Academic Scientific JournalsDNA barcoding of commercially important marine fish species Hipposcarus harid from the central Red Sea, Saudi Arabia
DOI:
https://doi.org/10.26881/oahs-2024.2.02Keywords:
mitochondrial DNA, COI genes, marine fish, coral reef fish, fish populationAbstract
In this study, the collected fish species were identified based on morphological observations and then evaluated by DNA barcoding. The COI gene has been recognized as a biological marker for fish species identification and the objective of this study is to analyze the variable region of the COI gene in subunit I. The mitochondrial cytochrome (COI) oxidase subunit I gene was analyzed as a suitable molecular maker for the identification of three specimens of the fish species Hipposcarus harid, widely distributed in the Red Sea. The COI gene sequences in the variable region revealed variations among the fish species. The COI gene sequences in the variable region were similar to the variable region of Hipposcarus harid collected from the Northern Red Sea and all three were named: H. harid H13, H. harid H2c, and H. harid H12. The identification of the fish species collected from the Red Sea in Saudi Arabia would help ichthyologists improve the management, conservation and monitoring of economically important long-nose parrotfish species in Saudi Arabia.
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Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research, 25, 3389–3402. https:// doi.org/10.1093/nar/25.17.3389 PMID:9254694.
Alwany, M. A., Thaler, E., & Stachowitsch, M. (2009). Parrotfish bioerosion on Egyptian Red Sea reefs. Journal of Experimental Marine Biology and Ecology, 371, 170–176. https://doi.org/10.1016/j.jembe.2009.01.019.
Antil, S., Abraham, J. S., Sripoorna, S., Maurya, S., Dagar, J., Makhija, S., Bhagat, P., Gupta, R., Sood, U., Lal, R., & Toteja, R. (2023). DNA barcoding, an effective tool for species identification: A review. Molecular Biology Reports, 50(1), 761–775. https://doi.org/10.1007/s11033-022-08015-7. PMID:36308581.
Bektas, Y., Aksu, İ., Kaya, C., Bayçelebi, E., & Turan, D. (2022). DNA barcoding and species delimitation of the genus Oxynoemacheilus (Teleostei: Nemacheilidae) in Anatolia. Journal of Fish Biology, 101(3), 505–514. https://doi.org/10.1111/jfb.15114 PMID:35607971.
Bingpeng, X., Heshan, L., Zhilan, Z., Chunguang, W., Yanguo, W., Jianjun, W. (2018). DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One, 13(6), e0198109. https://doi.org/10.1371/journal.pone.0198109.
Bhattacharjee, M. J., Laskar, B. A., Dhar, B., & Ghosh, S. K. (2012). Identification and re-evaluation of freshwater catfishes through DNA barcoding. PLoS One, 7, e49950. Advance online publication. https://doi.org/10.1371/journal.pone.0049950 PMID:23166801.
Cermakova, E., Lencova, S., Mukherjee, S., Horka, P., Vobruba, S., Demnerova, K., & Zdenkova, K. (2023). Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art. Foods, 12(1), 228. https:// doi.org/10.3390/foods12010228 PMID:36613444.
Charendoff, J. A., Edwards, C. B., Pedersen, N. E., Petrovic, V., Zgliczynski, B., Sandin, S. A., & Smith, J. E. (2023, June 10). Variability in composition of parrotfish bite scars across space and over time on a central Pacific atoll. Coral Reefs, 42, 905–918. Advance online publication. https://doi.org/10.1007/s00338-023-02392-6.
Chakraborty, C., Doss, C. G. P., Patra, B. C., & Bandyopadhyay, S. (2014). DNA barcoding to map the microbial communities: Current advances and future directions. Applied Microbiology and Biotechnology, 98(8), 3425–3436. https://doi.org/10.1007/s00253-014-5550-9 PMID:24522727.
Chakraborty, M., & Ghosh, S. K. (2014). An assessment of the DNA barcodes of Indian freshwater fishes. Gene, 537(1), 20–28. https://doi.org/10.1016/j.gene.2013.12.047 PMID:24378233.
Chang, C. H., Shao, K. T., Lin, H. Y., Chiu, Y. C., Lee, M. Y., Liu, S. H., & Lin, P. L. (2017). DNA barcodes of the native rayfinned fishes in Taiwan. Molecular Ecology Resources, 17(4), 796–805. https://doi.org/10.1111/1755-0998.12601 PMID:27717215.
Dawson, T. P., Jackson, S. T., House, J. I., Prentice, I. C., & Mace, G. M. (2011). Beyond predictions: Biodiversity conservation in a changing climate. Science, 332, 53–58. https://doi. org/10.1126/science.1200303 PMID:21454781.
Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797. https://doi.org/10.1093/nar/ gkh340 PMID:15034147.
