Pertanika Journal of Tropical Agricultural Science
Pertanika Journal Home Facebook
Pertanika · Universiti Putra Malaysia Press

Pertanika Journal of Tropical Agricultural Science

Official journal of Universiti Putra Malaysia for peer-reviewed research across tropical agriculture and allied agricultural sciences.

e-ISSN 2231-8542 ISSN 1511-3701
Browse latest issue Author guidelines Submit Here
Research article

Species Identification of Sea Bamboo (Isis hippuris) using COI-based DNA Barcoding

La Ode Alirman Afu, Anis Chamidah, Uun Yanuhar and Maftuch

Volume 46, Issue 4 November 2023 Published 27 November 2023
https://doi.org/10.47836/pjtas.46.4.17
KeywordsCOI gene analysis, conservation, DNA barcoding, management strategies, sea bamboo (Isis hippuris)
Article content

Abstract

Conservation and effective management of marine ecosystems and biodiversity requires accurate species identification. This study classifies sea bamboo (Isis hippuris) specimens using DNA barcoding, a technique widely recognized for its speed, accuracy, and objectivity. This study examines the cytochrome c oxidase subunit I (COI) gene analysis for species identification. Isis hippuris was collected from two stations (coral and seagrass areas) of Tanjung Tiram Waters, South Konawe, Southeast Sulawesi. Genomic DNA was extracted from the base, main, and lateral stem of I. hippuris. Polymerase chain reaction (PCR) was used to amplify the mtDNA of I. hippuris with HCO2198 and LCO1490 primers. The highest quality PCR product based on the COI gene was chosen for sequencing analysis. The study revealed that COI gene analysis could only be performed on the base and main stem of the I. hippuris. Samples from coral and seagrass-coral areas on lateral stems were not further analyzed due to low concentration and purity values, which could potentially fail DNA sequencing. Each part of I. hippuris may have unique genetic differences. This study highlights the advantages of DNA sequencing in providing a unique genetic fingerprint for each species, enabling accurate species identification. This research provides insight into using DNA barcoding for sea bamboo species identification.
Supporting literature

