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First DNA Barcoding-based Inventory of Suez Gulf Fishes in Egypt and its Implication for Species Diversity

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Abstract

The Suez Gulf is one of the most important water bodies north of the Red Sea that contribute significantly in fish production in Egypt. The current study represents the first molecular identification of marine fish species from the Suez Gulf in Egypt based on DNA barcoding. A total of 96 DNA barcodes using a 662 bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 32 species that represent 26 genera and 19 families. The average genetic divergence based on Kimura two-parameter model between families and species were 0.274 and 0.256, respectively. The genetic distance among families varied greatly with the lowest genetic distance of 0.190 obtained between Carangidae and Atherindae, while Sphyraenidae and Moronidae had genetic distance of 0.472. The percent GC content was above average across species and ranged between 51.74% in Acanthopagrus bifasciatus and 66.37% in Lagocephalus guentheri. The Neighbor Joining tree showed clear clustering of the 19 fish families with species of the same family formed a single cluster. The findings of the current study support that COI barcode effectively identified Suez Gulf fish species. Moreover, the results of the current study will establish the first DNA barcode records for Suez Gulf fishes in Egypt which will contribute in future fish species identification in the Suez Gulf and the Red Sea.

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REFERENCES

  1. Abbas, E.M., Takayanagi, A., Shimizu, N., and Kato, M., Methylation status and chromatin structure of the myostatin gene promoter region in the sea perch Lateolabrax japonicus (Perciformes), Genet. Mol. Res., 2011, vol. 10, no. 4, pp. 3306–3315. https://doi.org/10.4238/2011.december.8.7

    Article  CAS  PubMed  Google Scholar 

  2. Abbas, E., Abdelsalam, K., Geba, K.M., et al., Genetic and morphological identification of some crabs from the Gulf of Suez, Northern Red Sea, Egypt, Egypt. J. Aquat. Res., 2016, vol. 42, no. 3, pp. 319–329. https://doi.org/10.1016/j.ejar.2016.08.003

    Article  Google Scholar 

  3. Abbas, E., Soliman, T., El-Magd, M., et al., Phylogeny and DNA barcoding of the family Sparidae inferred from mitochondrial DNA of the Egyptian waters, J. Fish. Aquat. Sci., 2017, vol. 12, no. 2, pp. 73–81. https://doi.org/10.3923/jfas.2017

    Article  CAS  Google Scholar 

  4. Abbas, E.M., Geba, K.M., and Sharawy, Z.Z., Molecular and biometric characterizations of the Western king prawn Melicertus latisulcatus (Kishinouye, 1896) in the Egyptian Red Sea, Egypt, Egypt. J. Aquat. Biol. Fish., 2018, vol 22, no. 1, pp. 1–14. https://doi.org/10.21608/EJABF.2018.7181

    Article  Google Scholar 

  5. Ahmed, M.I., Sabrah, M.M., Heneish, R.A., and El-Alwany, M., DNA barcoding uncover cryptic diversity in goat fishes (family: Mullidae) across the Egyptian coastal waters, Pak. J. Biol. Sci., 2016, vol. 19, no. 2, pp. 65–70. https://doi.org/10.3923/pjbs.2016.65.70

    Article  PubMed  Google Scholar 

  6. Akel, S.H. and Karachle, P.K., The marine ichthyofauna of Egypt, Egypt. J. Aquat. Biol. Fish., 2017, vol. 21, no. 3, pp. 81–116. https://doi.org/10.21608/EJABF.2017.4130

    Article  Google Scholar 

  7. Ali, F.S., Ismail, M., and Mamoon, A., Comparative molecular identification of genus Dicentrarchus using mitochondrial genes and internal transcribed spacer region, Egypt. J. Aquat. Biol. Fish., 2019, vol. 23 no. 3, pp. 371–384. https://doi.org/10.21608/EJABF.2019.47385

    Article  Google Scholar 

  8. Ali, F.S., Ismail, M., and Aly, W., DNA barcoding to characterize biodiversity of freshwater fishes of Egypt, Mol. Biol. Rep., 2020, vol. 47, pp. 5865–5877. https://doi.org/10.1007/s11033-020-05657-3

