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The Utility of Otx1B Gene Sequence in Evaluating Some Epinephelus species Evolutionary Variations Compared with Other Ray-finned Fishes

DOI: 10.18805/IJAR.B-1338    | Article Id: B-1338 | Page : 666-672
Citation :- The Utility of Otx1B Gene Sequence in Evaluating Some Epinephelus species Evolutionary Variations Compared with Other Ray-finned Fishes.Indian Journal of Animal Research.2022.(56):666-672
A.M. Shaikh-Omar, Y.M. Saad, Z.M. Al-Hasawi yasser_saad19@yahoo.com
Address : Faculty of Sciences, Biological Sciences Department, King Abdulaziz University, Jeddah-80200, KSA.
Submitted Date : 14-11-2020
Accepted Date : 10-02-2021

Abstract

Background: The application of molecular methods for evaluating the Epinephelus species evolutionary variations is considered the backbone for the conservation process for these biological resources. 
Methods: In this study, the utility of the Otx1B gene sequence variations was evaluated for the identification of some Red Sea Epinephelus species (E. areolatus, E. malabaricus, E. summana, E. radiatus and E. chlorostigma) compared with other ray-finned fishes. Some Otx1B gene fragments were isolated, purified, sequenced, analyzed (663 bp) and submitted to NCBI. 
Result: A total of 140 single nucleotide polymorphisms were identified among the evaluated fishes. The phylogenetic relations among the evaluated fishes were reconstructed using the Maximum Likelihood and Neighbor-Joining methods. The genus Epinephelus was distantly related to the group formed by genera Chlorurus, Scarus and Oxycheilinus. The DNA polymorphism and sequence conservation values were calculated. The estimated Otx1B gene fragment sequences have proven their ability to detect speciation in each studied fish genera.

