DNA BARCODING APPLICATION OF MITOCHONDRIAL COI GENE TO IDENTIFY SOME FISH SPECIES OF FAMILY GOBIIDAE IN VIETNAM
Keywords:DNA barcoding, COI, Gobiidae, Vietnam.
AbstractThe family Gobiidae is a relatively high abundance family of coastal fish with about 2000 species in 210 genera described. In Vietnam, the study on Gobiidae is very complex due to the large number of species, small size and high morphological variation which makes difficulties in identification and classification. In this study, the DNA barcoding technique has been used through mitochondrial cytochrome oxidase I (COI) gene to classify 30 specimens of Gobiidae from three coastal areas (North, Central and South) in Vietnam to evaluate the effectiveness compared to the morphological classification method. Results showed that 26 species belonging to 21 genera were determined by the COI barcode while 19 species (17 genera) were determined when using morphological method. Mahidolia mystacina was new recorded in Vietnam. The DNA barcodes of COI gene developed in this study could be useful for estimating phylogenetic diversity as well as other studies of gobiids in terms of conservation, management and utilization of fisheries resources in Vietnam. In addition, the results showed the high potentiality in using COI barcode to identify marine fish.
Eschmeyer, W. N., and Fong, J. D., 2015. Species by family/subfamily in the Catalog of Fishes. San Francisco, CA: California Academy of Sciences.
Nelson, J., 2006. Fishes of the world. 4th edn. New York: John Wiley and Sons, Inc.
Mai Dinh Yen, Nguyen Van Trong, Nguyen Van Thien, Le Hoang Yen, and Hua Bach Loan, 1992. Identification of freshwater fish in Southern Vietnam. Science and Technics Publishing House, Hanoi.
Nguyen Thanh Tung, Nguyen, N. D., and Lam, N. C., 2005. Aquatic species in Vinh Long province. Department of Agriculture and Rural Development, Vinh Long province. 165 p.
Ngo Truc Binh, 2009. Biological characteristics of goby fishes in Tra Vinh Province. Master thesis. Can Tho University.
Tran Dac Dinh, Shibukawa, K., Nguyen, T. P., Ha, P. H., Tran, X. L., Mai, V. H., Utsugi, K., 2013. Fishes of the Mekong Delta, Vietnam. Can Tho University Publishing House, Can Tho. 174 p.
Diep Anh Tuan, Dinh Minh Quang, Tran Dac Dinh, 2014. Study on species composition of Gobiidae distributed in coast of Soc Trang province. Journal of Sciences VNU, 30(3), 68–76.
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., Stoeckle, M. Y., Zemlak, T. S., and Francis, C. M., 2004. Identification of birds through DNA barcodes. PLoS Biology, 2(10), e312.
Hubert, N., Hanner, R., Holm, E., Mandrak, N. E., Taylor, E., Burridge, M., Watkinson, D., Dumont, P., Curry, A., Bentzen, P., Zhang, J., April, J., and Bernatchez, L., 2008. Identifying Canadian freshwater fishes through DNA barcodes. PLoS one, 3(6), e2490.
Feng, Y., Li, Q. I., Kong, L., and Zheng, X., 2011. COI‐based DNA barcoding of Arcoida species (Bivalvia: Pteriomorphia) along the coast of China. Molecular Ecology Resources, 11(3), 435–441.
Jeon, H. B., Choi, S. H., and Suk, H. Y., 2012. Exploring the utility of partial cytochrome c oxidase subunit 1 for DNA barcoding of gobies. Journal of Animal Systematics, Evolution and Diversity, 28(4), 269–278.
Viswambharan, D., Pavan-Kumar, A., Singh, D. P., Jaiswar, A. K., Chakraborty, S. K., Nair, J. R., and Lakra, W. S., 2015. DNA barcoding of gobiid fishes (Perciformes, Gobioidei). Mitochondrial DNA, 26(1), 15–19.
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. 1800 p.
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.
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), 19. DOI 10,1186/s40555-014-0085-4.
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., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G., 2007. Clustal W and Clustal X version 2.0. bioinformatics, 23(21), 2947–2948.
Nguyen Nhat Thi, 2000. Animal of Vietnam volume 2, Gobioidei. Science and Technics Publishing House, Hanoi.
Tran Dinh, Nguyen Nhat Thi, 1985. List of marine fish in Vietnam. Proceedings of Marine Science Research, Hai Phong Marine Research Institute, Pp. 19–45.
Truong Thu Khoa and Tran Thi Thu Huong, 1993. Identification of freshwater fish in the Mekong delta. Bookstore of Can Tho University.
Do Thi Cat Tuong, Nguyen Van Long, 2015. Species composition and distribution of goby (Gobiidae) in coral reefs at Nha Trang bay. Collection of Marine Research Works, 21(2), 124–135.
Nguyen Nhat Thi and Nguyen Van Quan, 2004. Biodiversity and potential resources of coral reef fish in the Spratly islands. Journal of Marine Science and Technology, 4(4), 47–64.
Nguyen Van Quan, 2005. Resources of coral reef fish in Ha Long bay - Quang Ninh. Journal of Marine Science and Technology, 5(2), 39–51.
Nguyen Van Long, 2013. Coral reef fishes in the coastal waters of Phu Yen. Journal of Marine Science and Technology, 13 (1): 31-40.
Satapoomin, U., 2000. A preliminary checklist of coral reef fishes of the Gulf of Thailand, South China Sea. Raffles Bulletin of Zoology, 48(1), 31–54.
Allen, G. R., and Werner, T. B., 2002. Coral reef fish assessment in the ‘coral triangle’of southeastern Asia. Environmental Biology of Fishes, 65(2), 209–214.
Adrim, M., Chen, I. S., Chen, Z. P., Lim, K. K., Tan, H. H., Yusuf, Y., and Jaafar, Z., 2004. Marine fishes recorded from the Anambas and Natuna islands, South China Sea. The Raffles Bulletin of Zoology, (Supplement 11), 117–130.
Thai Thi Lan Phuong, Dang Thuy Binh, 2015. Goby Species Diversity In Vietnam Based On Morphological And Genetic Characteristics. Journal of Fisheries Science and Technology, (Special Issue).
Duong Thuy Yen and Truong Ngoc Trinh, 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, 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(2), 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.