    Article  CAS  PubMed  Google Scholar 

  9. Ardura, A., Planes, S., and Garcia-Vazquez, E., Applications of DNA barcoding to fish landings: Authentication and diversity assessment, ZooKeys, 2013, vol. 365, pp. 49–65. https://doi.org/10.3897/zookeys.365.6409

    Article  Google Scholar 

  10. Bariche, M., Torres, M., Smith, C., et al., Red Sea fishes in the Mediterranean Sea: a preliminary investigation of a biological invasion using DNA barcoding, J. Biogeogr., 2015, vol. 42, no. 12, pp. 2363–2373. https://doi.org/10.1111/jbi.12595

    Article  Google Scholar 

  11. Bergsten, J., Bilton, D., Fujisawa, T., et al., The effect of geographical scale of sampling on DNA barcoding, Syst. Biol., 2012, vol. 61, no. 5, pp. 851–869. https://doi.org/10.1093/sysbio/sys037

    Article  PubMed  PubMed Central  Google Scholar 

  12. Bingpeng, X., Heshan, L., Zhilan, Z., et al., DNA barcoding for identification of fish species in the Taiwan Strait, PLoS One, 2018, vol. 13, no. 6, art. ID e0198109. https://doi.org/10.1371/journal.pone.0198109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Dayrat, B., Towards integrative taxonomy, Biol. J. Linn. Soc., 2005, vol. 85, no. 3, pp. 407–415. https://doi.org/10.1111/j.1095-8312.2005.00503.x

    Article  Google Scholar 

  14. Deichmann, J.L., Mulcahy, D.G., Vanthomme, H., et al., How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation, PLoS One, 2017, vol. 12, no. 11, art. ID e0187283. https://doi.org/10.1371/journal.pone.0187283

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. DiBattista, J.D., Roberts, M.B., Bouwmeester, J., et al., A review of contemporary patterns of endemism for shallow water reef fauna in the Red Sea, J. Biogeogr., 2016, vol. 43, no. 3, pp. 423–439. https://doi.org/10.1111/jbi.12649

    Article  Google Scholar 

  16. Fish Statistics Yearbook, 2019, Cairo: Gen. Auth. Fish Resour. Dev., 2019, vol. 27.

  17. Folmer, O., Black, M., Hoeh, W., et al., DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates, Mol. Mar. Biol. Biotechnol., 1994, vol. 3, no. 5, pp. 294–299.

    CAS  PubMed  Google Scholar 

  18. Froese, R. and Pauly, D., FishBase, in Species 2000 & ITIS Catalogue of Life, Roskov, Y., Abucay, L., Orrell, T., et al., Eds., Leiden: Species 2000: Naturalis, 2017. https://www.catalogueoflife.org/col.

  19. Galal-Khallaf, A., Osman, A.G.M., El-Ganainy, A., et al., Mitochondrial genetic markers for authentication of major Red Sea grouper species (Perciformes: Serranidae) in Egypt: a tool for enhancing fisheries management and species conservation, Gene, 2019, vol. 689, pp. 235–245 https://doi.org/10.1016/j.gene.2018.12.021

    Article  CAS  PubMed  Google Scholar 

  20. Golani, D. and Fricke, R., Checklist of the Red Sea fishes with delineation of the Suez Gulf, Gulf of Aqaba, endemism and Lessepsian migrants, Zootaxa, 2018, vol. 4509, no. 1, pp. 1–215. https://doi.org/10.11646/zootaxa.4509.1.1

    Article  PubMed  Google Scholar 

  21. Golani, D. and Ritte, U., Genetic relationship in goat fishes (Mullidae: Perciformes) of the Red Sea and the Mediterranean, with remarks on Suez Canal migrants, Sci. Mar., 1999, vol. 63, no. 2, pp. 129–135. https://doi.org/10.3989/scimar.1999.63n2129

    Article  Google Scholar 

  22. Hajibabaei, M., Singer, G.A., Hebert, P.D., and Hickey, D.A., DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics, Trends Genet., 2007, vol. 23, no. 4, pp. 167–172. https://doi.org/10.1016/j.tig.2007.02.001

