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All Journal HAYATI Journal of Biosciences Media Teknologi Hasil Perikanan Jurnal MIPA PHARMACON JURNAL ILMIAH PLATAX Jurnal Bios Logos JURNAL BIOMEDIK Jurnal Ilmu Alam dan Lingkungan The Studies of Social Sciences Jurnal Perempuan dan Anak Indonesia ZOOTEC Makara Journal of Science Jurnal Ilmiah Sains Heca Journal of Applied Sciences Grimsa Journal of Science Engineering and Technology Kalwedo Sains (KASA)
BEIVY JONATHAN KOLONDAM
Department of Biology, Faculty of Mathematics and Natural Sciences, University of Sam Ratulangi, Kampus UNSRAT Bahu, Manado 95115
Agriculture, Biological Sciences & Forestry Humanities Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Decision Sciences, Operations Research & Management Earth & Planetary Sciences Economics, Econometrics & Finance Education Engineering Environmental Science Health Professions Immunology & microbiology Languange, Linguistic, Communication & Media Law, Crime, Criminology & Criminal Justice Mathematics Medicine & Pharmacology Physics Social Sciences Veterinary Other

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Journal : JURNAL ILMIAH PLATAX

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PCR-RFLP Design for Authentication of Red Snapper Species Based on CYB Gene Timbuleng, Kevin; Kolondam, Beivy J; Katili, Deidy
Jurnal Ilmiah Platax Vol. 9 No. 1 (2021): ISSUE JANUARY - JUNE 2021
Publisher : Sam Ratulangi University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35800/jip.9.1.2021.33541

Abstract

The PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) technique is a species identification method that can facilitate food inspection agencies to overcome mislabelling. In addition, this technique is simple, fast, powerful, and cheap compared to DNA barcodes. This study aimed to accommodate the problem in determining restriction endonuclease enzymes for the digestion of PCR end products through the design of snapper species authentication using the CYB gene in silico. Differentiation of CYB gene sequences with DNA barcoding showed that all species could be differentiated with the highest similarity level in Red Fish (Sebastes) species by 98.9% and snapper species between L. malabaricus and L. erythropterus by 99.8%. Enzyme tracing based on sequences variation of snapper species with substitution species found three potential enzymes from the CYB gene sequence, namely, Accl, Fnu4HI, and Tsp45I. Where all these enzymes can discriminate red snapper species among other.Key words: PCR-RFLP; CYB gene; Red snapperAbstrakTeknik PCR-RFLP (polymerase chain reaction-restriction fragment length polymorphism) merupakan metode identifikasi spesies yang dapat memfasilitasi lembaga inspeksi makanan untuk mengatasi mislabelling. Selain itu, teknik ini sederhana, cepat, kuat, dan murah dibandingkan dengan barcode DNA. Penelitian ini bertujuan untuk mengakomodasi masalah dalam menentukan enzim restriksi endonuklease untuk digesti produk akhir PCR lewat perancangan autentikasi spesies ikan kakap menggunakan gen CYB secara in silico. Diferensiasi sekuens gen CYB dengan DNA barcoding menunjukkan semua spesies dapat dibedakan dengan tingkat kesamaan tertinggi pada spesies Red Fish (Sebastes) sebesar 98,9% dan spesies kakap antara L. malabaricus dan L. erythropterus sebesar 99,8%. Penelusuran enzim berdasarkan variasi sekuens spesies kakap dengan spesies substitusi ditemukan sebanyak tiga enzim yang berpotensi yaitu, Accl, Fnu4HI, dan Tsp45I. Semua enzim tersebut dapat memdiskriminasikan spesies kakap merah dari spesies lainnya.Kata kunci: PCR-RFLP; gen CYB; ikan kakap merah
Evaluation of 16S rRNA Gene Sequence for DNA Barcoding of Tuna Fish Kolondam, Beivy J
Jurnal Ilmiah Platax Vol. 10 No. 1 (2022): ISSUE JANUARY-JUNE 2022
Publisher : Sam Ratulangi University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.35800/jip.v10i1.38861