FAO. (2018). Fishery and aquaculture statistics. Global Capture Production 1950-2016 (FishstatJ). FAO Fisheries and Aquaculture Department, Rome. www.fao.org/fishery/ statistics/software/fishstatj/en.
Fišer Pečnikar, Ž., & Buzan, E. V. (2014). 20 years since the introduction of DNA barcoding: From theory to application. Journal of Applied Genetics, 55(1), 43–52. https://doi. org/10.1007/s13353-013-0180-y PMID:24203863.
Friedlander, A. M., Donovan, M. K., Stamoulis, K. A., Williams, I. D., Brown, E. K., Conklin, E. J., DeMartini, E. E., Rodgers, K. S., Sparks, R. T., & Walsh, W. J. (2018). Human-induced gradients of reef fish declines in the Hawaiian Archipelago viewed through the lens of traditional management boundaries. Aquatic Conservation, 28, 146–157. https://doi.org/10.1002/aqc.2832.
Folmer, O., Black, M., Hoeh, W., Lutz, R., & Vrijenhoek, R. (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology, 3, 294–299. PMID:7881515.
Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings. Biological Sciences, 270(1512), 313–321. https://doi.org/10.1098/rspb.2002.2218 PMID:12614582.
Hollingsworth, P. M., Graham, S. W., & Little, D. P. (2011). Choosing and using a plant DNA barcode. PLoS One, 6(5), e19254. https://doi.org/10.1371/journal.pone.0019254 PMID:21637336.
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., & Bernatchez, L. (2008). Identifying Canadian freshwater fishes through DNA barcodes. PLoS One, 3, e2490. Advance online publication. https://doi.org/10.1371/journal.pone.0002490 PMID:22423312.
Hubert, N., Meyer, C. P., Bruggemann, H. J., Guérin, F., Komeno, R. J., Espiau, B., Causse, R., Williams, J. T., & Planes, S. (2012). Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centreof-overlap hypothesis. PLoS One, 7, e28987. https://doi. org/10.1371/journal.pone.0028987 PMID:22438862.
Kar, C., Purkayastha, A., Limna Mol, V. P., & Sureshkumar, S. (2022). Comprehensive review and diversity analysis of coral-reef associated fishes from Southern India. Regional Studies in Marine Science, 56, 102657. Advance online publication. https://doi.org/10.1016/j.rsma.2022.102657.
Karahan, A., Douek, J., Paz, G., Stern, N., Kideys, A. E., Shaish, L., Goren, M., & Rinkevich, B. (2017). Employing DNA barcoding as taxonomy and conservation tools for fish species censuses at the southeastern Mediterranean, a hot-spot area for biological invasion. Journal for Nature Conservation. 36: 1–9. Advance online publication. https://doi.org/10.1016/j.jnc.2017.01.004.
Lakra, W. S., Verma, M. S., Goswami, M., Lal, K. K., Mohindra, V., Punia, P., Gopalakrishnan, A., Singh, K. V., Ward, R. D., & Hebert, P. (2011). DNA barcoding Indian marine fishes. Molecular Ecology Resources, 11(1), 60–71. https://doi.org/10.1111/j.1755-0998.2010.02894.x PMID:21429101.
Lara, A., Ponce de León, J. L., Rodríguez, R., Casane, D., Côté, G., Bernatchez, L., & García-Machado, E. (2010). DNA barcoding of Cuban freshwater fishes: Evidence for cryptic species and taxonomic conflicts. Molecular Ecology Resources, 10(3), 421–430. https://doi.org/10.1111/j.1755-0998.2009.02785.x PMID:21565041.
Lokrantz, J., Nystrom, M., Thyresson, M., & Johansson, C. (2008). The non-linear relationship between body size and function in parrotfishes. Coral Reefs, 27, 967–974. https:// doi.org/10.1007/s00338-008-0394-3.
Macali, A., Semenov, A., Paladini de Mendoza, F., Dinoi, A., Bergami, E., & Tiralongo, F. (2020). Relative influence of environmental factors on biodiversity and behavioural traits of a rare mesopelagic fish, Trachipterus trachypterus (Gmelin, 1789), in a continental shelf front of the Mediterranean Sea. Journal of Marine Science and Engineering, 8(8), 581. https://doi.org/10.3390/ jmse8080581.
Meier, R., Zhang, G. Y., & Ali, F. (2008). The Use of Mean Instead of Smallest Interspecific Distances Exaggerates the Size of the “Barcoding Gap” and Leads to Misidentification. Systematic Biology 57(5): 809–13. Advance online publication. https://doi.org/10.1080/10635150802406343.
