DNA barcoding for identification of some fish species (Carangidae) in Vietnam coastal area

Pham The Thu; Nguyen Manh Linh; Nguyen Van Quan; Pham Van Chien; Dao Huong Ly; Le Ba Hoang Hiep

doi:10.15625/1859-3097/19/4/14909

Author affiliations

Authors

Pham The Thu Institute of Marine Environment and Resources, VAST, Vietnam
Nguyen Manh Linh Institute of Marine Environment and Resources, VAST, Vietnam
Nguyen Van Quan Institute of Marine Environment and Resources, VAST, Vietnam
Pham Van Chien Institute of Marine Environment and Resources, VAST, Vietnam
Dao Huong Ly Institute of Marine Environment and Resources, VAST, Vietnam
Le Ba Hoang Hiep VNU University of Sciences, Vietnam National University, Hanoi, Vietnam

DOI:

https://doi.org/10.15625/1859-3097/19/4/14909

Keywords:

DNA barcoding, COI, Carangidae, Vietnam.

Abstract

Carangidae family has got about 148 species belonging to 32 genera. In Vietnam, Carangidae is of high commercial value and playing an important role in the ecosystem. In the context Vietnam has received yellow card for seafood since Nov. 2017 by the EU, in which one of the main reasons was related to the restriction of traceability. In this study, DNA barcoding technique of mitochondrial cytochrome oxidase I (COI) gene was used to classify 56 specimens of Carangidae from three coastal areas (Northern, Central and Southern) in Vietnam to evaluate the effectiveness compared to the morphological classification method. Results showed that 21 species belonging to 16 genera were determined by the COI barcode while 18 species (16 genera) were determined when using morphological method. Seriola quinqueradiata and Trachinotus anak were newly recorded in Vietnam. From 56 sequences with 660 bp of mtDNA (COI), total 27 haplotypes were detected; haplotype diversity (h) and nucleotide diversity (π) were 0.903 ± 0.00060 and 0.14%, respectively. The DNA barcodes of COI gene of 21 species in Carangidae which were developed in this study could be used as a basis for comparison and traceability of their products. In addition, the results showed the high potentiality in using COI barcode to identify Carangidae fish in Vietnam.

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References

Thanh Nguyen, 2018. Three major challenges to remove the “yellow card” from the EC. Customs newspaper. http://cafef.vn/ba-thach-thuc-lon-de-go-the-vang-tu-ec-20180621141126282.chn.

Hanner, R., Floyd, R., Bernard, A., Collette, B. B., and Shivji, M., 2011. DNA barcoding of billfishes. Mitochondrial DNA, 22(sup1), 27–36.

Costa, F. O., and Carvalho, G. R., 2007. The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of Fish. Genomics, Society and Policy, 3(2), 29–40.

Fox, C., Taylor, M. I., Pereyra, R., and Rico, C., 2005. Mapping of the spawning grounds of Irish Sea gadoids using genetic identification of planktonic eggs. Mol Ecol, 14, 879–884.

Trivedi, S., Aloufi, A. A., Ansari, A. A., and Ghosh, S. K., 2016. Role of DNA barcoding in marine biodiversity assessment and conservation: an update. Saudi journal of biological sciences, 23(2), 161–171.

Moore, W. S., 1995. Inferring phylogenies from mtDNA variation: mitochondrial‐gene trees versus nuclear‐gene trees. Evolution, 49(4), 718–726.

Hebert, P. D., Cywinska, A., Ball, S. L., and Dewaard, J. R., 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(1512), 313–321.

Hebert, P. D., Ratnasingham, S., and De Waard, J. R., 2003. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences, 270(suppl_1), S96–S99.

Hebert, P. D., Stoeckle, M. Y., Zemlak, T. S., and Francis, C. M., 2004. Identification of birds through DNA barcodes. PLoS biology, 2(10), e312.

