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DNA barcoding of coastal ray-finned fishes in Vietnam

DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were...

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Autores principales: Thu, Pham The, Huang, Wen-Chien, Chou, Tak-Kei, Van Quan, Nguyen, Van Chien, Pham, Li, Fan, Shao, Kwang-Tsao, Liao, Te-Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752846/
https://www.ncbi.nlm.nih.gov/pubmed/31536551
http://dx.doi.org/10.1371/journal.pone.0222631
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author Thu, Pham The
Huang, Wen-Chien
Chou, Tak-Kei
Van Quan, Nguyen
Van Chien, Pham
Li, Fan
Shao, Kwang-Tsao
Liao, Te-Yu
author_facet Thu, Pham The
Huang, Wen-Chien
Chou, Tak-Kei
Van Quan, Nguyen
Van Chien, Pham
Li, Fan
Shao, Kwang-Tsao
Liao, Te-Yu
author_sort Thu, Pham The
collection PubMed
description DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam.
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spelling pubmed-67528462019-09-27 DNA barcoding of coastal ray-finned fishes in Vietnam Thu, Pham The Huang, Wen-Chien Chou, Tak-Kei Van Quan, Nguyen Van Chien, Pham Li, Fan Shao, Kwang-Tsao Liao, Te-Yu PLoS One Research Article DNA barcoding based on a fragment of the cytochrome c oxidase subunit I (COI) gene is widely applied in species identification and biodiversity studies. The aim of this study was to establish a comprehensive barcoding database of coastal ray-finned fishes in Vietnam. A total of 3,638 specimens were collected from fish landing sites in northern, central and southern Vietnam. Seven hundred and sixty-five COI sequences of ray-finned fishes were generated, belonging to 458 species, 273 genera, 113 families and 43 orders. A total of 59 species were newly recorded in Vietnam and sequences of six species were new to the Genbank and BOLD online databases. Only 32 species cannot be annotated to species level because difficulty in morphological identifications and their Kimura-2-Parameter (K2P) genetic distances to most similar sequences were more than 2%. Moreover, intra-specific genetic distances in some species are also higher than 2%, implying the existence of putative cryptic species. The mean K2P genetic distances within species, genera, families, orders and classes were 0.34%, 12.14%, 17.39%, 21.42%, and 24.80, respectively. Species compositions are quite different with only 16 common species among northern, central and southern Vietnam. This may attribute to multiple habitats and environmental factors across the 3,260 km Vietnamese coastline. Our results confirmed that DNA barcoding is an efficient and reliable tool for coastal fish identification in Vietnam, and also established a reliable DNA barcode reference library for these fishes. DNA barcodes will contribute to future efforts to achieve better monitoring, conservation, and management of fisheries in Vietnam. Public Library of Science 2019-09-19 /pmc/articles/PMC6752846/ /pubmed/31536551 http://dx.doi.org/10.1371/journal.pone.0222631 Text en © 2019 Thu et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Thu, Pham The
Huang, Wen-Chien
Chou, Tak-Kei
Van Quan, Nguyen
Van Chien, Pham
Li, Fan
Shao, Kwang-Tsao
Liao, Te-Yu
DNA barcoding of coastal ray-finned fishes in Vietnam
title DNA barcoding of coastal ray-finned fishes in Vietnam
title_full DNA barcoding of coastal ray-finned fishes in Vietnam
title_fullStr DNA barcoding of coastal ray-finned fishes in Vietnam
title_full_unstemmed DNA barcoding of coastal ray-finned fishes in Vietnam
title_short DNA barcoding of coastal ray-finned fishes in Vietnam
title_sort dna barcoding of coastal ray-finned fishes in vietnam
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752846/
https://www.ncbi.nlm.nih.gov/pubmed/31536551
http://dx.doi.org/10.1371/journal.pone.0222631
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