DNA barcoding for identification of fish species in the Taiwan Strait
DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and...
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| Veröffentlicht in: | PloS one 2018-06, Vol.13 (6), p.e0198109-e0198109 |
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| creator | Bingpeng, Xing Heshan, Lin Zhilan, Zhang Chunguang, Wang Yanguo, Wang Jianjun, Wang |
| description | DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species. |
| doi_str_mv | 10.1371/journal.pone.0198109 |
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The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0198109</identifier><identifier>PMID: 29856794</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Base Composition ; Base pairs ; Biodiversity ; Biology and life sciences ; Classification ; Climate change ; COI protein ; Commercial fishing ; Computer and information sciences ; Cytochrome ; Cytochrome-c oxidase ; Deoxyribonucleic acid ; DNA ; DNA barcoding ; DNA Barcoding, Taxonomic ; DNA sequencing ; DNA, Mitochondrial - genetics ; Earth Sciences ; Ecology ; Ecology and Environmental Sciences ; Ecosystem biology ; Ecosystems ; Electron Transport Complex IV - genetics ; Evolution ; Fish ; Fisheries management ; Fishes ; Fishes - classification ; Fishes - genetics ; Fishing ; Gene sequencing ; Genera ; Genetic aspects ; Genetic Markers ; Genomes ; Identification ; Identification and classification ; Interspecific ; Laboratories ; Marine biology ; Mitochondria ; Morphology ; Nucleotide sequence ; Oceanography ; Oceans and Seas ; Research and analysis methods ; Species ; Species classification ; Studies ; Taxonomy ; Trends</subject><ispartof>PloS one, 2018-06, Vol.13 (6), p.e0198109-e0198109</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Bingpeng 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. 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High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.</description><subject>Animals</subject><subject>Base Composition</subject><subject>Base pairs</subject><subject>Biodiversity</subject><subject>Biology and life sciences</subject><subject>Classification</subject><subject>Climate change</subject><subject>COI protein</subject><subject>Commercial fishing</subject><subject>Computer and information sciences</subject><subject>Cytochrome</subject><subject>Cytochrome-c oxidase</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA barcoding</subject><subject>DNA Barcoding, Taxonomic</subject><subject>DNA sequencing</subject><subject>DNA, Mitochondrial - genetics</subject><subject>Earth Sciences</subject><subject>Ecology</subject><subject>Ecology and Environmental Sciences</subject><subject>Ecosystem biology</subject><subject>Ecosystems</subject><subject>Electron Transport Complex IV - 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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>Bingpeng, Xing</au><au>Heshan, Lin</au><au>Zhilan, Zhang</au><au>Chunguang, Wang</au><au>Yanguo, Wang</au><au>Jianjun, Wang</au><au>Fugmann, Sebastian D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DNA barcoding for identification of fish species in the Taiwan Strait</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2018-06-01</date><risdate>2018</risdate><volume>13</volume><issue>6</issue><spage>e0198109</spage><epage>e0198109</epage><pages>e0198109-e0198109</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene in the mitochondrial genome is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding reference database of fishes in the Taiwan Strait and evaluate the applicability of using the COI gene for the identification of fish at the species level. A total of 284 mitochondrial COI barcode sequences were obtained from 85 genera, 38 families and 12 orders of fishes. The mean length of the sequences was 655 base pairs. The average Kimura two parameter (K2P) distances within species, genera, families, orders and classes were 0.21%, 6.50%, 23.70% and 25.60%, respectively. The mean interspecific distance was 31-fold higher than the mean intraspecific distance. The K2P neighbor-joining trees based on the sequence generally clustered species in accordance with their taxonomic classifications. High efficiency of species identification was demonstrated in the present study by DNA barcoding, and we conclude that COI sequencing can be used to identify fish species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>29856794</pmid><doi>10.1371/journal.pone.0198109</doi><tpages>e0198109</tpages><orcidid>https://orcid.org/0000-0002-4963-6574</orcidid><orcidid>https://orcid.org/0000-0003-2390-0207</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Animals Base Composition Base pairs Biodiversity Biology and life sciences Classification Climate change COI protein Commercial fishing Computer and information sciences Cytochrome Cytochrome-c oxidase Deoxyribonucleic acid DNA DNA barcoding DNA Barcoding, Taxonomic DNA sequencing DNA, Mitochondrial - genetics Earth Sciences Ecology Ecology and Environmental Sciences Ecosystem biology Ecosystems Electron Transport Complex IV - genetics Evolution Fish Fisheries management Fishes Fishes - classification Fishes - genetics Fishing Gene sequencing Genera Genetic aspects Genetic Markers Genomes Identification Identification and classification Interspecific Laboratories Marine biology Mitochondria Morphology Nucleotide sequence Oceanography Oceans and Seas Research and analysis methods Species Species classification Studies Taxonomy Trends |
| title | DNA barcoding for identification of fish species in the Taiwan Strait |
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