Keywords

Epinephelus Evolution Fish Genetics Otx1B

References

  1. Alam, A., Chadha, N.K., Kumar, A., Chakraborty, S.K., Joshi, K.D., Sawant, P.B., Das, S.C.S., Kumar, J., Kumar, T. (2020). DNA barcoding and biometric investigation on the invasive oreochromis niloticus (Linnaeus, 1758) from the River Yamuna of Uttar Pradesh. Indian Journal of Animal Research. 54: 856-863.
  2. Cawthorn, D., Harris, A.S., Witthuhn, R. (2012). Evaluation of the 16S and 12S rRNA genes as universal markers for the identification of commercial fish species in South Africa. Gene. 491: 40-48.
  3. Chen, W., Shen, Y., Gan, X., Wang, X., He, S. (2016). Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong). Ecol. Evol. 6:6023-6036.
  4. Deepti, V.A., Shrikanya, K.V., Sujatha, K. (2014). Taxonomic studies and phylogenetic relationship of seven spotted groupers species of genus Epinephelus (Pisces: Serranidae) off Visakhapatnam, middle-east coast of India. Indian Journal of Geo-Marine Sciences. 12: 2254-2268.
  5. Eknath, A. (1995). Managing aquatic genetic resources. Management example 4: The Nile tilapia. International center for living Aquatic resources Management (ICLARM), MCP.O. Box 2631, Makati, Metro Manila 0718, Philippines. 1995.
  6. FAO (1993). Groupers of the World, 16(1993)125. [Heemstra P.C. and Randall J.E.], FAO 1993. 
  7. Giacomo, B., Dennis, A.P. (1992). Molecular phylogeny of the prickly shark, Echinorhinus cookei, based on a nuclear (18S rRNA) and a mitochondrial (cytochrome b) gene. Molecular Phylogenetics and Evolution, 2: 161-167.
  8. Hobbs, J. A., Lynne, V., Dean, R., Geoffrey, P., Philip, L. (2013). High genetic diversity in geographically remote populations of endemic and widespread coral reef angelfishes (genus: Centropyge). Diversity. 5: 39-50.
  9. Hillis, D., Moritz, C., Mable, B. (1996). Molecular Systematics, 2nd ed. Sinauer Associates, Sunderland, MA. 655 pp.
  10. Kim, Y.K., Lee, C.H., Lee, Y.D., Han, S.H. (2017). Development of species-specific PCR for the identification of three grouper fish species (Epinephelus septemfasciatus, E. bruneus and E. akaara). Indian Journal of Animal Research. 53: 482-484.
  11. Lee, D.J., Kim, I.C. (2020). The new freshwater crab belongs to the genus Geothelphusa as inferred from mitochondrial and nuclear DNA markers. Indian Journal of Animal Research. 54:424-429
  12. Lleonart, J., Taconet, M., Lamboeuf, M. (2006). Integrating information on marine species identification for fishery purposes. Mar Ecol. Prog. Ser. 316: 231-238.
  13. Liu, Q., Takashi, S., Satoshi, K., Nobuaki, O., Hirofumi, Y., Motohiro, T., Yuya, S., Takuma, S., Yoji, N., Motohiko, T., Yuya, S., Takuma, S., Yoji, N., Motohiko, S., Suwit, W., Akiyuki, O. (2013). A genetic linkage map of kelp grouper (Epinephelus bruneus) based on microsatellite markers. Aquaculture. 415: 63-81. 
  14. Manorama, M., Arti, G., Kuldeep, K., Rajeev, K., Vindhya, M. (2017). Genetic divergence in natural and farm populations of Pengba fish, Osteobrama belangeri (Valenciennes, 1844), an endemic fish of North-East India derived from mtDNA ATPase 6/8 gene. Mitochondrial DNA Part B.2, 658-661.
  15. Matthew, T., Philip, A. (2007). A molecular phylogeny of the groupers of the subfamily Epinephelinae (Serranidae) with a revised classification of the Epinephelini. Ichthyol. Res. 54: 1-17.
  16. Ornjira, P., Narongrit, M., Surin, P., Kornsorn, S. (2018). Complete mitochondrial genome of mouthbrooding fighting fish (Betta pi) compared with bubble nesting fighting fish (B. splendens). Mitochondrial DNA Part B. 3: 6-8. 
  17. Park, L., Brainard, M., Dightman, D. (1993). Low levels of intraspecific variation in the mitochondrial DNA of chum salmon (Oncoryhnchus keta). Mol. Mar. Biol. Biotech. 2: 362-370. 
  18. Popovic, J., Stevanovic, M. (2009). Remarkable evolutionary conservation of SOX14 orthologues. J. Genet. 88: 15-    24. 
  19. Redwan, E.M., Korim, S., Samra, A., Saad, Y.M., Almhedar, H.A., Uversky, V.N. (2018). Variability of some milk-associated genes and proteins in several breeds of Saudi Arabian camels. Protein Journal. 37: 333-352. 
  20. Saad, Y.M., Abuzinadah, O.A., El-Domyati, F.M., Sabir, J.M. (2012). Analysis of genetic signature for some Plectropomus species based on some dominant DNA markers. Life Sci. J. 9: 2370-2375. 
  21. Saad, Y.M., Abuzinadah, O.A., El-Domyati, F.M. (2013). Monitoring of genetic diversity in some parrotfish species based on inter simple sequence repeat polymorphism. Life Sci. J. 10: 1841-1846.
  22. Saad, Y.M., El-Sebaie, H.A. (2017). The efficiency of Cytochrome oxidase subunit 1 gene (cox1) in reconstruction of phylogenetic relations among some Crustacean species. Qulified by the 19th International Conference on Animal Production, Mating and Breeding (ICAPMB), (27-28 July, 2017), Istanbul, Turkey.
  23. Santini, S., Bernardi, G. (2005). Organization and base composition of Tilapia Hox genes: implications for the evolution of Hox clusters in fish. Gene. 346: 51-61.
  24. Smith, L.L., Jennifer, L., Michael, E., Todd, S., Mark, W. (2008). Phylogenetic relationships and the evolution of regulatory gene sequences in the parrotfishes. Molecular Phylogenetics and Evolution. 49:136-152.
  25. Sun, L.F., Li, J., Liang, X.F., Yi, T.L., Fang, L., Sun, J., He, Y.H., Luo, X.N., Dou, Y.Q., Yang, M. (2015). Microsatellite DNA markers and their correlation with growth traits in mandarin fish (Siniperca chuatsi). Genet. Mol. Res. 14: 19128-19135.
  26. Tamura, K., Stecher, G., Peterson, D., Filipski, K. (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution. 30: 2725-2729. 
  27. Volff, J.N. (2004). Genome evolution and biodiversity in teleost fish. Heredity. 94: 280-294.
  28. Vignal, A., Milan, D., Sancristoba, M., Eggen, A. (2002). A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 3: 275-305. 
  29. Wang, Z., Wang, Y., Lin, L., Qiu, S., Ben, X. (2002). Genetic polymorphisms in wild and cultured large yellow croaker Pseudosciaena crocea using AFLP fingerprinting. Journal of Fishery Sciences of China. 9: 198-202.
  30. Ward, R.D., Tyler, S.Z., Bronwyn, H.I., Peter, R.L., Paul, D.N. (2005). DNA barcoding Australia’s fish species. Phil. Trans R. Soc. B. 60: 1847-1857.
  31. Yu, H., You, X., Li, J., Zhang, X., Zhang, S., Jiang, S., Lin, X., Lin, H.R., Meng, Z., Shi, Q. (2018). A genome-wide association study on growth traits in orange-spotted grouper (Epinephelus coioides) with RAD-seq genotyping. Sci. China Life Sci. 61: 934-946.

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