DNA barcoding of coastal ray-finned fishes in Vietnam
Autoři:
Pham The Thu aff001; Wen-Chien Huang aff002; Tak-Kei Chou aff004; Nguyen Van Quan aff001; Pham Van Chien aff001; Fan Li aff004; Kwang-Tsao Shao aff005; Te-Yu Liao aff004
Působiště autorů:
Institute of Marine Environment and Resources, Vietnam Academy of Science and Technology, Hai Phong, Vietnam
aff001; Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, Taiwan
aff002; Doctoral Degree Program in Marine Biotechnology, Academia Sinica, Taipei, Taiwan
aff003; Department of Oceanography, National Sun Yat-sen University, Kaohsiung, Taiwan
aff004; Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
aff005; Institute of Marine Biology, National Taiwan Ocean University, Keelung, Taiwan
aff006
Vyšlo v časopise:
PLoS ONE 14(9)
Kategorie:
Research Article
doi:
https://doi.org/10.1371/journal.pone.0222631
Souhrn
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.
Klíčová slova:
Biology and life sciences – Molecular biology – Molecular biology techniques – DNA barcoding – Evolutionary biology – Evolutionary systematics – Molecular systematics – Taxonomy – Organisms – Eukaryota – Animals – Vertebrates – Fish – Marine fish – Marine biology – Ecology – Biodiversity – Agriculture – Fisheries – Research and analysis methods – Database and informatics methods – Biological databases – Bioinformatics – Sequence analysis – Sequence databases – Computer and information sciences – Data management – Earth sciences – Marine and aquatic sciences – People and places – Geographical locations – Asia – Vietnam – Ecology and environmental sciences
Zdroje
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.
2. Frézal L, Leblois R. Four years of DNA barcoding: current advances and prospects. Infection, Genetics and Evolution. 2008;8(5):727–36. doi: 10.1016/j.meegid.2008.05.005 18573351
3. 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.
4. Kaur S. DNA Barcoding and Its Applications. International Journal of Engineering Research and General Science. 2015;3(2):602–4.
5. 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. doi: 10.1098/rstb.2005.1716 16214743
6. Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, et al. Identifying Canadian freshwater fishes through DNA barcodes. PLoS one. 2008;3(6):e2490. doi: 10.1371/journal.pone.0002490 22423312
7. Valdez-Moreno M, Ivanova N, Elías-Gutiérrez M, Contreras-Balderas S, Hebert P. Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. Journal of Fish Biology. 2009;74(2):377–402. doi: 10.1111/j.1095-8649.2008.02077.x 20735566
8. Ward RD, Hanner R, Hebert PD. The campaign to DNA barcode all fishes, FISH-BOL. Journal of fish biology. 2009;74(2):329–56. doi: 10.1111/j.1095-8649.2008.02080.x 20735564
9. Becker S, Hanner R, Steinke D. Five years of FISH-BOL: brief status report. Mitochondrial DNA. 2011;22(sup1):3–9.
10. Mecklenburg CW, Møller PR, Steinke D. Biodiversity of arctic marine fishes: taxonomy and zoogeography. Marine Biodiversity. 2011;41(1):109–40.
11. Galimberti A, De Mattia F, Losa A, Bruni I, Federici S, Casiraghi M, et al. DNA barcoding as a new tool for food traceability. Food Research International. 2013;50(1):55–63.
12. Costa FO, Landi M, Martins R, Costa MH, Costa ME, Carneiro M, et al. A ranking system for reference libraries of DNA barcodes: application to marine fish species from Portugal. PLoS One. 2012;7(4):e35858. doi: 10.1371/journal.pone.0035858 22558244
13. Steinke D, Zemlak TS, Boutillier JA, Hebert PDN. DNA barcoding of Pacific Canada’s fishes. Marine Biology. 2009;156(12):2641. doi: 10.1007/s00227-009-1284-0
14. Zhang J. Species identification of marine fishes in China with DNA barcoding. Evidence-Based Complementary and Alternative Medicine. 2011;2011:10. http://dx.doi.org/10.1155/2011/978253.
15. Zhang J, Hanner R. Molecular approach to the identification of fish in the South China Sea. PLoS One. 2012;7(2):e30621. doi: 10.1371/journal.pone.0030621 22363454
16. Bingpeng X, Heshan L, Zhilan Z, Chunguang W, Yanguo W, Jianjun W. DNA barcoding for identification of fish species in the Taiwan Strait. PloS one. 2018;13(6):e0198109. doi: 10.1371/journal.pone.0198109 29856794
17. Wang L, Wu Z, Liu M, Liu W, Zhao W, Liu H, et al. DNA barcoding of marine fish species from Rongcheng Bay, China. PeerJ. 2018;6:e5013. doi: 10.7717/peerj.5013 29967722
18. Lakra W, Verma M, Goswami M, Lal KK, Mohindra V, Punia P, et al. DNA barcoding Indian marine fishes. Molecular Ecology Resources. 2011;11(1):60–71. doi: 10.1111/j.1755-0998.2010.02894.x 21429101
19. Chang C-H, Shao K-T, Lin H-Y, Chiu Y-C, Lee M-Y, Liu S-H, et al. DNA barcodes of the native ray-finned fishes in Taiwan2017. 796–805 p.
