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DNA Barcoding of Red Algae (Rhodophyta) in Ternate Island Sea, North Maluku, Indonesia
Corresponding Author(s) : Muhammad Janib Achmad
Jurnal Ilmiah Perikanan dan Kelautan, Vol. 16 No. 1 (2024): JURNAL ILMIAH PERIKANAN DAN KELAUTAN
Abstract
Abstract
Ternate Island is located on the North Maluku Sea. The North Maluku Sea region includes the Wallacea area and the world's coral triangle. One of the organisms commonly found in this sea is red algae. Study aimed to determine the red algae species by phylogenetic tree analysis based on the rbcL gene as a DNA marker. The preserved red algae tissue samples were extracted with the Geneaid GP100 DNA Extraction Kit Plant. The DNA sample was amplified and then visualized by 1% agarose gel electrophoresis. The amplicon products were sequenced and then aligned with the rbcL gene database that was available at the NCBI gene bank. The phylogenetic tree was constructed using the UPGMA method. The results showed that red algae were identified into four species: namely Gibsmithia hawaiiensis (98.65%), C_rbcL sample was identical to Amansieae sp. (91.50%), D_rbcL sample was identical to Peyssonnelia sp. (95.54%), and G_rbcL sample was similar to Portieria hornemanniI (96.15%). Based on phylogenetic tree analysis, Gibsmithia hawaiiensis from North Maluku is closely related to species from Raja Ampat, West Papua, Indonesia, followed by the Philippines species. Special findings were found to carry out phylogenetic reconstructions that can answer inter-species kinship. The general finding is that the markers used can be used for phylogenetic construction. Phylogenetic construction of Peyssonnelia sp. in North Maluku is related to species from South Africa. North Maluku's Portieria hornemannii is closely related to a species from Korea.
Highlight Research
- This study provides initial information about the DNA barcoding of red algae.
- Important for management purposes and determining the status of red algae in the future.
- This scientific information also provides an understanding of the relationships among red algae species in the world's oceans.
- Global warming has changed the temperature of seawater and affected the population of marine organisms.
Keywords
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- Achmad, M. J., Djamhur, M., Fabanyo, M. A., & Akbar, N. (2019). DNA barcoding application of garfish (Hemirhampus sp.) in North Maluku Sea. Journal of ichthyology of Indonesia, 19(3):463-473.
- Achmad, M. J., Yudiati, E., Azhar, N., & Alghazeer, R. (2023). Chloroform fraction from methanol extract of starfish Acanthaster planci stimulates Catfish (Clarias sp.) macrophage immunomodulatory activity. Jurnal Kelautan Tropis, 26(1):95-104.
- Akbar, N., & Aris, M. (2018). Genetic population structure of yellowfin tuna (Thunnus albacares) as based data of fish conservation in North Mallucas sea. Omni-Akuatika, 14(3):75-85.
- Akbar, N., Zamani, N. P., & Madduppa, H. H. (2014). Genetic diversity of yellowfin tuna (Thunnus albacares) from two populations in the Moluccas Sea, Indonesia. Depik, 3(1):65-73.
- Alshehri, M. A., Aziz, A. T., lzahrani, O., Alasmari, A., Ibrahim, S., Osman, G., & Bahattab. (2019). DNA barcoding and species identification for some Saudi Arabia Seaweeds using rbcL Gene. Journal of Pure and Applied Microbiology, 13(4):2035-2044.
- Amelia, R., & Tanod, W. A. (2016). Antioxidant content of red algae Eucheuma cottonii with different drying methods. KAUDERNI: Journal of Fisheries, Marine and Aquatic Science, 1(1):1-6.
- Amaranggana, L., & Wathoni, N. (2017). Manfaat alga merah (Rhodophyta) sebagai sumber obat dari bahan alam. Majalah Farmasetika, 2(1):16-19.
- Annisaqois, M., Gerung, G. S., Wullur, S., Sumilat, D. A., Wagey, B. T., Mandagi, S. V. (2018). Molecular analysis of DNA red algae (Rhodophyta) Kappaphycus sp. Jurnal Pesisir dan Laut Tropis, 1(1):107-112.
- Aris, M., Muchdar, F., & Labenua, R. (2021). Study of seaweed Kappaphycus alvarezii explants growth in the different salinity concentrations. Jurnal Ilmiah Perikanan dan Kelautan, 13(1):97–105.
- Aziz, L., & Chasani, A. R. (2020). Comparison of the structure and macroalgae composition in Drini and Krakal Beach. Jurnal Kelautan: Indonesian Journal of Marine Science and Technology, 13(2):75-86.