Abstract

For fish product authentication, DNA barcoding has been a reliable tool. This is due to its requirement of a small amount of tissue sample in order to conduct a full analysis for species identification. This research aimed to conduct an assessment for the use of 16S rRNA gene sequence for tuna fish identification through DNA barcoding. Previous in silico studies using the COI gene and CYB gene were conducted using the same tuna fish specimens. A comparison of 16S rRNA gene sequence between Bluefin tuna (five species), Yellowfin tuna (three species), and another group of tuna (five species) showed the reliability of this gene in differentiating all species represented by the respective specimens. The multiple sequence alignment of 1695 bp in this research is reliable for accurate identification. All specimens of Thunnus (Bluefin group and Yellowfin group) were able to be differentiated with other genera (Auxis, Euthynnus, and Katsuwonus) group in 27 sites. The other tuna fish genera group members are similar in 27 sites and the member Thunnus group has a polymorphism in the same location. The similarity among the Bluefin group is 99.3% to 99.8%. The similarity among Yellowfin group is 99.6% to 99.9%. The similarity among the other group is 97.5% to 99.5%. In conclusion, the 16S rRNA gene is a reliable marker for DNA barcoding of tuna fish.Keywords: DNA barcoding; 16S rRNA gene; tuna fishAbstrakUntuk kepentingan autentikasi produk-produk dari ikan, DNA barcoding merupakan perangkat yang dapat diandalkan. Ini disebabkan karena metode ini hanya membutuhkan sedikit sampel jaringan untuk analisis identifikasi spesies. Penelitian ini bertujuan untuk melakukan asesmen penggunaan sekuens gen 16S rRNA untuk identifikasi ikan tuna melalui DNA barcoding. Studi in silico sebelumnya untuk gen COI dan gen CYB dilaksanakan menggunakan spesimen ikan tuna yang sama. Perbandingan sekuens gen 16S rRNA antara kelompok ikan tuna Bluefin (lima spesies), kelompok ikan tuna Yellowfin (tiga spesies), dan kelompok ikan tuna jenis lain (lima spesies) menunjukkan kemampuan gen ini dalam membedakan semua spesies. Dari hasil yang diperoleh, penjajaran multisekuens dari 1695 bp dapat diandalkan untuk indentifikasi yang akurat. Semua spesimen genus Thunnus (kelompok Bluefin dan kelompok Yellowfin) dapat dibedakan dengan spesimen lainnya pada 27 titik nukleotida. Kelompok tuna jenis lain juga memiliki nukleotida yang seragam di 27 lokasi dibandingkan dengan yang dari genus Thunnus. Tingkat kesamaan antar spesimen kelompok tuna Bluefin yaitu 99,3% sampai 99,8%. Tingkat kesamaan antar spesimen kelompok tuna Yellowfin yaitu 99,6% sampai 99,9%. Tingkat kesamaan antar kelompok tuna jenis lain yaitu 97,5% sampai 99,5%. Dari penelitian ini dapat disimpulkan bahwa gen 16S rRNA merupakan gen yang dapat diandalkan untuk DNA barcoding ikan tuna.Kata-kata kunci: DNA barcoding; gen 16S rRNA; ikan tuna
Co-Authors Abas, Abdul Hawil Adelfia Papu Agustina Monalisa Tangapo Akihary, Claudia Valleria Arthur G. Pinaria Balansa, Endrile Golmen Bernadus, Zefanya Bernadus, Zefanya G Dantje Tarore Deidy Katili Edwin de Queljoe Edy F Lengkong, Edy F Edy Lengkong Eka Julianti Fatimawali . Feky R. Mantiri Fitri Elizabrth Br Hasibuan Indra Polii, Indra J Polii-Mandang J. Polii, Mandang Johanis Pelealu Johanis Pelealu Koneri , Roni Laksono Trisnantoro Lalu Wahyudi Lisa Ruga Loho, Jesica C. M. Magani, Alce K Makagansa, Marbela Mamahit, Juliet Merry Eva Mangindaan, Glanny Mantang, Wianita Marnix L. D. Langoy Marnix L.D. Langoy Marnix Langoy Meiranty C. Pangerapan, Meiranty C. Mende, Pingkan S. Mende, Pingkan Stela Nelsyani Pasappa Olivia H Abram Pahlevi, Dylan R. Pience Veralyn Maabuat Presticilla D Irawan Presticilla D Irawan Presticilla D Irawan, Presticilla D Roni Koneri Runtunuwu Semuel Runtunuwu, Semuel Salaki, Christina Leta Sari, Nadia Warda Sekar Saroyo Saroyo Susan Marlein Mambu Susan Marlein Mambu Tambuwun, Jenifer Timbuleng, Kevin Trina E Tallei Trina E Tallei Trina Ekawati Tallei TRINA EKAWATI TALLEI TRINA EKAWATI TALLEI