20. Alien GR, Amaoka K, Anderson WD Jr, Bellwood DR, Bohlke EB, Bradbury MG, et al. A checklist of the fishes of the South China Sea. The Raffles Bulletin of Zoology. 2000;(8):569–667.
21. Zakaria-Ismail M. Zoogeography and biodiversity of the freshwater fishes of Southeast Asia. Ecology and conservation of Southeast Asian marine and freshwater environments including wetlands: Springer; 1994. p. 41–8.
22. Aquino LMG, Tango JM, Canoy RJC, Fontanilla IKC, Basiao ZU, Ong PS, et al. DNA barcoding of fishes of Laguna de Bay, Philippines. Mitochondrial DNA. 2011;22(4):143–53. doi: 10.3109/19401736.2011.624613 22040082
23. Alcantara SG, Yambot AV. DNA barcoding of commercially important grouper species (Perciformes, Serranidae) in the Philippines. Mitochondrial DNA Part A. 2016;27(6):3837–45.
24. Abdullah ML, Nor SM, Naim DM. Use of DNA barcode in the identification of catfishes (Siluriformes: Ariidae) from Malaysia. Biodiversitas Journal of Biological Diversity. 2017;18(4):1358–66.
25. Jaafar TNAM, Taylor MI, Nor SAM, de Bruyn M, Carvalho GR. DNA barcoding reveals cryptic diversity within commercially exploited Indo-Malay Carangidae (Teleosteii: Perciformes). PLoS One. 2012;7(11):e49623. doi: 10.1371/journal.pone.0049623 23209586
26. Ayudhaya PT, Muangmai N, Banjongsat N, Singchat W, Janekitkarn S, Peyachoknagul S, et al. Unveiling cryptic diversity of the anemonefish genera Amphiprion and Premnas (Perciformes: Pomacentridae) in Thailand with mitochondrial DNA barcodes. Agriculture and Natural Resources. 2017;51(3):198–205.
27. Nguyen ML, Nguyen VQ, Pham VC, Dao HL, Dinh VN, Dam TL. DNA barcoding application of mitochondrial COI gene to identify some fish of family Gobiidae in Vietnam. Vietnam Journal of Marine Science and Technology. 2018;18(4):443–51.
28. Pham TT, Furukawa M. Impact of Sea Level Rise on Coastal Zone of Vietnam. Bull Faculty Sci Univ Ryukyus. 2007;84.
29. Rojana-anawat P, Pradit S, Sukramongkol N, Siriraksophon S, editors. Temperature, salinity, dissolved oxygen and water masses of Vietnamese waters. Proceedings of the SEAFDEC Seminar on Fishery Resources in the South China Sea, Area IV: Vietnamese Waters; 2001; Thailand: Southeast Asian Fisheries Development Center.
30. Ngo-Duc T. Climate change in the coastal regions of Vietnam. Coastal Disasters and Climate Change in Vietnam: Elsevier; 2014. p. 175–98.
31. Fang G, Wang G, Fang Y, Fang W. A review on the South China Sea western boundary current. Acta Oceanologica Sinica. 2012;31(5):1–10.
32. Nguyen KH. Fish fauna of Vietnam. Collection of Marine Research Works 1995;IV:121–6.
33. Bui DC, Chu TV, Nguyen HD. Marine fisheries resources—Basic development of marine fisheries industry in Vietnam. In Proceedings of Marine Fisheries Research, Research Institute for Marine Fisheries, Vietnam Ministry of Fisheries, 560 p. 2001;II:200–10.
34. Dao MS, Pham T, editors. Management of coastal fisheries in Vietnam. Assessment, Management and Future Directions for Coastal Fisheries in Asian Countries: WorldFish Center Conference Proceedings; 2003.
35. Nguyen H, Hien P, Lebailly P. Vietnam’s fisheries and aquaculture development’s policy: are exports performance targets sustainable. 2017.
36. Lutaenko KA. Proceedings of the Workshop Coastal Marine Biodiversity and Bioresources of Vietnam and Adjacent Areas to the South China Sea, NhaTrang, Vietnam, November 24–25, 2011. 2011:Vladivostok-NhaTrang: Dalnauka, 2011. 123 pp.
37. Duong TY, Nguyen K, Bui SN, Nguyen VT, Nguyen BL, Tran DD. DNA barcodes and morphology of P. krempfi, P. mekongensis, and P. elongatus. Vietnam Journal of Biotechnology. 2016;14(1):29–37.
38. Vu DHQ, Le TTP, Tran TO, Le TT, Dang TB. Phylogenetic relationships of freshwater fish in Vietnamese Mekong. International Conference on Biological, Environment and Food Engineering (BEFE-2015) May 15–16, 2015 Singapore. 2015:58–61. http://dx.doi.org/10.15242/IICBE.C0515014.