- Chojnacka, K., Saeid, A., Witkowska, Z., & Tuhy, L. (2012). Biologically active compounds in seaweed extracts-the prospects for the application. The Open Conference Proceedings Journal, 3(1):20-28.
- Djakatara, P. D., Gerung, G. S., Ginting, E. L., Sondak, C. F. A., Rumampuk, N. D. C., & Mantiri, D. M. H. (2018). Amplifikasi DNA alga merah (Rhodophyta) Eucheuma sp. Jurnal Pesisir dan Laut Tropis, 2(1):26-30.
- Ghazali, M., Rahmawati, R., Astuti, S. P., & Sukiman, (2018). Diversity of red algae (Rhodophyta) on mangrove ecosystem in Ekas Villages, East Lombok District. Fish Scientiae, 8(1):1-12.
- Hamdan, N., Samad, A. A., Hidayat, T., & Salleh, F. M. (2013). Phylogenetic analysis of eight Malaysian pineapple cultivars using a chloroplast marker (rcbL gene). Jurnal Teknologi, 64(2):29-33.
- Hengkengbala, I. R., Gerung, G. S., & Wullur, S. (2018). DNA extraction and amplification of the rbcL (ribulose-1,5- bisphosphate carboxylase/oxygenase large subunit) gene of red seaweed Gracilaria sp. from Bahoi Waters, North Minahasa Regency. Journal of Aquatic Science & Management, 6(2):33-38.
- Istifada, D. S., & Saptarini, N. M. (2018). Review jurnal: aktivitas senyawa bioaktif alga merah (Rhodophyta) sebagai antimikroba. Farmaka, 16(1):367-373.
- Ji, S. G., Huo, K. K., Jun, W., & Pan, S. L. (2008). A molecular phylogenetic study of Huperziaceae based on chloroplast rbcL and psbA-trnH sequences. Journal of Systematics and Evolution, 46(2):213-219.
- Julyasih, K. S. M., Ristiati, N. P., & Arnyana, I. B. P. (2020). Potensi Alga Merah dan Alga Hijau untuk Menghambat Pertumbuhan Bakteri Eschericia coli. Agrotrop, 10(1):11-17.
- Kristanto, A. H., & Kusrini, E. (2007). The role of environmental factors in fish breeding. Media Akuakultur, 2(1):183-188.
- Leliaert, F., Payo, A. D., Gurgel, C. F. D., Schils, T., Draisma, S. G. A., Saunders, G. W., Kamiya, M., Sherwood, A. R., Lin, S. M., Huisman, J. M., Gall, L. L., Anderson, R. J., Bolton, J. J., Mattio, L., Zubia, M., Spokes, T., Vieira, C., Payri, C. E., Coppejans, E., D'hondt, S., Verbruggen, H., & De Clerk, O. (2018). Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria. Journal of Biogeography, 45(10):2299-2313.
- Leatemia, S. P. O., Isma, Pattiasina, T. F., & Saleky, D. (2021). Morphology and genetic character of Lunella sp. Agricola, 11(1):24-34.
- Lim, P. E., Tan, J., Phang, S. M., Nikmatullah, A., Hong, D. D., Sunarpi, H., & Hurtado, A. Q. (2013). Genetic diversity of Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta) in Southeast Asia. Journal of Applied Phycology, 25(6):1253-1272.
- Meinita, M. D. N., Akromah, N., Ansriyani, N., Setijanto, Herwanto, D., & Liu, T. (2021). Molecular identification of Gracilaria species (Gracilariales, Rhodophyta) obtained from the South Coast of Java Island, Indonesia. Biodiversitas, 22(7):3046-3056.
- Nei, M., & Kumar. S. (2000). Molecular evolution and phylogenetics. Oxford: Oxford University Press.
- Oryza, D., Mahanal, S., & Sari, M. S. (2017). Identifikasi Rhodophyta sebagai bahan ajar di perguruan tinggi. Jurnal Pendidikan, 2(3):309-314.
- Pasaribu, H.N., Rumengan I.F.M., Wullur, S., Manoppo, H., Rimper, J.RTSL., & Tumbol, R.A.2023. Phylogenetic position of eurihaline rotifer Brachionus sp. originated from Tumpaan Waters, South Minahasa, North Sulawesi. Jurnal Bios Logos, 13 (1):1-6. DOI:
- Ragan, M. A., Bird, C. J., Rice, E. L., Gutell, R. R., Murphy, C. A., & Singh, R. K. (1994). A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proceedings of the National Academy of Sciences of the United States of America, 91(15):7276-7280.