    Article  CAS  PubMed  Google Scholar 

  23. Hall, T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser., 1999, vol. 41, pp. 95–98.

    CAS  Google Scholar 

  24. Halldén, C., Nilsson, N.O., Rading, I.M., and Säll, T., Evaluation of RFLP and RAPD markers in a comparison of Brassica napus breeding lines, Theor. Appl. Genet., 1994, vol. 88, pp. 123–128. https://doi.org/10.1007/BF00222404

    Article  PubMed  Google Scholar 

  25. Hebert, P.D., Cywinska, A., Ball, S.L., and deWaard, J.R., Biological identifications through DNA barcodes, Proc. R. Soc. B, 2003, vol. 270, pp. 313–321. https://doi.org/10.1098/rspb.2002.2218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Hinchliff, C.E. and Smith, S.A., Some limitations of public sequence data for phylogenetic inference (in plants), PLoS One, 2014, vol. 9, no. 7, art. ID e98986. https://doi.org/10.1371/journal.pone.0098986

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Hubert, N., Hanner, R., Holm, E., et al., Identifying Canadian freshwater fish through DNA barcodes, PLoS One, 2008, vol. 3, no. 6, art. ID e2490. https://doi.org/10.1371/journal.pone.0002490

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Ibrahim, N., Abbas, E. M., El-Seedy, A., et al., DNA barcoding and comparative genetic diversification among species of family Sparidae in the coastal waters of Egypt, Egypt. J. Aquat. Biol. Fish., 2020, vol. 24, no. 3, pp. 333–349. https://doi.org/10.21608/EJABF.2020.91939

    Article  Google Scholar 

  29. Johnston, I.G. and Williams, B.P., Evolutionary inference across eukaryotes identifies specific pressures favoring mitochondrial gene retention, Cell Syst., 2016, vol. 2, pp. 101–111. https://doi.org/10.1016/j.cels.2016.01.013

    Article  CAS  PubMed  Google Scholar 

  30. Jukes, T.H. and Cantor, C.R., Evolution of protein molecules, in Mammalian Protein Metabolism, Munro, H.N., Ed., New York: Academic, 1969.

    Google Scholar 

  31. Kemp, J.M., Zoogeography of the coral reef fishes of the northeastern Gulf of Aden, with eight new records of coral reef fishes from Arabia, Fauna Arab., 2000, vol. 18, pp. 293–322.

    Google Scholar 

  32. Keskin, E. and Atar, H.H., DNA barcoding commercially important fish species of Turkey, Mol. Ecol. Res., 2013, vol. 13, no. 5, pp. 788–797. https://doi.org/10.1111/1755-0998.12120

    Article  CAS  Google Scholar 

  33. Kimura, M., A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, J. Mol. Evol., 1980, vol. 16, no. 2, pp. 111–120. https://doi.org/10.1007/BF01731581

    Article  CAS  PubMed  Google Scholar 

  34. Kochzius, M., Antoniou, A., Botla, S., et al., Identifying fishes through DNA barcodes and microarrays, PLoS One, 2010, vol. 5, no. 9, art. ID e12620. https://doi.org/10.1371/journal.pone.0012620

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K., MEGA X: molecular evolutionary genetics analysis across computing platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Lakra, W.S., Verma, M.S., Goswami, M., Lal, K.K., Mohindra, V., Punia, P., Gopalakrishnan, A., Singh, K.V., Ward, R.D., and Hebert, P., DNA barcoding Indian marine fishes, Mol. Ecol. Resour., 2011, vol. 11, no. 1, pp. 60–71. https://doi.org/10.1111/j.1755-0998.2010.02894.x

    Article  CAS  PubMed  Google Scholar 

  37. Landi, M., Dimech, M., Arculeo, M., et al., DNA barcoding for species assignment: the case of Mediterranean marine fishes, PLoS One, 2014, vol. 9 no. 9, art. ID e106135. https://doi.org/10.1371/journal.pone.0106135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Lleonart, J., Taconet, M., and Lamboeuf, M., Integrating information on marine species identification for fishery purposes, Mar. Ecol.: Prog. Ser., 2006, vol. 316, pp. 231–238. https://doi.org/10.3354/meps316231