References

  1. Bineesh, K. K., Gopalakrishnan, A., Akhilesh, K. V., Sajeela, K. A., Abdussamad, E. M., Pillai, N. G. K., Basheer, V. S., Jena, J. K., & Ward, R. D. (2017). DNA barcoding reveals species composition of sharks and rays in the Indian commercial fishery. Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 28(4), 458–472. https://doi.org/10.3109/19401736.2015.1137900
  2. 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
  3. Ceruso, M., Mascolo, C., Anastasio, A., Pepe, T., & Sordino, P. (2019). Frauds and fish species authentication: Study of the complete mitochondrial genome of some Sparidae to provide specific barcode markers. Food Control, 103, 36-47. https://doi.org/10.1016/j.foodcont.2019.03.028
  4. Clark, L. F. (2015). The current status of DNA barcoding technology for species identification in fish value chains. Food Policy, 54, 85-94. https://doi.org/10.1016/j.foodpol.2015.05.005
  5. Cooke, S. J., Martins, E. G., Struthers, D. P., Gutowsky, L. F., Power, M., Doka, S. E., Dettmers, J. M., Crook, D. A., Lucas, M. C., Holbrook, C. M., & Krueger, C. C. (2016). A moving target-incorporating knowledge of the spatial ecology of fish into the assessment and management of freshwater fish populations. Environmental Monitoring and Assessment, 188(4), 239. https://doi.org/10.1007/s10661-016-5228-0
  6. Cooper, E. W. T., Torntore, S. J., Leung, A. S. M., Shadbolt, T., & Dawe, C. (2011). Guide to the identification of precious and semi-precious corals in commercial trade. https://www.traffic.org/site/assets/files/5642/guide_to_the_identification_of_precious_and_semi-precious_corals_in_commercial_trade.pdf
  7. Díaz, S., Settele, J., Brondízio, E. S., Ngo, H. T., Guèze, M., Agard, J., Arneth, A., Balvanera, P., Brauman, K., Butchart, S. H., Chan, K. M., Garibaldi, L. A., Ichii, K., Liu, J., Mazhenchery Subramanian, S., Midgley, G., Miloslavich, P., Molnár, Z., Obura, D., … Zayas, C. N. (Eds.). (2019). Summary for policymakers of the global assessment report on biodiversity and ecosystem services. Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. https://doi.org/10.5281/zenodo.3553579
  8. Dieffenbach, C. W., Lowe, T. M., & Dveksler, G. S. (1993). General concepts for PCR primer design. PCR Methods and Applications, 3(3), S30–S37. https://doi.org/10.1101/gr.3.3.s30
  9. Drancourt, M., Bollet, C., Carlioz, A., Martelin, R., Gayral, J. P., & Raoult, D. (2000). 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. Journal of Clinical Microbiology, 38(10), 3623–3630. https://doi.org/10.1128/JCM.38.10.3623-3630.2000
  10. Edrus, I. N., & Suman, A. (2013). Kebijakan perlindungan dan konservasi hewan oktokoralian/bambu laut (Isis hippuris Linnaeus 1758) [Policy for the protection and conservation of octocoralians/sea bamboo (Isis hippuris Linnaeus 1758)]. Jurnal Kebijakan Perikanan Indonesia, 5(2), 107-112. https://doi.org/10.15578/JKPI.5.2.2013.107-112
  11. Han, Z. Q., Gao, T. X., Yanagimoto, T., & Sakurai, Y. (2008). Genetic population structure of Nibea albiflora in the Yellow Sea and East China Sea. Fisheries Science, 74, 544-552. https://doi.org/10.1111/j.1444-2906.2008.01557.x
  12. Hebert, P. D., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B: Biological Sciences, 270(1512), 313-321. https://doi.org/10.1098/rspb.2002.2218
  13. Hellberg, R. S., Pollack, S. J., & Hanner, R. H. (2016). Seafood species identification using DNA sequencing. In A. M. Naaum & R. H. Hanner (Eds.), Food safety and quality systems in developing countries (pp. 113-132). Academic Press. https://doi.org/10.1016/B978-0-12-801592-6.00006-1
  14. Hoegh-Guldberg, O., & Bruno, J. F. (2010). The impact of climate change on the world’s marine ecosystems. Science, 328(5985), 1523-1528. https://doi.org/10.1126/science.1189930
  15. Kumar, A., & Verma, A. K. (2017). Biodiversity loss and its ecological impact in India. International Journal on Biological Sciences, 8(2), 156-160.
  16. Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547-1549. https://doi.org/10.1093/molbev/msy096
  17. Kuske, C. R., Barns, S. M., Grow, C. C., Merrill, L., & Dunbar, J. (2006). Environmental survey for four pathogenic bacteria and closely related species using phylogenetic and functional genes. Journal of Forensic Sciences, 51(3), 548–558. https://doi.org/10.1111/j.1556-4029.2006.00131.x
  18. Laxmi, R., Arya, S., Sultana, A., & Das, S. K. (2015). Assessment and impact of industrial effluents on River Yamuna ecosystem. International Journal of Current Research, 7(9), 19956-19963.
  19. Lind, C. U., Evans, B. S., Knauer, J., Taylor, J. J. U., & Jerry, D. R. (2009). Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima). Aquaculture, 286(1-2), 12-19. https://doi.org/10.1016/j.aquaculture.2008.09.009
