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Vol. 14 No. 2 (2022): JURNAL ILMIAH PERIKANAN DAN KELAUTAN

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Molecular Genetics DNA Barcoding

DNA Barcoding on Indian Ocean Squid, Uroteuthis duvaucelii (D'Orbigny, 1835) (Cephalopoda: Loliginidae) from the Java Sea, Indonesia

https://doi.org/10.20473/jipk.v14i2.33448
Norma Afiati
Department of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.
https://orcid.org/0000-0001-9788-4815
Subagiyo Subagiyo
Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.
https://orcid.org/0000-0002-8446-9038
Christina Retna Handayani
Directorate for Aquaculture Development and Fish Health, Directorate General of Aquaculture, Ministry of Marine Affairs and Fisheries of the Republic of Indonesia, Central Jakarta, 10110.
https://orcid.org/0000-0003-4135-8546
Retno Hartati
Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.
https://orcid.org/0000-0002-3131-5166
Nenik Kholilah
Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.
https://orcid.org/0000-0002-8335-3498

Corresponding Author(s) : Norma Afiati

normaafiati.na@gmail.com

Jurnal Ilmiah Perikanan dan Kelautan, Vol. 14 No. 2 (2022): JURNAL ILMIAH PERIKANAN DAN KELAUTAN

Abstract

Highlight Research

  1. The possibility of U. duvauceli be a polymorph cryptic species is further reinforced by the results of the present study.
  2. Phylogenetic analysis showed two separate clusters though did not perfectly segregate north to the south waters.
  3. Individuals in cluster II from the south coast showed the highest polymorphism levels by 40 segregating sites (S), compared to only 2-4 sites in that of cluster I
  4. Frequencies of A, C, G, and T in mitochondrial DNA of all specimens skewed toward A and T, with T being the most preferred and G being the least preferred nucleotide
  5. All specimens showed no amino acid frequency for glutamic acid. Further, all four individuals in cluster II (south coast) were also have no amino acid frequencies for aspartic acid and valine as well.


Abstract

Uroteuthis duvauceli (D' Orbigny, 1835) also known as the Indian Ocean Squidis a highly important commercial marine organism along the Java coast, Indonesia. Based on genetic variation this species-complex are polymorphic and cryptic. In the present study, the genetic diversity and stock structure of loliginid squid U. duvauceli is investigatedusing a mitochondrial gene cytochrome oxidase subunit I (COI). Samples were collected by hand-jigging onboard of an 8hp small fisher-boat equipped with a few lamps during May to August 2015, May 2016 and August to November 2018. Sample collection started at dusk until midnight. The attractor was a weighed-quill attached to nylon string, manually immersed into the water and pulled quickly and continuously for about 3-5 minutes at each effort. The determination was conducted with BLAST. Phylogenetic analysis showed two separate clusters with 100% bootstrap value, in which cluster II from Palabuhanratu has divergences of 5.9 - 7.0%, compared to cluster I.  Genetic variations exist within and among individuals over the locations. Palabuhanratu individuals have the highest polymorphism levels compared to other locations as shown by 40 segregating sites (S). Frequencies of A, C, G, and T in mtDNA of the 20 specimens U. duvauceli are biased toward A and T, with T being the most favoured and G being the least favoured nucleotide. All specimen showed no amino acid frequency for glutamic acid and all four individuals in cluster II (south coast) also have no amino acid frequencies for aspartic acid and valine as well.

