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. 2019 Sep 19;14(9):e0222631.
doi: 10.1371/journal.pone.0222631. eCollection 2019.

DNA barcoding of coastal ray-finned fishes in Vietnam

Pham The Thu  1 , Wen-Chien Huang  2   3   4 , Tak-Kei Chou  4 , Nguyen Van Quan  1 , Pham Van Chien  1 , Fan Li  4 , Kwang-Tsao Shao  5   6 , Te-Yu Liao  4
Affiliations

DNA barcoding of coastal ray-finned fishes in Vietnam

Pham The Thu et al. PLoS One. .

Abstract

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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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Three sampling areas along the coast of Vietnam.
N comprises Do Son (20.719536, 106.793336) and Ha Long (20.948599, 107.083191) of Hai Phong–Quang Ninh Provinces; C comprises Phan Rang (11.591625, 109.046675; 11.546292, 109.025067) of Ninh Thuan Province; S comprises Tac Cau (9.876155, 105.124151) and Ha Tien (10.378664, 104.485162) of Kien Giang Province. GPS coordinates are for the major fish markets visited every day.
Fig 2
Fig 2. Variation of taxonomic levels in each area.
Data include records from [27].
Fig 3
Fig 3. Distribution of K2P distances (percent) for mitochondrial COI (707 sequences, 500 bp) at different taxonomic levels.
Data include records from [27].
See this image and copyright information in PMC

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References

    1. Hebert PD, Cywinska A, Ball SL. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London B: Biological Sciences. 2003;270(1512):313–21. - PMC - PubMed
    1. Frézal L, Leblois R. Four years of DNA barcoding: current advances and prospects. Infection, Genetics and Evolution. 2008;8(5):727–36. 10.1016/j.meegid.2008.05.005 - DOI - PubMed
    1. Leray M, Knowlton N. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proceedings of the National Academy of Sciences. 2015;112(7):2076–81. - PMC - PubMed
    1. Kaur S. DNA Barcoding and Its Applications. International Journal of Engineering Research and General Science. 2015;3(2):602–4.
    1. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD. DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society of London B: Biological Sciences. 2005;360(1462):1847–57. 10.1098/rstb.2005.1716 - DOI - PMC - PubMed

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Grants and funding

This study was funded by Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 106.06-2018.31 to the Vietnamese side and Ministry of Science and Technology (104-2611-M-110-004; 105-2923-B-110-001-MY3; 106-2611-M-110-008) to the Taiwanese side. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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