39. Tran TO, Vu DHQ, Dang TB. Phylogenetic Relationships of Emperors (Lethrinidae) and Snappers (Lutjanidae) in Vietnam based on Mitochondrial DNA Sequences. International Conference on Biological, Environment and Food Engineering (BEFE-2015) May 15–16, 2015 Singapore. 2015:62–5. http://dx.doi.org/10.15242/IICBE.C0515016.
40. Tran TVT, Phan KL, Durand J-D. Diversity and distribution of cryptic species within the Mugil cephalus species complex in Vietnam. Mitochondrial DNA Part A. 2017;28(4):493–501. doi: 10.3109/24701394.2016.1143467
41. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular biology and evolution. 2018;35(6):1547–9. doi: 10.1093/molbev/msy096 29722887
42. Arroyave J, Stiassny ML. DNA barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae). Ecology and evolution. 2014;4(23):4534–42. doi: 10.1002/ece3.1321 25512849
43. Tran D, Nguyen NT. List of marine fish in Vietnam. Marine research collection 1985:19–45.
44. Nguyen KH. Fauna of Vietnam: Hanoi Science and Technology publisher; 2001. 324 p.
45. Nguyen NT, Nguyen VQ. Biodiversity and living resources of the coral reef fish in Vietnam marine waters: Hanoi Science and Technology publisher; 2005. 120 p.
46. Seishi K, Hisashi I, Nguyen VQ, Pham TD. Fishes of Ha Long Bay: Fisheries Research Laboratory, Mie University; 2018. 314 p.
47. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of molecular evolution. 1980;16(2):111–20. doi: 10.1007/bf01731581 7463489
48. Ward RD. DNA barcode divergence among species and genera of birds and fishes. Molecular ecology resources. 2009;9(4):1077–85. doi: 10.1111/j.1755-0998.2009.02541.x 21564845
49. Betancur-R R, Wiley EO, Arratia G, Acero A, Bailly N, Miya M, et al. Phylogenetic classification of bony fishes. BMC Evolutionary Biology. 2017;17(1):162. doi: 10.1186/s12862-017-0958-3 28683774
50. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular biology and evolution. 1993;10(3):512–26. doi: 10.1093/oxfordjournals.molbev.a040023 8336541
51. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985;39(4):783–91. doi: 10.1111/j.1558-5646.1985.tb00420.x 28561359
52. Landi M, Dimech M, Arculeo M, Biondo G, Martins R, Carneiro M, et al. DNA barcoding for species assignment: the case of Mediterranean marine fishes. PLoS One. 2014;9(9):e106135. doi: 10.1371/journal.pone.0106135 25222272
53. Srivathsan A, Meier R. On the inappropriate use of Kimura-2-parameter (K2P) divergences in the DNA-barcoding literature. Cladistics. 2012;28(2):190–4.
54. Reid B, Le M, McCord W, Iverson J, Georges A, Bergmann T, et al. Comparing and combining distance-based and character-based approaches for barcoding turtles. Molecular Ecology Resources. 2011;11(6):956–67. doi: 10.1111/j.1755-0998.2011.03032.x 21635698
55. Zhang J. Species identification of marine fishes in China with DNA barcoding. Evidence-Based Complementary and Alternative Medicine. 2011;2011.
56. Lavery S, Clements KD, Hickey A. Molecular identification of cryptogenic/invasive gobies in New Zealand: Ministry of Fisheries; 2006.
57. Bellwood D, Klanten S, Cowman P, Pratchett M, Konow N, Van Herwerden L. Evolutionary history of the butterflyfishes (f: Chaetodontidae) and the rise of coral feeding fishes. Journal of evolutionary biology. 2010;23(2):335–49. doi: 10.1111/j.1420-9101.2009.01904.x 20487131
58. Tang KL, Fielitz C. Phylogeny of moray eels (Anguilliformes: Muraenidae), with a revised classification of true eels (Teleostei: Elopomorpha: Anguilliformes). Mitochondrial DNA. 2013;24(1):55–66. doi: 10.3109/19401736.2012.710226 22967094
59. Guo Y, Bai Q, Yan T, Wang Z, Liu C. Mitogenomes of genus Pristipomoides, Lutjanus and Pterocaesio confirm Caesionidae nests in Lutjanidae. Mitochondrial DNA Part A. 2016;27(3):2198–9.
60. Ikejima K, Ishiguro NB, Wada M, Kita-Tsukamoto K, Nishida M. Molecular phylogeny and possible scenario of ponyfish (Perciformes: Leiognathidae) evolution. Molecular Phylogenetics and Evolution. 2004;31(3):904–9. doi: 10.1016/j.ympev.2003.10.006 15120388
61. Kaga T. Phylogenetic systematics of the family Sillaginidae (Percomorpha: order Perciformes). Zootaxa. 2013;3642(1):1–105.
62. Qu L, Ma C, Ma H, Dong Y, Wang W, Ren G, et al. The complete mitochondrial genome of Stolephorus commersonii. Mitochondrial DNA Part B. 2017;2(2):573–4.
Článek vyšel v časopise
PLOS One
2019 Číslo 9
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