- Ratnawati, P., Simatupang, N. F., Masak, P. R. P., Paul, N. A., & Zuccarello, G. C. (2020). Genetic diversity analysis of cultivated Kappaphycus in Indonesian seaweed farms using COI gene. Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology, 15(2):65-72.
- Rohani-Ghadikolaei, K., Abdulalian, E., & Ng, W. K. (2011). Evaluation of the proximate, fatty acid and mineral composition of representative green, brown and red seaweeds from the Persian Gulf of Iran as potential food and feed resources. Journal of Food Science and Technology, 49(6):774-80.
- Samman, A., & Achmad, M. J. (2023). Diversitas dan distribusi alga merah (Rhodophyta) di Perairan Pulau Ternate. Jurnal Kelautan Tropis, 26(1):148-154.
- Singkoh, M. F. O., Mantiri, D. M. H., Lumenta, C., & Manoppo, H. (2019). Identification bioactive compounds of algae Halymenia durvillei. Jurnal Bios Logos, 9(1):21-27.
- Schmitz, F., & Hauptfleisch, P. (1897). Ceramiaceae. In A. Engler and K. Prantl (Ed.), Die natürlichen Pflanzenfamilien. (pp. 481-504). Leipzig: Verlag von Wilhelm Engelmann.
- Subagio, & Kasim, M. S. H. (2019). Identifikasi rumput laut (Seaweed) di perairan Pantai Cemara, Jerowaru Lombok Timur sebagai bahan informasi keanekaragaman hayati bagi masyarakat. JISIP: Jurnal Ilmu Sosial dan Pendidikan, 3(1):308-321.
- Sukiman, Chikmawati, T., & Aryanti, N. S. (2014). Classification and key identification of red algae (Rhodophyta) species in West Java. Prosiding Semnas Biodiversitas, 3(2):135-139.
- Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12):2725-2729.
- Thenu, T. (1997). A Taxonomic study of seaweeds of North Sulawesi, Indonesia. Vancouver: University of British Columbia.
- Waryono, T. (2001). Biogeografi alga makro (rumput) laut di kawasan pesisir Indonesia. Kumpulan Makalah Periode 1987-2008, 1-6.
- Winowoda, S. D., Singkoh, M. F. O., & Siahaan, R. (2020). Wealth and potential of macroalgae bioactive compounds on the Atep Oki Coast, district of Minahasa, North Sulawesi. Jurnal Pesisir dan Laut Tropis, 8(3):7-16.
- Wirawan, I. G. P., Sasadara, M. M. V., Wijaya, I. N., Krinandika, A. A. K. (2021). DNA barcoding in molecular identification and phylogenetic relationship of beneficial wild Balinese red algae, Bulung sangu (Gracilaria sp.). Bali Medical Journal, 10(1):82-88.
- Woelkerling, W. J. (1990). Introduction red alga. In K. M. Cole, & R. G. Sheath (Ed.), Biology of the red algae. (pp. 1-6). Cambridge: Cambridge University Press.
- Yusron, E. (2005). Utilization of genetic diversity in the management of marine biological resources. Oseana, 30(2):29-34.
References
Achmad, M. J., Djamhur, M., Fabanyo, M. A., & Akbar, N. (2019). DNA barcoding application of garfish (Hemirhampus sp.) in North Maluku Sea. Journal of ichthyology of Indonesia, 19(3):463-473.
Achmad, M. J., Yudiati, E., Azhar, N., & Alghazeer, R. (2023). Chloroform fraction from methanol extract of starfish Acanthaster planci stimulates Catfish (Clarias sp.) macrophage immunomodulatory activity. Jurnal Kelautan Tropis, 26(1):95-104.
Akbar, N., & Aris, M. (2018). Genetic population structure of yellowfin tuna (Thunnus albacares) as based data of fish conservation in North Mallucas sea. Omni-Akuatika, 14(3):75-85.
Akbar, N., Zamani, N. P., & Madduppa, H. H. (2014). Genetic diversity of yellowfin tuna (Thunnus albacares) from two populations in the Moluccas Sea, Indonesia. Depik, 3(1):65-73.
Alshehri, M. A., Aziz, A. T., lzahrani, O., Alasmari, A., Ibrahim, S., Osman, G., & Bahattab. (2019). DNA barcoding and species identification for some Saudi Arabia Seaweeds using rbcL Gene. Journal of Pure and Applied Microbiology, 13(4):2035-2044.