    Article  Google Scholar 

  39. Mehanna, S. and El-Gammal, F., Suez Gulf fisheries: current status, assessment and management, J. King Abdulaziz Univ., Mar. Sci., 2007, vol. 18, no. 1, pp. 3–18. https://doi.org/10.4197/mar.18-1.1

    Article  Google Scholar 

  40. Nei, M. and Miller, J.C., A simple method for estimating average number of nucleotide substitutions within and between populations from restriction data, Genetics, 1990, vol. 125, no. 4, pp. 873–879.

    Article  CAS  Google Scholar 

  41. Neumann, A.C. and McGill, D.A., Circulation of the Red Sea in early summer, Deep-Sea Res., 1961, vol. 8, nos. 3–4, pp. 223–235. https://doi.org/10.1016/0146-6313(61)90023-5

    Article  Google Scholar 

  42. Nneji, L.M., Adeola, A.C., Okeyoyin, A.O., et al., Assessing the effectiveness of molecular data for species identification and diversity studies of Nigerian herpetofauna, Mitochondrial DNA, Part B, 2019, vol. 4 no. 1, pp. 589–593. https://doi.org/10.1080/23802359.2018.1561219

    Article  Google Scholar 

  43. Pappalardo, A.M., Cuttitta, A., Sardella, A., et al., DNA barcoding and COI sequence variation in Mediterranean lantern fishes larvae, Hydrobiologia, 2015, vol. 749, pp. 155–167. https://doi.org/10.1007/s10750-014-2161-5

    Article  CAS  Google Scholar 

  44. Por, F.D., Lessepsian Migration: The Influx of Red Sea Biota into the Mediterranean by Way of the Suez Canal, Ecol. Stud. Ser., vol. 23, Berlin: Springer-Verlag, 1978, pp 1–229.

  45. Puillandre, N., Lambert, A., Brouillet, S., and Achaz, G., ABGD, Automatic Barcode Gap Discovery for primary species delimitation, Mol. Ecol., 2011, vol. 21, no. 8, pp. 1864–1877. https://doi.org/10.1111/j.1365-294X.2011.05239.x

    Article  PubMed  Google Scholar 

  46. Rasmussen, H., Scheier, M., and Greenhouse, J., Optimism and physical health: a meta-analytic review, Ann. Behav. Med., 2009, vol. 37, no. 3, pp. 239–256. https://doi.org/10.1007/s12160-009-9111-x

    Article  PubMed  Google Scholar 

  47. Ratnasingham, S. and Hebert, P.D.N., A DNA-based registry for all animal species: the Barcode Index Number (BIN) system, PLoS One, 2013, vol. 8, no. 7, art. ID e66213. https://doi.org/10.1371/journ al.pone.0066213

  48. Roberts, C.M., McClean, C.J., Veron, J.E.N., et al., Marine biodiversity hotspots and conservation priorities for tropical reefs, Science, 2002, vol. 295, no. 5558, pp. 1280–1284. https://doi.org/10.1126/science.1067728

    Article  CAS  PubMed  Google Scholar 

  49. Rozas, J., Ferrer-Mata, A., Sánchez-DelBarrio, J.C., et al., DnaSP 6: DNA sequence polymorphism analysis of large data sets, Mol. Biol. Evol., 2017, vol. 34, no. 12, pp. 3299–3302. https://doi.org/10.1093/molbev/msx248

    Article  CAS  PubMed  Google Scholar 

  50. Saitou, N. and Nei, M., The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 1987, vol. 4, no. 4, pp. 406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

    Article  CAS  PubMed  Google Scholar 

  51. Samuels, D.C., Life span is related to the free energy of mitochondrial DNA, Mech. Ageing Dev., 2005, vol. 126, pp. 1123–1129. https://doi.org/10.1016/j.mad.2005.05.003

    Article  CAS  PubMed  Google Scholar 

  52. Steinke, D., Zemlak, T., and Hebert, P., Barcoding nemo: DNA-based identifications for the ornamental fish trade, PLoS One, 2009, vol. 4, no. 7, art. ID e6300. https://doi.org/10.1371/journal.pone.0006300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Tikochinski, Y., Shainin, I., Hyams, Y., et al., Genetic evidence for an undescribed species previously considered as Sillago sihama from the northern Red Sea, Mar. Biol. Res., 2013, vol. 9, no. 3, pp. 309–315.

