DOI QR코드

DOI QR Code

Genetic diversity of spotted scat (Scatophagus argus) in Vietnam based on COI genes

  • Received : 2022.02.03
  • Accepted : 2022.10.30
  • Published : 2022.12.31

Abstract

A spotted scat, Scatophagus argus, has a high nutritional value and is among Asia's most widely consumed fish species. Thua Thien Hue's consumption market considers this species to be of high economic value and requires protection and conservation of the population. However, the studies on the identification and genetic diversity of S. argus distributed in Vietnam are still lacking. Therefore, mitochondrial cytochrome c oxidase subunit I (COI) gene was utilized to distinguish different populations and investigate the genetic diversity of two populations of S. argus from Tam Giang lagoon, Thua Thien Hue province (n = 31) and Ca Mau province (n = 14). The sequencing results indicated 13 distinct haplotypes among 45 sequences. Five single nucleotide polymorphisms were observed to distinguish Hue spotted scat population. The S. argus population in Ca Mau province was higher haplotype diversity (Hd) and nucleotide diversity (π) than those of Thua Thien Hue province, which demonstrates that there are minor differences between haplotypes. There were genetic distances ranging from 0%-4% within the populations and 6.67% between the two populations. In addition to the sequencing, the comparison of morphology, biology, culture, and the growth rate was sufficient to distinguish the spotted scat S. argus in Thua Thien Hue from Ca Mau.

Keywords

Acknowledgement

This study was supported by the Department of Scientific and Technologies of Thua Thien Hue Province, Vietnam under grant number TTH.2018-KC.02.