Keywords

Uroteuthis duvaucelimtDNACOIJava SeaIndonesia
Norma Afiati, Subagiyo, S., Handayani, C. R., Hartati, R., & Kholilah, N. (2022). DNA Barcoding on Indian Ocean Squid, <I>Uroteuthis duvaucelii</I> (D’Orbigny, 1835) (Cephalopoda: Loliginidae) from the Java Sea, Indonesia. Jurnal Ilmiah Perikanan Dan Kelautan, 14(2), 231–245. https://doi.org/10.20473/jipk.v14i2.33448
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References
  1. Afiati, N., Subagiyo, Widyorini, N., & Harwanto, D. (2013). Inventory on landed mollusc from South coast of Central Java (Report in Bahasa Indonesia). Semarang: Universitas Diponegoro.
  2. Afiati, N., Puspanusari, D. M., & Subagiyo. (2017). Allometric study of Urotheutis (Photololigo) duvauceli (d'Orbigny 1835) from Northern Coast of Java, Indonesia. Proceedings of the Pakistan Academy of Science B. Life and Environmental Sciences, 54(1):21-37.
  3. Anderson, F. E., Engelke, R., Jarrett, K., Valinassab, T., Mohamed, K. S., Asokan, P. K., Zacharia, P. U., Nootmorn, P., Chotiyaputta, C., & Dunning, M. (2011). Phylogeny of the Sepia pharaonis species complex (Cephalopoda: Sepiida) based on analyses of mitochondrial and nuclear DNA sequence data. Journal of Molluscan Studies, 77(1):65-75.
  4. Andujar, C., Arribas, P., Yu, D. W., Vogler, A. P., & Emerson, B. C. (2018). Why the COI barcode should be the community DNA metabarcode for the metazoa. Molecular Ecology, 27(20):3968-3975.
  6. Arkhipkin, A. I., Rodhouse, P. G. K., Pierce, G. J., Sauer, W., Sakai, M., Allcock, L., Arguelles, J., & Zeidberg, L. D. (2015). World squid fisheries. Reviews in Fisheries Science & Aquaculture, 23(2):92-252.
  7. Badhe, M. R., Pavan-Kumar, A., Gireesh-Babu, P., Nandanpapwar, P., Chaudhari, A., Jaiswar, A. K., Krishna, G., G., & Lakra W. S. (2013). DNA barcoding of selected cephalopods from Indian coast. Indian Journal of Animal Sciences, 83(8):862-866.
  8. Barcaccia, G., Lucchin, M., & Cassandro, M. (2016). DNA barcoding as a molecular tool to track down mislabeling and food piracy. Diversity, 8(1):2.
  9. Bonnaud, L., Boucher-Rodoni, R., & Monnerot, M. (1994). Phylogeny of decapod cephalopods based on partial 16S rDNA nucleotide sequences. Comptes Rendus de l'Académie des Sciences de Paris, 317(6):581-588.
  10. Bonnaud, L., Boucher-Rodoni, R., & Monnerot, M. (1997). Phylogeny of cephalopods inferred from mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 7(1):44-54.
  11. BPS-Statistics Indonesia. (2019). Statistical yearbook of Indonesia. Indonesia: BPS-Statistics Indonesia.
  12. Canapa, A., Barucca, M., Marinelli, A., & Olmo, E. (2001). A molecular phylogeny of Heterodonta (Bivalvia) based on small ribosomal subunit RNA sequences. Molecular Phylogenetics and Evolution, 21(1):156-161.
  13. Carlini, D. C., & Graves, J. E. (1999). Phylogenetic analysis of cytochrome C oxidase I sequences to determine higher-level relationships within the coleoid cephalopods. Bulletin of Marine Science, 64(1):57-76.
  14. Chakraborty, K., & Joy, M. (2020). High-value compounds from the molluscs of marine and estuarine ecosystems as prospective functional food ingredients: An overview. Food Research International, 137:109637.
  15. Chen, J., Li, Q., Kong, L., & Yu. H. (2011). How DNA Barcodes Complement Taxonomy and Explore Species Diversity: The Case Study of a Poorly Understood Marine Fauna. PLoS ONE, 6(6):e21326.
  17. Cheng, R., Zheng, X., Ma, Y., & Li, Q. (2013). The complete mitochondrial genomes of two Octopods Cistopus chinensis and Cistopus taiwanicus: Revealing the phylogenetic position of the genus Cistopus within the order Octopoda. PLoS ONE, 8(12):e84216.
  18. Dai, L., Zheng, X., Kong, L., & Li, Q. (2012). DNA barcoding analysis of Coleoidea (Mollusca: Cephalopoda) from Chinese waters. Molecular Ecology Resources, 12(3):437-447.
  19. DeSalle, R., & Goldstein, P. (2019). Review and interpretation of trends in DNA barcoding. Frontiers in Ecology and Evolution, 7:1-11.
  21. Ereshefsky, M., & Matthen, M. (2005). Taxonomy, polymorphism, and history: An introduction to population structure theory. Philosophy of Science, 7(1):1-21.
  22. FAO. (2015). The state of world fisheries and aquaculture. Rome: FAO.
  23. FAO. (2021). World food and agriculture-statistical yearbook 2021. Rome: FAO.
  24. Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39(4):783-791.
  25. 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(5):294-299.