Costa, F. O., DeWaard, J. R., Boutillier, J., Ratnasingham, S., Dooh, R. T., Hajibabaei, M., and Hebert, P. D., 2007. Biological identifications through DNA barcodes: the case of the Crustacea. Canadian Journal of Fisheries and Aquatic Sciences, 64(2), 272–295.

Mikkelsen, N. T., Schander, C., and Willassen, E., 2007. Local scale DNA barcoding of bivalves (Mollusca): a case study. Zoologica Scripta, 36(5), 455–463.

Nelson, J. S., 2006. Fishes of the world. 4th edn. New York: John Wiley & Sons.

Food and Agriculture Organization of the United Nations: Fisheries and Aquaculture Department (URL http://www.fao.org/ fishery/statistics/en).

Tran Thi Hong Hoa, Vo Van Quang, Nguyen Phi Uy Vu, Le Thi Thu Thao, Tran Cong Thinh, 2014. Species composition of exploited fishes in Van Phong bay, Khanh Hoa province. Collection of Marine Research, 20, 70–88.

Vu Viet Ha, Nguyen Viet Nghia, 2012. Species composition and productivity for fishing of pelagic fish by gill net in central and southeastern waters of Vietnam. Final report topics. Research Institute for Marine Fisheries, Hai Phong.

Dao Manh Son, 2005. Research on resources and ability to exploit large pelagic fish in the offshore waters of the Central and Southeast regions. Final report of project at ministry level. Research Institute for Marine Fisheries, Hai Phong.

Froese R., Pauly D. (Editors), 2012. FishBase. World Wide Web electronic publication. www.fishbase.org, version (04/2012).

Laroche, W. A., 1984. Carangidae: development. Ontogeny and systematics of fishes. Am. Soc. Ichthyol. Herpetol.

Rainboth, W. J., 1996. Fishes of the cambodian mekong. Food & Agriculture Org.

Nakabō, T. (Ed.), 2002. Fishes of Japan: with pictorial keys to the species (Vol. 1). Tokai University Press.

Chou, C. E., Liao, T. Y., Chang, H. W., and Chang, S. K., 2015. Population structure of Hirundichthys oxycephalus in the northwestern Pacific inferred from mitochondrial cytochrome oxidase I gene. Zoological Studies, 54(1), 1–9. DOI 10,1186/s40555-014-0085-4.

Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., and Hebert, P. D., 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462), 1847–1857. doi: 10,1098/rstb,2005,1716.

Hall, T. A., 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. In Nucleic acids symposium series (Vol. 41, No. 41, pp. 95–98). [London]: Information Retrieval Ltd., c1979–c2000.

Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., ... and Thompson, J. D., 2007. Clustal W and Clustal X version 2.0. Bioinformatics, 23(21), 2947–2948.

Rozas, J., Sánchez-DelBarrio, J. C., Messeguer, X., and Rozas, R., 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19(18), 2496–2497.

Le Thi Thu Thao, Vo Van Quang, Nguyen Phi Uy Vu, 2010. Correct and update the scientific names of fish (family Carangidae) in Vietnamese seawaters. Collection of Marine Research Works, 17, 216–224.

Nguyen Van Luc, Le Thi Thu Thao, Nguyen Phi Uy Vu, 2007. List of marine fish in Vietnam. Vol. 19. Marine fish: Perciformes (Carangidae, Mullidae, Chaetodontidae, Labridae, Scombridae). Science and Technics Publishing House, Hanoi. 199 p.

Lai Duy Phuong, Nguyen Quang Hung, 2017. Atlas of common coral reef fish in Vietnam. Agriculture Publishers, Hanoi. pp. 105–111.

Hoang Ngoc Thao, Nguyen Thi Yen, Ho Anh Tuan, Nguyen Kim Tien, 2017. Species composition of fish in estuary area of Mai Giang river in Quynh Luu and Hoang Mai districts, Nghe An province. Proceedings of 7th National Scientific Conference on Ecology and Biological Resources. pp. 382–387.

