKbH3_0Khhj18uuX_2fPfxyyz2-wawTfr2Pww2XPHIJ8D5ouxNhhc11kSvQ4BVfV0OMU6GkKktuTmx907XTV9uwvTW8B-g</recordid><startdate>20170914</startdate><enddate>20170914</enddate><creator>Wu, Fan</creator><creator>Ma, Jinxing</creator><creator>Meng, Yuqin</creator><creator>Zhang, Daiyu</creator><creator>Pascal Muvunyi, Blaise</creator><creator>Luo, Kai</creator><creator>Di, Hongyan</creator><creator>Guo, Wenli</creator><creator>Wang, Yanrong</creator><creator>Feng, Baochang</creator><creator>Zhang, Jiyu</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-3230-8996</orcidid></search><sort><creationdate>20170914</creationdate><title>Potential DNA barcodes for Melilotus species based on five single loci and their combinations</title><author>Wu, Fan ; Ma, Jinxing ; Meng, Yuqin ; Zhang, Daiyu ; Pascal Muvunyi, Blaise ; Luo, Kai ; Di, Hongyan ; Guo, Wenli ; Wang, Yanrong ; Feng, Baochang ; Zhang, Jiyu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-ef5da64e2dda40d2f46ad13999509017da76b6aea035a9861fcdae64a85087743</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Analysis</topic><topic>Bar codes</topic><topic>Biology and life sciences</topic><topic>Breeding of animals</topic><topic>Chloroplasts - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Fan</au><au>Ma, Jinxing</au><au>Meng, Yuqin</au><au>Zhang, Daiyu</au><au>Pascal Muvunyi, Blaise</au><au>Luo, Kai</au><au>Di, Hongyan</au><au>Guo, Wenli</au><au>Wang, Yanrong</au><au>Feng, Baochang</au><au>Zhang, Jiyu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Potential DNA barcodes for Melilotus species based on five single loci and their combinations</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-09-14</date><risdate>2017</risdate><volume>12</volume><issue>9</issue><spage>e0182693</spage><epage>e0182693</epage><pages>e0182693-e0182693</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes. Based on inter-specific divergence, we analysed sequences and confirmed that each candidate barcode was able to identify some of the 18 species. The resolution of a single barcode and its combinations ranged from 33.33% to 88.89%. Analysis of pairwise distances showed that matK+rbcL+trnL-F+trnH-psbA+ITS (MRTPI) had the greatest value and rbcL the least. Barcode gap values and similarity value analyses confirmed these trends. The results indicated that an ITS region, successfully identifying 13 of 18 species, was the most appropriate single barcode and that the combination of all five potential barcodes identified 16 of the 18 species. We conclude that MRTPI is the most effective tool for Melilotus species identification. Taking full advantage of the barcode system, a clear taxonomic relationship can be applied to identify Melilotus species and enhance their practical production.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28910286</pmid><doi>10.1371/journal.pone.0182693</doi><tpages>e0182693</tpages><orcidid>https://orcid.org/0000-0002-3230-8996</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2017-09, Vol.12 (9), p.e0182693-e0182693 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1938827284 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Analysis Bar codes Biology and life sciences Breeding of animals Chloroplasts - genetics Computer and information sciences Deoxyribonucleic acid Divergence DNA DNA Barcoding, Taxonomic - methods DNA sequencing DNA, Chloroplast - genetics DNA, Intergenic DNA, Plant - genetics Ecosystems Flowers & plants Gene sequencing Genetic aspects Genetic Loci Genetic Variation Grasslands Herbal medicine Laboratories Loci Melilotus - classification Melilotus - genetics Mutation Phylogenetics Phylogeny Quality control Research and Analysis Methods Sequence Analysis, DNA - methods Spacer Species Studies Sweet clover |
| title | Potential DNA barcodes for Melilotus species based on five single loci and their combinations |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-08T08%3A57%3A44IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Potential%20DNA%20barcodes%20for%20Melilotus%20species%20based%20on%20five%20single%20loci%20and%20their%20combinations&rft.jtitle=PloS%20one&rft.au=Wu,%20Fan&rft.date=2017-09-14&rft.volume=12&rft.issue=9&rft.spage=e0182693&rft.epage=e0182693&rft.pages=e0182693-e0182693&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0182693&rft_dat=%3Cgale_plos_%3EA504553739%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1938827284&rft_id=info:pmid/28910286&rft_galeid=A504553739&rft_doaj_id=oai_doaj_org_article_04e01bada3564b77900cd484bd2c62ce&rfr_iscdi=true |