  26. Gebhardt, K., & Knebelsberger, T. (2015). Identification of cephalopod species from the North and Baltic Seas using morphology, COI and 18S rDNA sequences. Helgoland Marine Research, 69:259-271.
  27. Haye, P. A., Segovina, N.I., Muñiz-Herrera, N. C., Gálvez, F. E., Martí­nez, A., Meynard, A., Pardo-Gandarillas, M. C., Poulin, E., & Faugeron, S. (2014). Phylogeographic structure in benthic marine invertebrates of southeast Pacific Coast of Chile with differing dispersal potential. PLoS ONE, 9(2):e88613.
  28. Huang, J., Zhang, A., Mao, S., & Huang, Y. (2013). DNA barcoding and species boundary delimitation of selected species of Chinese Acridoidea (Orthoptera: Caelifera). PLoS ONE, 8(12):e82400.
  29. Hubert, N., & Hanner, R. (2015). DNA barcoding, species delineation and taxonomy: A historical perspective. DNA Barcodes, 3:44-58.
  30. Hunsicker, M. E., Essington, T. E., Watson, R., & Sumaila, U. R. (2010). The contribution of cephalopods to global marine fisheries: can we have our squid and eat them too? Fish and Fisheries, 11:421-438.
  31. Inshore Fisheries Management (Zambia, South Africa). (2014). Squid permit conditions (commercial fishery) fishing season: 2014 – DAFF.
  32. Islam, R., Pradit, S., Hajisamae, S., Perngmak, P., & Fazrul, H. (2016). Size and growth variation at maturity of two common squid species in the South China Sea. Russian Journal of Agricultural and Socio-Economic Sciences (RJOAS), 7(55):18-24.
  33. Jereb, P., & Roper, C. F. E. (2010). Cephalopods of the world. An annotated and illustrated catalogue of cephalopod species known to date. Volume 2. Myopsid and oegopsida squids. Rome: FAO.
  34. Katugin, O. N., Chichvarkhina, O. V., Zolotova, A. O., & Chichvarkhin, A. Y. (2017). DNA barcoding for squids of the family Gonatidae (Cephalopoda: Teuthida) from the boreal North Pacific. Mitochondrial DNA Part A. DNA Mapping, Sequencing, and Analysis, 28(1):41-49.
  35. Kholilah, N., Afiati, N., & Subagiyo. (2020). Characterization of Some Commercially Important Octopus (Mollusca: Cephalopoda) from Indonesian Waters using Mitochondrial DNA Cytochrome Oxidase Sub-Unit I (Mt-DNA COI). Indonesian Journal of Marine Sciences 26(1):17-26.
  36. Kim, D. W., Yoo, W. G., Park, H. C., Yoo, H. S., Kang, D. W., Jin, S. D., Min, H. K., Paek, W. K., & Lim, J. (2012). DNA barcoding of fish, insects, and shellfish in Korea. Genomics Information, 10(3):206-211.
  38. Kimura, M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16:111-120.
  39. Krishnan, S., Chakraborty, K., & Vijayagopal, P. (2019). Nutritional profiling of selected species of edible marine molluscs from the south-west coast of India. Indian Journal of Fisheries, 66(1):56-63.
  40. Librado, P., & Rozas, J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11):1451-1452.
  41. Mather, J. A., & Anderson, R. C. (2007). Ethics and invertebrates: a cephalopod perspective. Diseases of Aquatic Organisms, 75:119-129.
  43. Mugnai, F., Meglécz, E., CoMBoMed group, Abbiati, M., Bavestrello, G., Bertasi, F., Bo, M., Capa, M., Chenuil, A., Colangelo, M. A., De Clerck, O., Gutiérrez, J. M., Lattanzi, L., Leduc, M., Martin, D., Matterson, K. O., Mikac, B., Plaisance, L., Ponti, M., Riesgo, A., Rossi, V., Turicchia, E., Waeschenbach, A., Wangensteen, O. S., & Constantini, F. (2021). Are well-studied marine biodiversity hotspots still blackspots for animal barcoding? Global Ecology and Conservation, 32:e01909.
  44. Munasinghe, D. H. N., & Thushari, G. G.N. (2014). Length - weight relationship and molecular phylogenetic analysis to infer status of Uroteuthis duvaucelii (d'Orbigny 1835) population in the southern coastal region of Sri Lanka. International Journal of Fisheries and Aquatic Studies, 2(1):223-231.
  45. Nieuwenhove, A. H. M. V., Ratsimbazafy, H. A., & Kochzius. M. (2019). Cryptic diversity and limited connectivity in Octopuses: Recommendations for fisheries management. PLoS ONE, 14(5):1-20.
  47. Okutani, T. (2005). Past, present and future studies on cephalopod diversity in Tropical West Pacific. Phuket Marine Biological Center Research Bulletin, 66:39-50.
  48. Pratasik, S. B., Marsoedi, D., Arfiati, & Setyohadi, D. (2016). Mitochondrial CO1 genetic marker-based species diversity of cuttlefish (Cephalopod; Mollusk) in Manado Bay and Lembeh Strait, North Sulawesi, Indonesia. AACL Bioflux, 9(6):1345-1354.
