• icon+90(535) 849 84 68
  • iconnwsa.akademi@hotmail.com
  • icon Fırat Akademi Samsun-Türkiye

> Detaylı Arama

Article Details

Article Details

  • Article Code : FIRAT-AKADEMI-9241-5791
  • Article Type : Derleme
  • Publication Number : 5A0238
  • Page Number : 144-153
  • Doi : 10.12739/NWSA.2025.20.4.5A0238
  • Abstract Reading : 125
  • Download : 36
  • Atıf Sayısı : 0
  • Share :

  • PDF Download

Issue Details

  • Year : 2025
  • Volume : 20
  • Issue : 4
  • Number of Articles Published : 4
  • Published Date : 1.10.2025

Cover Download Context Page Download
Dergi Kapağı
Ecological Life Sciences

Serial Number : 5A
ISSN No. : 1308-7258
Release Interval (in a Year) : 4 Issues

Sibel DOĞAN 1 , Hediye Gozbil2

Keywords

USING MITOCHONDRIAL GENOMES AND COI-BASED DNA BARCODING IN AQUACULTURE

Sibel DOĞAN 1 , Hediye Gozbil2

Aquatic resources constitute one of the most important biological assets worldwide in terms of natural ecosystems, human nutrition, and economic sustainability. The effective management of fisheries and aquaculture activities is closely linked to accurate species identification, monitoring of biodiversity, and the elucidation of genetic stock structure. In this context, the mitochondrial genome (mtDNA) has become a widely used molecular marker in fisheries research due to its small genome size, relatively high mutation rate, maternal inheritance, and lack of recombination. The mitochondrial cytochrome c oxidase subunit I (COI) gene is recognized as the standard DNA barcode region for animals and enables rapid, reliable, and highly accurate identification of fish species in particular. COI-based DNA barcoding provides significant advantages in the identification of morphologically similar species, the detection of cryptic taxa, and the assessment of both intra- and interspecific genetic variation. Furthermore, COI barcode data are effectively utilized to investigate the population structure, phylogenetic relationships, and evolutionary history of fish species.

Keywords
Aquaculture, mitochondrial DNA, DNA Barcoding, Cytochrome C Oxidase Subunit I (COI), Species Identification,

Details
   

Authors

Sibel DOĞAN (1) (Corresponding Author)
Fırat University
sbarata@firat.edu.tr | 0000-0003-4569-5435

Hediye Gozbil (2)

Tarim ve Orman Bakanligi
hediyediyar@gmail.com | 0009-0006-8759-2951

Supporting Institution

 :

Project Number

 :

Thanks

 :
References
[1] Elyasigorji, Z., Izadpanah, M., Hadi, F., et al. (2023). Mitochondrial genes as strong molecular markers for species identification. Nucleus, 66(1):81–93. https://doi.org/10.1007/s13237-022-00393-4

[2] Xing, B., Lin, L., and Wu, Q., (2025). Application of mitochondrial genomes to species identification and evolution. Electronic Journal of Biotechnology, 76:39–48.

[3] Ladoukakis, E.D. and Zouros, E., (2017). Evolution and inheritance of animal mitochondrial DNA: Rules and exceptions. Journal of Biological Research–Thessaloniki, 24:2.

[4] Dong, Z., Wang, Y., Li, C., et al., (2021). Mitochondrial DNA as a molecular marker in insect ecology: Current status and future prospects. Annals of the Entomological Society of America, 114(4):470–476. https://doi.org/10.1093/aesa/saab020

[5] Gendron, E.M., Qing, X., Sevigny, J.L., et al., (2024). Comparative mitochondrial genomics in Nematoda reveal variation in compositional biases and substitution rates. BMC Genomics, 25(1):615. https://doi.org/10.1186/s12864-024-10500-1

[6] Keskin, E. and Atar, H.H., (2013). DNA barcoding commercially important fish species of Turkey. Molecular Ecology Resources, 13(5):788–797.

[7] Zangl, L., Daill, D., Schweiger, S., Gassner, G., and Koblmüller, S., (2020). A reference DNA barcode library for Austrian amphibians and reptiles. PLoS ONE, 15(3):e0229353.

[8] Bucklin, A., Peijnenburg, K.T.C.A., Kosobokova, K.N., et al., (2021). Toward a global reference database of COI barcodes for marine zooplankton. Marine Biology, 168:78. https://doi.org/10.1007/s00227-021-03887-y

[9] Bingpeng, X., Heshan, L., Zhilan, Z., Chunguang, W., Yanguo, W., and 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

[10] Hahn, A. and Zuryn, S., (2019). Mitochondrial genome mutations that generate reactive oxygen species. Antioxidants, 8(9):392. https://doi.org/10.3390/antiox8090392.