Radulovici, A. E., Archambault, P., & Dufresne, F. (2010). DNA barcodes for marine biodiversity: Moving fast forward? Diversity, 2, 450–472. https://doi.org/10.3390/d2040450.
Schindel, D. E., Stoeckle, M. Y., Milensky, C., Trizna, M., Schmidt, B., Gebhard, C., & Graves, G. (2011). Project description: DNA barcodes of bird species in the national museum of natural history, smithsonian institution, USA. ZooKeys, 152, 87–92. https://doi.org/10.3897/zookeys.152.2473 PMID:22287908.
Shan, B., Liu, Y., Yang, C., Zhao, Y., Zhang, G., Wu, Q., & Sun, D. (2021). DNA barcoding of fish in mischief reef—Fish diversity of a reef fish community from Nansha Islands. Frontiers in Marine Science, 7, 618954. https://doi.org/10.3389/fmars.2020.618954.
Shellem, C. T., Ellis, J. I., Coker, D. J., & Berumen, M. L. (2021). Red Sea fish market assessments indicate high species diversity and potential overexploitation. Fisheries Research, 239, 105922. https://doi.org/10.1016/j.fishres.2021.105922.
Steinke, D., Zemlak, T. S., Boutillier, J. A., & Hebert, P. D. (2009). DNA barcoding of Pacific Canada’s fishes. Marine Biology, 156(12), 2641–2647. https://doi.org/10.1007/s00227-009-1284-0.
Takahara, T., Minamoto, T., & Doi, H. (2013). Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS One, 8, e56584. Advance online publication. https://doi.org/10.1371/ journal.pone.0056584 PMID:23437177.
Tavares, E. S., & Baker, A. J. (2008). Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evolutionary Biology, 8(1), 81. https://doi. org/10.1186/1471-2148-8-81 PMID:18328107.
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673–4680. https://doi. org/10.1093/nar/22.22.4673 PMID:7984417.
Trontelj, P., Machino, Y., & Sket, B. (2005). Phylogenetic and phylogeographic relationships in the crayfish genus Austropotamobius inferred from mitochondrial COI gene sequences. Molecular Phylogenetics and Evolution, 34(1), 212–226. https://doi.org/10.1016/j.ympev.2004.09.010 PMID:15579394.
Valentini, A., Pompanon, F., & Taberlet, P. (2009). DNA barcoding for ecologists. Trends in Ecology & Evolution, 24(2), 110–117. https://doi.org/10.1016/j.tree.2008.09.011 PMID:19100655.
van Rooij, J. M., Bruggemann, J. H., Videler, J. J., & Breeman, A. M. (1995). Plastic growth of the herbivorous reef fish Sparisomaviride—Field evidence for a trade-off between growth and reproduction. Marine Ecology Progress Series, 122, 93–105. https://doi.org/10.3354/meps122093.
Wang, W., Ma, C., Chen, W., Zhang, H., Kang, W., Ni, Y., & Ma, L. (2017). Population genetic diversity of Chinese sea bass (Lateolabrax maculatus) from southeast coastal regions of China based on mitochondrial COI gene sequences. Biochemical Systematics and Ecology, 71, 114–120. https://doi.org/10.1016/j.bse.2017.01.002.
Weigt, L. A., Baldwin, C. C., Driskell, A., Smith, D. G., Ormos, A., & Reyier, E. A. (2012). Using DNA barcoding to assess Caribbean reef fish biodiversity: Expanding taxonomic and geographic coverage. PLoS One, 7, e41059. https://doi.org/10.1371/journal.pone.0041059 PMID:22815912.
Zhang, J. B., & Hanner, R. (2011). DNA barcoding is a useful tool for the identification of marine fishes from Japan. Biochemical Systematics and Ecology 39(1), 31–42. Advance online publication. https://doi.org/10.1016/j. bse.2010.12.017.
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1847–1857. https://doi.org/10.1098/rstb.2005.1716 PMID:16214743.
Xu, L., Van Damme, K., Li, H., Ji, Y., Wang, X., & Du, F. (2019). A molecular approach to the identification of marine fish of the Dongsha Islands (South China Sea). Fisheries Research, 213, 105–112. https://doi.org/10.1016/j.fishres.2019.01.011.
Zhang, D. X., & Hewitt, G. M. (1996). Nuclear integrations: Challenges for mitochondrial DNA markers. Trends in Ecology & Evolution, 11(6), 247–251. https://doi.org/10.1016/0169-5347(96)10031-8.
Zou, R., Liang, C., Dai, M., Wang, X., Zhang, X., & Song, Z. (2020). DNA barcoding and phylogenetic analysis of bagrid catfish in China based on mitochondrial COI gene. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis, 31(2), 73–80. https://doi.org/10.1080/24701394.2020.1735379 PMID:32126856.