Tong Xuan Tam, Nguyen Thi Nhu Han, 2014. Constructing a database for fish species in Can Gio, Ho Chi Minh city. Journal of Science, Ho Chi Minh University of Education, 74-81.

Nguyen Huu Phung, Le Trong Phan, Nguyen Nhat Thi, Nguyen Phi Binh, Do Thi Nhu Nhung, Nguyen Van Luc, 1995. List of marine fish in Vietnam. Vol. III. Science and Technics Publishing House.

Nguyen Nhat Thi, Nguyen Van Quan. 2005. Biodiversity and potential resources of coral reef fish in Vietnam. Science and Technics Publishing House, pp.73–74.

Nguyen Van Hoan, Nguyen Huu Duc, 2012. Study on the structure of fish species composition in Tam Giang-Cau Hai lagoon system, Thua Thien-Hue province. Journal of Biology, 34(1), 20–30.

Lin, P. L., and Shao, K. T., 1999. A Review of the Carangid Fishes (Family Carangidae) from Taiwan with Descriptions of Four New Records. Zoological Studies, 38(1), 33–68.

Mat, T. J., Taylor, M. I., Mohd, S. N., and Carvalho, G. R., 2012. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PloS one, 7(11), e49623-e49623. doi:10.1371/journal.pone.0049623.

Yoshida, T., Motomura, H., Musikasinthorn, P., and Matsuura, K., (eds.), 2013. Fish of northern Gulf of Thailand. National Museum of Nature and Science, Tsukuba, Research Institute for Humanity and Nature, Kyoto, and Kagoshima University Museum, Kagoshima. Vii, 114–122.

Gushiken, S., 1988. Phylogenetic relationships of the perciform genera of the family Carangidae. Ichthyological Research, 34(4), 443–461.

Kijima, A., Taniguchi, N., and Ochiai, A., 1986. Genetic relationships in the family Carangidae. In Uyeno T, Arai R, Taniuchi T, Matsuura K. Indo-Pacific fish biology: proceedings of the Second International Conference on Indo-Pacific Fishes. Ichthylog Soc Japan Tokyo (pp. 840–848).

Smith-Vaniz, W. F., 1984. Carangidae: relationships. Ontogeny and systematics of fishes, 1, 640–670.

Reed, D. L., Carpenter, K. E., and Martin, J. D., 2002. Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches. Molecular Phylogenetics and Evolution, 23(3), 513–524.

Yen, D. T., and Trinh, T. N., 2013. Morphological comparison between new phenotype and wild strains of climbing perch (Anabas testudineus). Journal of Science, Can Tho University, 86–95.

Duong Thuy Yen, 2014. Sequence comparison of DNA barcoding genes between new phenotype and wild strains of climbing perch (Anabas testudineus Bloch, 1792). Journal of Science, Can Tho University, (30), 29–36.

Nguyen Phuong Thao and Duong Thuy Yen, 2014. Comparing morphological characteristics and DNA barcoding of two goby species Butis butis and Butis humeralis. Journal of Science, Can Tho University, (40), 23–30

Docker, M. F., and Heath, D. D., 2003. Genetic comparison between sympatric anadromous steelhead and freshwater resident rainbow trout in British Columbia, Canada. Conservation Genetics, 4(2), 227–231.

Pearse, D. E., Hayes, S. A., Bond, M. H., Hanson, C. V., Anderson, E. C., Macfarlane, R. B., and Garza, J. C., 2009. Over the falls? Rapid evolution of ecotypic differentiation in steelhead/rainbow trout (Oncorhynchus mykiss). Journal of Heredity, 100(5), 515–525.

Ardura, A., Linde, A. R., Moreira, J. C., and Garcia-Vazquez, E., 2010. DNA barcoding for conservation and management of Amazonian commercial fish. Biological Conservation, 143(6), 1438–1443.