[11] Nosek, J. and Tomáška, L., (2003). Mitochondrial genome diversity: Evolution of the molecular architecture and replication strategy. Current Genetics, 44:73–84.

[12] Roger, A.J., Muñoz-Gómez, S.A., and Kamikawa, R., (2017). The origin and diversification of mitochondria. Current Biology, 27(21):R1177–R1192.

[13] Zardoya, R., (2020). Recent advances in understanding mitochondrial genome diversity. F1000Research, 9:270.

[14] Sato, M. and Sato, K., (2013). Maternal inheritance of mitochondrial DNA by diverse mechanisms. Biochimica et Biophysica Acta, 1833(8):1979–1984.

[15] Allio, R., Donega, S., Galtier, N., et al., (2017). Large variation in the ratio of mitochondrial to nuclear mutation rate across animals: Implications for genetic diversity and the use of mitochondrial DNA as a molecular marker. Molecular Biology and Evolution, 34(11):2762–2772. https://doi.org/10.1093/molbev/msx197

[16] Patwardhan, A., Ray, S., and Roy, A., (2014). Molecular markers in phylogenetic studies: A review. Journal of Phylogenetics and Evolutionary Biology, 2(2):131.

[17] Gendron, E.M., Sevigny, J.L., Byiringiro, I., et al., (2023). Nematode mitochondrial metagenomics: A new tool for biodiversity analysis. Molecular Ecology Resources, 23(5):975–989. https://doi.org/10.1111/1755-0998.13761

[18] Thomsen, P.F. and Willerslev, E., (2015). Environmental DNA: An emerging tool in conservation. Biological Conservation, 183:4–18.

[19] Hebert, P.D.N., (2003). Cytochrome c oxidase I divergence among closely related species. Proceedings of the Royal Society B, 270:S96–S99.

[20] Hebert, P.D.N. and Gregory, T.R., (2005). The promise of DNA barcoding. Systematic Biology, 54(5):852–859.

[21] White, D.J., Wolff, J.N., Pierson, M., et al., (2008). Revealing the complexities of mtDNA inheritance. Molecular Ecology, 17(23):4925–4942.

[22] Rubinoff, D. and Holland, B.S., (2005). Mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic inference. Systematic Biology, 54(6):952–961.

[23] Barata, S.D., Dörücü, M., and Gürses, M., (2022). Identification and Molecular Investigation of Diplostomum in Capoeta umbla Caught from Freshwater Sources, Turkey. Genetics of Aquatic Organisms, 6(2):GA454. http://doi.org/10.4194/GA454

[24] Barata, S.D., Dörücü, M., Saglam, N., Gürses, M., and Otlu, Ö., (2023). Molecular Diversity of Diplostomum spathaceum (Digenea: Diplostomidae) on the Capoeta umbla and Cyprinus carpio (Cypriniformes) Using Mitochondrial DNA Barcode. Turkish Journal of Fisheries and Aquatic Sciences, 23(2):TRJFAS20576. https://doi.org/10.4194/TRJFAS20576

[25] Bucklin, A., Steinke, D., and Blanco-Bercial, L., (2011). DNA barcoding of marine Metazoa. Annual Review of Marine Science, 3:471–508.

[26] Li, M., Schönberg, A., Schaefer, M., et al., (2010). Detecting heteroplasmy from mtDNA genomes. American Journal of Human Genetics, 87(2):237–249.

[27] Ivanova, N.V., Zemlak, T.S., Hanner, R.H., and Hebert, P.D.N. (2007). Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes, 7(4):544–548.

[28] Ward, R.D., Costa, F.O., Holmes, B.H., and Steinke, D., (2005). DNA barcoding of fishes. Philosophical Transactions of the Royal Society B, 360:1847–1857.

[29] Ward, R.D., Hanner, R., and Hebert, P.D.N., (2009). The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology, 74:329–356.

[30] Ward, R.D., Costa, F.O., Holmes, B.H., and Steinke, D., (2008). DNA barcoding of shared fish species from the North Atlantic and Australasia. Aquatic Biology, 3:71–78.

[31] Zemlak, T.S., Ward, R.D., Connell, A.D., Holmes, B.H., and Hebert, P.D.N., (2009). DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources, 9(1):237–242.

[32] Hubert, N., Hanner, R., Holm, E., et al., (2008). Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE, 3(6):e2490.