  20. Lunt, I. D., Byrne, M., Hellmann, J. J., Mitchell, N. J., Garnett, S. T., Hayward, M. W., Martin, T. G., Mcdonald-maddden, E., Williams, S. E., & Zander, K. K. (2013). Using assisted colonisation to conserve biodiversity and restore ecosystem function under climate change. Biological Conservation, 157, 172–177. https://doi.org/10.1016/j.biocon.2012.08.034
  21. Meriam, T., Wafa, T., Khawla, T., Tarek, H., Abdeljelil, G., & Mhamed, E. (2015). Genetic diversity and population structure of Sepia officinalis from the Tunisian cost revealed by mitochondrial COI sequences. Molecular Biology Reports, 42, 77-86. https://doi.org/10.1007/s11033-014-3743-z
  22. Muhammad, H., Iqbal, Z., Iqbal, M. U., Younas, T., & Bashir, Q. (2016). An efficient method for DNA isolation from fish fin. Pakistan Journal of Agricultural Science, 53(4), 843-850. https://doi.org/10.21162/PAKJAS%2F16.3998
  23. Ovenden, J. R., Berry, O., Welch, D. J., Buckworth, R. C., & Dichmont, C. M. (2013). Ocean’s eleven: A critical evaluation of the role of population, evolutionary and molecular genetics in the management of wild fisheries. Fish and Fisheries, 16(1), 125-159. https://doi.org/10.1111/faf.12052
  24. Ozturk, A. R., & Can, T. (2017). A multiplex primer design algorithm for target amplification of continuous genomic regions. BMC Bioinformatics, 18, 306. https://doi.org/10.1186/s12859-017-1716-7
  25. Palumbi, S. R. (2003). Population genetics, demographic connectivity, and the design of marine reserves. Ecological Applications, 13(sp1), 146-158. https://doi.org/10.1890/1051-0761(2003)013[0146:PGDCAT]2.0.CO;2
  26. Perwati, L. K. (2009). Analisis derajat ploidi dan pengaruhnya terhadap variasi ukuran stomata dan spora pada Adiantum raddianum [Analysis of ploidy degree and its effect on variations in stomata and spore size in Adiantum raddianum]. Bioma: Berkala Ilmiah Biologi, 11(2), 39-44. https://doi.org/10.14710/bioma.11.2.39-44
  27. Pimm, S. L., Jenkins, C. N., Abell, R., Brooks, T. M., Gittleman, J. L., Joppa, L. N., Raven, P. H., Roberts, C. M., & Sexton, J. O. (2014). The biodiversity of species and their rates of extinction, distribution, and protection. Science, 344(6187), 1246752. https://doi.org/10.1126/science.1246752
  28. Posthouwer, C., Veldman, S., Abihudi, S., Otieno, J. N., van Andel, T. R., & de Boer, H. J. (2018). Quantitative market survey of non-woody plants sold at Kariakoo Market in Dar es Salaam, Tanzania. Journal of Ethnopharmacology, 222, 280-287. https://doi.org/10.1016/j.jep.2018.04.039
  29. Ravago-Gotanco, R., & Kim, K. M. (2019). Regional genetic structure of sandfish Holothuria (Metriatyla) scabra populations across the Philippine archipelago. Fisheries Research, 209, 143-155. https://doi.org/10.1016/J.FISHRES.2018.09.021
  30. Saad, Y. (2019). Analysis of 16s mitochondrial ribosomal DNA sequence variations and phylogenetic relations among some Serranidae fishes. South African Journal of Animal Science, 49(1), 80-89. https://doi.org/10.4314/sajas.v49i1.10
  31. Sari, A., Duran, M., Sen, A., & Bardakci, F. (2015). Investigation of Chironomidae (Diptera) relationships using mitochondrial COI gene. Biochemical Systematics and Ecology, 59, 229-238. https://doi.org/10.1016/j.bse.2015.01.005
  32. Thai, B. T., Pham, T. A., & Austin, G. M. (2006). Genetic diversity of common carp in Vietnam using direct sequencing and SSCP analysis of the mitochondrial DNA control region. Aquaculture, 258(1-4), 228-240. https://doi.org/10.1016/j.aquaculture.2006.03.025
  33. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., & Higgins, D. G. (1997). The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25(24), 4876-4882. https://doi.org/10.1093/nar/25.24.4876
  34. Verma, A. K. (2017). Genetic diversity as buffer in biodiversity. Indian Journal of Biology, 4(1), 61-63. https://doi.org/10.21088/ijb.2394.1391.4117.9
  35. Verma, A. K. (2018). Ecological balance: An indispensable need for human. Journal of Experimental Zoology India, 21(1), 407-409.
  36. Wallace, L. J., Boilard, S. M. A. L., Eagle, S. H. C., Spall, J. L., Shokralla, S., & Hajibabaei, M. (2012). DNA barcodes for everyday life: Routine authentication of Natural Health Products. Food Research International, 49(1), 446-452. https://doi.org/10.1016/j.foodres.2012.07.048
  37. Wang, B., Xie, F., Li, J. N., Wang, G., Li, C., & Jiang, J. P. (2017). Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau. PeerJ, 5, e3770. https://doi.org/10.7717/peerj.3770
  38. Watson, J. E. M., Rao, M., Ai-Li, K., & Yan, X. (2012). Climate change adaptation planning for biodiversity conservation: A review. Advances in Climate Change Research, 3(1), 1-11. https://doi.org/10.3724/SP.J.1248.2012.00001
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License .