  49. Raupach, M. J, Barco, A., Steinke, D., Beermann, J., Laakmann, S., Mohrbeck, I., Neumann, H., Kihara, T. C., Pointner, K., Radulovici, A., Segelken-Voigt, A., Wesse, C., & Knebelsberger, T. (2015). The Application of DNA barcodes for the identification of marine crustaceans from the North Sea and adjacent regions. PLoS ONE, 10(9):e0139421.
  50. Sabrah, M. M., El-Sayed, A. Y., & El-Ganiny, A. A. (2015). Fishery and population characteristics of the Indian squids Loligo duvauceli Orbigny, 1848 from trawl survey along the Northwest Red Sea. Egyptian Journal of Aquatic Research, 41(3):279-285.
  51. Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4):406-425.
  52. Sales, J. B. L, Shaw, P. W., Haimovici, M., Markaida, U., Cunha, D. B., Ready, J., Figueiredo-Ready, W. M. B., Schneider, H., & Sampaio, I. (2013). New molecular phylogeny of the squids of the family Loliginidae with emphasis on the genus Doryteuthis Naef, 1912: Mitochondrial and nuclear sequences indicate the presence of cryptic species in the Southern Atlantic Ocean. Molecular Phylogenetics and Evolution, 68(2):293-299.
  53. Sales, J. B. L, Shaw, Rodrigues-Filho, L. F. da S., Ferreira, Y. do S., Carneiro, J., Asp, N.E, Shaw, P.W., Haimovici, M., Markaida, U., Ready, J., Schneider, H., & Sampaio, I. (2017). Divergence of cryptic species of Doryteuthis plei Blainville, 1823 (Loliginidae, Cephalopoda) in the Western Atlantic Ocean is associated with the formation of the Caribbean Sea. Molecular Phylogenetics and Evolution, 106:44-54.
  54. Sanchez, G., Setiamarga, D. H. E., Tuanapaya, S., Tongtherm, K., Winkelmann, I. E., Schmidbaur, H., Umino, T., Albertin, C., Allcock, L., Perales-Raya, C., Gleadall, I., Strugnell, J. M., Simakov, O., & Nabhitabhata, J. (2018). Genus-level phylogeny of cephalopods using molecular markers: current status and problematic areas. PeerJ, 6:e4331.
  55. Siddique, M. A. M., Arshad, A., & Nurul-Amin, S. M. (2014). Length–weight relationships of the tropical cephalopod Uroteuthis chinensis (Gray, 1849) from Sabah, Malaysia. Zoology and Ecology, 24(3):215-218.
  56. Siddique, A. A. M., Khan, M. S. K., Habib, A., Bhuiyan, M. K. A., & Aftabuddin. S. (2016). Size frequency and length–weight relationships of three semi-tropical cephalopods, Indian squid Photololigo duvaucelii, needle cuttlefish Sepia aculeata, and spineless cuttlefish Sepiella inermis from the coastal waters of Bangladesh, .Bay of Bengal. Zoology and Ecology, 26(3):176-18.
  57. Sin, Y. W., Yau, C., & Chu, K. H. (2009). Morphological and genetic differentiation of two loliginid squids, Uroteuthis (Photololigo) chinensis and Uroteuthis (Photololigo) edulis (Cephalopoda: Loliginidae), in Asia. Journal of Experimental Marine Biology and Ecology, 369(1):22-30.
  58. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10):2731-2739.
  59. Thompson, D., Higgins, D. G., & Gibson, T. J. (1994). ClustalW: improving the sensitivity of progressive multiple sequence aligment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22):4673-4680.
  60. Troudet, J., Grandcolas, P., Blin, A., Vignes-Lebbe, R., & Legendre, F. (2017). Taxonomic bias in biodiversity data and societal preferences. Scientific Reports, 7(1):1-14.
  62. Yalla, S. K., & Mohanraju, R. (2018). DNA barcoding of commercially important cephalopods from Andaman Islands, India. Regional Studies in Marine Science, 25:100479.
  63. Zhang, M., Chen, J. L., Wang, P. C., Fu, C. Y., & Peng, H., (2017). Complete mitochondrial genome sequence of the human neuroblastoma cell line 751-NA. Genome Announcement, 5(46):e01185-17.
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Author Biographies

Norma Afiati, Department of Aquatic Resources Management, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.

Dept. of Aquatic Resources Management,

Professor.

Subagiyo Subagiyo, Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.
Department of Marine Science, Lecturer
Christina Retna Handayani, Directorate for Aquaculture Development and Fish Health, Directorate General of Aquaculture, Ministry of Marine Affairs and Fisheries of the Republic of Indonesia, Central Jakarta, 10110.
Research Centre for Brackish Water Aquaculture Development, Researcher
Retno Hartati, Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.
Department of Marine Science, Lecturer
Nenik Kholilah, Department of Marine Science, Faculty of Fisheries and Marine Science, Universitas Diponegoro, Semarang, Central Java, 50275.
Department of Marine Science, Academic Staff.
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