Amelia, R., & Tanod, W. A. (2016). Antioxidant content of red algae Eucheuma cottonii with different drying methods. KAUDERNI: Journal of Fisheries, Marine and Aquatic Science, 1(1):1-6.
Amaranggana, L., & Wathoni, N. (2017). Manfaat alga merah (Rhodophyta) sebagai sumber obat dari bahan alam. Majalah Farmasetika, 2(1):16-19.
Annisaqois, M., Gerung, G. S., Wullur, S., Sumilat, D. A., Wagey, B. T., Mandagi, S. V. (2018). Molecular analysis of DNA red algae (Rhodophyta) Kappaphycus sp. Jurnal Pesisir dan Laut Tropis, 1(1):107-112.
Aris, M., Muchdar, F., & Labenua, R. (2021). Study of seaweed Kappaphycus alvarezii explants growth in the different salinity concentrations. Jurnal Ilmiah Perikanan dan Kelautan, 13(1):97–105.
Aziz, L., & Chasani, A. R. (2020). Comparison of the structure and macroalgae composition in Drini and Krakal Beach. Jurnal Kelautan: Indonesian Journal of Marine Science and Technology, 13(2):75-86.
Chojnacka, K., Saeid, A., Witkowska, Z., & Tuhy, L. (2012). Biologically active compounds in seaweed extracts-the prospects for the application. The Open Conference Proceedings Journal, 3(1):20-28.
Djakatara, P. D., Gerung, G. S., Ginting, E. L., Sondak, C. F. A., Rumampuk, N. D. C., & Mantiri, D. M. H. (2018). Amplifikasi DNA alga merah (Rhodophyta) Eucheuma sp. Jurnal Pesisir dan Laut Tropis, 2(1):26-30.
Ghazali, M., Rahmawati, R., Astuti, S. P., & Sukiman, (2018). Diversity of red algae (Rhodophyta) on mangrove ecosystem in Ekas Villages, East Lombok District. Fish Scientiae, 8(1):1-12.
Hamdan, N., Samad, A. A., Hidayat, T., & Salleh, F. M. (2013). Phylogenetic analysis of eight Malaysian pineapple cultivars using a chloroplast marker (rcbL gene). Jurnal Teknologi, 64(2):29-33.
Hengkengbala, I. R., Gerung, G. S., & Wullur, S. (2018). DNA extraction and amplification of the rbcL (ribulose-1,5- bisphosphate carboxylase/oxygenase large subunit) gene of red seaweed Gracilaria sp. from Bahoi Waters, North Minahasa Regency. Journal of Aquatic Science & Management, 6(2):33-38.
Istifada, D. S., & Saptarini, N. M. (2018). Review jurnal: aktivitas senyawa bioaktif alga merah (Rhodophyta) sebagai antimikroba. Farmaka, 16(1):367-373.
Ji, S. G., Huo, K. K., Jun, W., & Pan, S. L. (2008). A molecular phylogenetic study of Huperziaceae based on chloroplast rbcL and psbA-trnH sequences. Journal of Systematics and Evolution, 46(2):213-219.
Julyasih, K. S. M., Ristiati, N. P., & Arnyana, I. B. P. (2020). Potensi Alga Merah dan Alga Hijau untuk Menghambat Pertumbuhan Bakteri Eschericia coli. Agrotrop, 10(1):11-17.
Kristanto, A. H., & Kusrini, E. (2007). The role of environmental factors in fish breeding. Media Akuakultur, 2(1):183-188.
Leliaert, F., Payo, A. D., Gurgel, C. F. D., Schils, T., Draisma, S. G. A., Saunders, G. W., Kamiya, M., Sherwood, A. R., Lin, S. M., Huisman, J. M., Gall, L. L., Anderson, R. J., Bolton, J. J., Mattio, L., Zubia, M., Spokes, T., Vieira, C., Payri, C. E., Coppejans, E., D'hondt, S., Verbruggen, H., & De Clerk, O. (2018). Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria. Journal of Biogeography, 45(10):2299-2313.
Leatemia, S. P. O., Isma, Pattiasina, T. F., & Saleky, D. (2021). Morphology and genetic character of Lunella sp. Agricola, 11(1):24-34.
Lim, P. E., Tan, J., Phang, S. M., Nikmatullah, A., Hong, D. D., Sunarpi, H., & Hurtado, A. Q. (2013). Genetic diversity of Kappaphycus Doty and Eucheuma J. Agardh (Solieriaceae, Rhodophyta) in Southeast Asia. Journal of Applied Phycology, 25(6):1253-1272.