    Article  Google Scholar 

  54. Triantafyllidis, A., Bobori, D., Koliamitra, C., et al., DNA barcoding analysis of fish species diversity in four north Greek lakes, Mitochondrial DNA, 2011, vol. 22, suppl. 1, pp. 37–42. https://doi.org/10.3109/19401736.2010.542242

    Article  CAS  PubMed  Google Scholar 

  55. Trivedi, S., Affan, R., Alessa, A., et al., DNA barcoding of Red Sea fishes from Saudi Arabia—the first approach, DNA Barcodes, 2014, vol. 2, pp. 17–20. https://doi.org/10.2478/dna-2014-0003

    Article  Google Scholar 

  56. Trivedi, S., Aloufi, A., Ansari, A., and Ghosh, S., Role of DNA barcoding in marine biodiversity assessment and conservation: an update, Saudi J. Biol. Sci., 2016, vol. 23, no. 2, pp. 161–171. https://doi.org/10.1016/j.sjbs.2015.01.001

    Article  CAS  PubMed  Google Scholar 

  57. Wang, Y.H., Duan, J.N, Shi, H.L., et al., Species identification of small fish in Xixuan Island coastal waters of Zhoushan using DNA barcoding, J. Appl. Ichthyol., 2020, vol. 36, pp. 75– 84. https://doi.org/10.1111/jai.13995

    Article  CAS  Google Scholar 

  58. Ward, R.D., Zemlak, T.S., Innes, B.H., Last, P.R., and Hebert, P.D.N., DNA barcoding Australia’s fish species, Philos. Trans. R. Soc., B, 2005, vol. 360, no. 1462, pp. 1847–1857. https://doi.org/10.1098/rstb.2005.1716

  59. Ward, R.D., Hanner, R.H., and Hebert, P.D.N., The campaign to DNA barcode all fishes, FISH–BOL, J. Fish Biol., 2009, vol. 74, no. 2, pp. 329–356. https://doi.org/10.1111/j.1095-8649.2008.02080.x

    Article  CAS  PubMed  Google Scholar 

  60. Weigt, L., Driskell, A., Baldwin, C., and Ormos, A., DNA barcoding fishes, Methods Mol. Biol., 2012, vol. 858, pp. 109–126. https://doi.org/10.1007/978-1-61779-591-6_6

    Article  CAS  PubMed  Google Scholar 

  61. Zhang, J. and Hanner, R., DNA barcoding is a useful tool for the identification of marine fishes from Japan, Biochem. Syst. Ecol., 2011, vol. 39, pp. 31–42. https://doi.org/10.1016/j.bse.2010.12.017

    Article  CAS  Google Scholar 

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ACKNOWLEDGMENTS

We deeply thank Dr. Ahmed Mamoon (Faculty of Agriculture Al-Azhar University, Nasr City, Cairo, Egypt) for his assistance in sequencing procedure.

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Authors and Affiliations

  1. Aquaculture Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt

    E. M. Abbas & F. S. Ali

  2. Genetics Department, Faculty of Agriculture, Menoufia University, Shibin El-Kom, Egypt

    M. Ismail

  3. Fisheries Division, National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt

    A. El-Ganainy

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  1. E. M. Abbas
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Statement on the welfare of animals. Ethical approval did not require as the samples were collected from the commercial fisheries then transferred frozen to the laboratory.

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Abbas, E.M., Ismail, M., El-Ganainy, A. et al. First DNA Barcoding-based Inventory of Suez Gulf Fishes in Egypt and its Implication for Species Diversity. J. Ichthyol. 61, 386–395 (2021). https://doi.org/10.1134/S0032945221030012

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