References

  1. Adamkewicz SL, Harasewych MG. Systematics and biogeography of the genus Donax (Bivalvia: Donacidae) in eastern North America. Am Malacol Bull. 1996;13:97-103.
  2. Ahmed MS, Chowdhury MMK, Nahar L. Molecular characterization of small indigenous fish species (SIS) of Bangladesh through DNA barcodes. Gene. 2019;684:53-7. https://doi.org/10.1016/j.gene.2018.10.048
  3. Ahmed MS, Datta SK, Saha T, Hossain Z. Molecular characterization of marine and coastal fishes of Bangladesh through DNA barcodes. Ecol Evol. 2021;11:3696-709. https://doi.org/10.1002/ece3.7355
  4. Anney MK, Antony A. Studies on some aspects of biology of two estuarine fishes Megalops cyprinoides and Scatophagus Argus [Ph.D. dissertation]. Kochi: Cochin University of Science and Technology; 1988.
  5. Barry TP, Fast AW. Natural history of the spotted scat (Scatophagus argus). In: Fast AW, editor. Spawning induction and pond culture of the spotted scat (Scatophagus argus Linnaeus) in the Philippines. Manoa: University of Hawaii at Manoa; 1988. p. 4-31.
  6. Bartlett SE, Davidson WS. Identification of Thunnus tuna species by the polymerase chain reaction and direct sequence analysis of their mitochondrial cytochrome b genes. Can J Fish Aquat Sci. 1991;48:309-17. https://doi.org/10.1139/f91-043
  7. Brown WM, George M Jr, Wilson AC. Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA. 1979;76:1967-71. https://doi.org/10.1073/pnas.76.4.1967
  8. Chakraborty M, Ghosh SK. An assessment of the DNA barcodes of Indian freshwater fishes. Gene. 2014;537:20-8. https://doi.org/10.1016/j.gene.2013.12.047
  9. Chandran A, Zacharia PU, Sanil NK. Ortholinea scatophagi (Myxosporea: Ortholineidae), a novel myxosporean infecting the spotted scat, Scatophagus argus (Linnaeus 1766) from southwest coast of India. Parasitol Int. 2020;75:102020.
  10. Frezal L, Leblois R. Four years of DNA barcoding: current advances and prospects. Infect Genet Evol. 2008;8:727-36. https://doi.org/10.1016/j.meegid.2008.05.005
  11. Froese R, Pauly D. Scatophagus argus (Linnaeus, 1766) [Internet]. FishBase. 2019 [cited 2021 Oct 5]. https://www.fishbase.de/summary/Scatophagus-argus.html
  12. Gregory TR, Witt JDS. Population size and genome size in fishes: a closer look. Genome. 2008;51:309-13. https://doi.org/10.1139/G08-003
  13. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999; 41: 95-98.
  14. Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc R Soc Lond B Biol Sci. 2003;270:313-21. https://doi.org/10.1098/rspb.2002.2218
  15. Hebert PDN, Gregory TR. The promise of DNA barcoding for taxonomy. Syst Biol. 2005;54:852-9. https://doi.org/10.1080/10635150500354886
  16. 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:e2490.
  17. Keskin E, Agdamar S, Tarkan AS. DNA barcoding common non-native freshwater fish species in Turkey: low genetic diversity but high population structuring. Mitochondrial DNA. 2013;24:276-87. https://doi.org/10.3109/19401736.2012.748041
  18. Khanh LV, Hai TN, Huong DTT, Phuong NT. Study on the reproductive biology of the spotted scat (Scatophagus argus) in the Mekong delta, Vietnam. Can Tho Univ J Sci. 2010;14:186-94.
  19. Lakra WS, Goswami M, Gopalakrishnan A. Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes, Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes. Mol Biol Rep. 2009;36:831-9. https://doi.org/10.1007/s11033-008-9252-1
  20. Lakra WS, Verma MS, Goswami M, Lal KK, Mohindra V, Punia P, et al. DNA barcoding Indian marine fishes. Mol Ecol Resour. 2011;11:60-71. https://doi.org/10.1111/j.1755-0998.2010.02894.x
  21. Liu SYV, Huang IH, Liu MY, Lin HD, Wang FY, Liao TY. Genetic stock structure of Terapon jarbua in Taiwanese waters. Mar Coast Fish. 2015;7:464-73. https://doi.org/10.1080/19425120.2015.1074966
  22. Locke SA, McLaughlin JD, Dayanandan S, Marcogliese DJ. Diversity and specificity in Diplostomum spp. metacercariae in freshwater fishes revealed by cytochrome c oxidase I and internal transcribed spacer sequences. Int J Parasitol. 2010;40:333-43. https://doi.org/10.1016/j.ijpara.2009.08.012
  23. Ma H, Ma C, Ma L. Population genetic diversity of mud crab (Scylla paramamosain) in Hainan Island of China based on mitochondrial DNA. Biochem Syst Ecol. 2011;39:434-40. https://doi.org/10.1016/j.bse.2011.06.005
  24. Martinez AS, Willoughby JR, Christie MR. Genetic diversity in fishes is influenced by habitat type and life-history variation. Ecol Evol. 2018;8:12022-31. https://doi.org/10.1002/ece3.4661
  25. McCusker MR, Bentzen P. Positive relationships between genetic diversity and abundance in fishes. Mol Ecol. 2010;19:4852-62. https://doi.org/10.1111/j.1365-294X.2010.04822.x
  26. Mindell DP. Phylogentic relationships among and within select avian orders based on mitochondrial DNA. Avian Mol Evol Syst. 1997:211-47.
  27. Mohammed-Geba K, El-Nab SESH, Awad E, Nofal AI. DNA barcoding identifies a unique haplotype of nile tilapia Oreochromis niloticus thriving in Egyptian freshwater and brackish water lakes. Int J Ecotoxicol Ecobiol. 2017;2:172-7.
  28. Moore WS. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution. 1995;49:718-26.
  29. Morin PA, Luikart G, Wayne RK, The SNP work group. SNPs in ecology, evolution and conservation. Trends Ecol Evol. 2004;19:208-16. https://doi.org/10.1016/j.tree.2004.01.009
  30.  Orsi JJ. A check list of the marine and freshwater fishes of Vietnam. Publ Seto Mar Biol Lab. 1974;21:153-77. https://doi.org/10.5134/175867
  31. Peng M, Zhu W, Yang C, Yao J, Chen H, Jiang W, et al. Genetic diversity of mitochondrial D-LOOP sequences in the spotted scat (Scatophagus argus) from different geographical populations along the northern coast of the South China Sea. J Appl Ichthyol. 2021;37:73-82. https://doi.org/10.1111/jai.14121
  32. Rozas J, Ferrer-Mata A, Sanchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, et al. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Mol Biol Evol. 2017;34:3299-302. https://doi.org/10.1093/molbev/msx248.
  33. Seeb JE, Carvalho G, Hauser L, Naish K, Roberts S, Seeb LW. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Mol Ecol Resour. 2011;11:1-8.
  34. Shen Y, Guan L, Wang D, Gan X. DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecol Evol. 2016;6:2702-13. https://doi.org/10.1002/ece3.2060
  35. Sivan G, Radhakrishnan CK. Food, feeding habits and biochemical composition of Scatophagus argus. Turk J Fish Aquat Sci. 2011;11:603-8.
  36. Thuy NTT, Binh MN, Chat TT, Han HTN. The characteristics of reproductive biology of spotted scat (Scatophagus argus Linnaeus, 1776) in Central Vietnam. Hue University J Science. 2015;104:241-53.
  37. Vijayan DK, Jayarani R, Singh DK, Chatterjee NS, Mathew S, Mohanty BP, et al. Comparative studies on nutrient profiling of two deep sea fish (Neoepinnula orientalis and Chlorophthalmus corniger) and brackish water fish (Scatophagus argus). J Basic Appl Zool. 2016;77:41-8. https://doi.org/10.1016/j.jobaz.2016.08.003
  38. Wang W, Ma C, Chen W, Zhang H, Kang W, Ni Y, et al. Population genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI gene sequences. Biochem Syst Ecol. 2017;71:114-20. https://doi.org/10.1016/j.bse.2017.01.002
  39. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. DNA barcoding Australia's fish species. Philos Trans R Soc Lond B Biol Sci. 2005;360:1847-57. https://doi.org/10.1098/rstb.2005.1716
  40. Yan YR, Hsu KC, Yi MR, Li B, Wang WK, Kang B, et al. Cryptic diversity of the spotted scat Scatophagus argus (Perciformes: Scatophagidae) in the South China Sea: pre-or post-production isolation. Mar Freshw Res. 2020;71:1640-50. https://doi.org/10.1071/MF19337
  41. Yen MD. Identification of freshwater fishes of South Vietnam. Ha Noi: Sci Tech; 1992.
  42. Zemlak TS, Ward RD, Connell AD, Holmes BH, Hebert PDN. DNA barcoding reveals overlooked marine fishes. Mol Ecol Resour. 2009;9:237-42.
  43. Zhang J, Hanner R. Molecular approach to the identification of fish in the South China Sea. PLOS ONE. 2012;7:e30621.
  44. Zhang JB, Hanner R. DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochem Syst Ecol. 2011;39:31-42. https://doi.org/10.1016/j.bse.2010.12.017