Meinita, M. D. N., Akromah, N., Ansriyani, N., Setijanto, Herwanto, D., & Liu, T. (2021). Molecular identification of Gracilaria species (Gracilariales, Rhodophyta) obtained from the South Coast of Java Island, Indonesia. Biodiversitas, 22(7):3046-3056.
Nei, M., & Kumar. S. (2000). Molecular evolution and phylogenetics. Oxford: Oxford University Press.
Oryza, D., Mahanal, S., & Sari, M. S. (2017). Identifikasi Rhodophyta sebagai bahan ajar di perguruan tinggi. Jurnal Pendidikan, 2(3):309-314.
Pasaribu, H.N., Rumengan I.F.M., Wullur, S., Manoppo, H., Rimper, J.RTSL., & Tumbol, R.A.2023. Phylogenetic position of eurihaline rotifer Brachionus sp. originated from Tumpaan Waters, South Minahasa, North Sulawesi. Jurnal Bios Logos, 13 (1):1-6. DOI:
Ragan, M. A., Bird, C. J., Rice, E. L., Gutell, R. R., Murphy, C. A., & Singh, R. K. (1994). A molecular phylogeny of the marine red algae (Rhodophyta) based on the nuclear small-subunit rRNA gene. Proceedings of the National Academy of Sciences of the United States of America, 91(15):7276-7280.
Ratnawati, P., Simatupang, N. F., Masak, P. R. P., Paul, N. A., & Zuccarello, G. C. (2020). Genetic diversity analysis of cultivated Kappaphycus in Indonesian seaweed farms using COI gene. Squalen Bulletin of Marine and Fisheries Postharvest and Biotechnology, 15(2):65-72.
Rohani-Ghadikolaei, K., Abdulalian, E., & Ng, W. K. (2011). Evaluation of the proximate, fatty acid and mineral composition of representative green, brown and red seaweeds from the Persian Gulf of Iran as potential food and feed resources. Journal of Food Science and Technology, 49(6):774-80.
Samman, A., & Achmad, M. J. (2023). Diversitas dan distribusi alga merah (Rhodophyta) di Perairan Pulau Ternate. Jurnal Kelautan Tropis, 26(1):148-154.
Singkoh, M. F. O., Mantiri, D. M. H., Lumenta, C., & Manoppo, H. (2019). Identification bioactive compounds of algae Halymenia durvillei. Jurnal Bios Logos, 9(1):21-27.
Schmitz, F., & Hauptfleisch, P. (1897). Ceramiaceae. In A. Engler and K. Prantl (Ed.), Die natürlichen Pflanzenfamilien. (pp. 481-504). Leipzig: Verlag von Wilhelm Engelmann.
Subagio, & Kasim, M. S. H. (2019). Identifikasi rumput laut (Seaweed) di perairan Pantai Cemara, Jerowaru Lombok Timur sebagai bahan informasi keanekaragaman hayati bagi masyarakat. JISIP: Jurnal Ilmu Sosial dan Pendidikan, 3(1):308-321.
Sukiman, Chikmawati, T., & Aryanti, N. S. (2014). Classification and key identification of red algae (Rhodophyta) species in West Java. Prosiding Semnas Biodiversitas, 3(2):135-139.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12):2725-2729.
Thenu, T. (1997). A Taxonomic study of seaweeds of North Sulawesi, Indonesia. Vancouver: University of British Columbia.
Waryono, T. (2001). Biogeografi alga makro (rumput) laut di kawasan pesisir Indonesia. Kumpulan Makalah Periode 1987-2008, 1-6.
Winowoda, S. D., Singkoh, M. F. O., & Siahaan, R. (2020). Wealth and potential of macroalgae bioactive compounds on the Atep Oki Coast, district of Minahasa, North Sulawesi. Jurnal Pesisir dan Laut Tropis, 8(3):7-16.
Wirawan, I. G. P., Sasadara, M. M. V., Wijaya, I. N., Krinandika, A. A. K. (2021). DNA barcoding in molecular identification and phylogenetic relationship of beneficial wild Balinese red algae, Bulung sangu (Gracilaria sp.). Bali Medical Journal, 10(1):82-88.
Woelkerling, W. J. (1990). Introduction red alga. In K. M. Cole, & R. G. Sheath (Ed.), Biology of the red algae. (pp. 1-6). Cambridge: Cambridge University Press.
Yusron, E. (2005). Utilization of genetic diversity in the management of marine biological resources. Oseana, 30(2):29-34.