Variasi Sekuens Gen COI untuk DNA Barcoding Ikan Tuna

DNA barcoding has been used for species identification of fishes, especially for fish product authentication. In tuna fish food products authentication, DNA barcoding is needed due to its requirement of small amount of samples for species identification. The COI gene, located in mitochondria of animal cells, is established as standard marker for animal DNA barcoding. This research aimed to study the variation in COI gene of tuna fish species in three groups, such as Bluefin tuna (five species), Yellowfin tuna (three species), and other tuna species (five species). The variation comparison showed that this gene can differentiate 11 out of 13 tuna species. The Thunnus orientalis and T. thynnus has 100% similarity over COI gene (identical). Therefore, another marker gene is required to differentiate this two species. Variation in COI gene has the ability to differentiate all species in the genus Thunnus with other genus (Auxis, Euthynnus, and Katsuwonus) by 29 nucleotide sites. Bluefin tuna group has one site unique to two other groups. Yellowfin tuna group did not have site for differentiation. Other tuna species has 33 nucleotide sites for differentiation with two other groups

Evaluation of 16S rRNA Gene Sequence for DNA Barcoding of Tuna Fish

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 tun

PCR-RFLP Design for Authentication of Red Snapper Species Based on CYB Gene

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 mera

Estimasi Densitas Tangkasi (Tarsius tarsier) di Luar Kawasan Hutan Hujan Tropis Dataran Rendah Sulawesi Utara Berdasarkan Sampling Duet Call

Telah dilakukan penelitian tentang densitas tangkasi (Tarsius tarsier) di luar kawasan hutan tropis dataran rendah Sulawesi Utara berdasarkan sampling duet call dengan tujuan untuk membandingkan densitasnya pada beberapa tipe habitat. Penelitian dilaksanakan di Kelurahan Batuputih untuk habitat pertanian, mangrove, dan semak; serta Gunung Klabat untuk habitat hutan dataran tinggi. Waktu penelitian dari bulan Mei sampai Juli 2013. Metode penelitian didasarkan pada sampling berdasarkan duet call dengan plot berbentuk lingkaran. Hasil penelitian menunjukkan densitas tangkasi ialah: 2,94 ekor/ha pada hutan dataran tinggi; 1,60 ekor/ha pada areal pertanian; 7,66 ekor/ha pada mangrove; dan 8,17 ekor/ha pada semak.A research about density of tangkasi (Tarsius tarsier) at the outside of lowland forest habitat in North Sulawesi has conducted to compare their density at several habitats based on the duet call. Research was done in Batuputih for farming area, mangrove, and shrub habitats and in Klabat Mountain for highland forest habitat. Time of research was May to July 2013. Method used was based on duet call sampling with circle plots. Results of this research were: density of tangkasi was 2.94 individuals/ha at highland forest, 1.60 individuals/ha at farming area, 7.66 individuals/ha at mangrove; and 8.17 individuals/ha at shrub

AMPLIFIKASI GEN COI DARI SAMPEL DARAH ULAR DENGAN MENGGUNAKAN BEBERAPA PASANGAN PRIMER UNIVERSAL

AMPLIFICATION OF COI GENE FROM SNAKE BLOOD SAMPLES USING TWO UNIVERSALPRIMER PAIRS. This study aims to amplify COI (Cytochrome Oxidase Subunit I) gene fragments from snake blood. Four samples were obtained from four different snake individuals that were captured in Tapahan Telu Waterfall, Kali Village, Minahasa Regency. Total DNA from the sample was isolated and then the COI gene was amplified through the PCR (Polymerase Chain Reaction) reaction using two primer pairs, LCO1490-HCO2198 and FF2d-FR1d. These four samples were successfully amplified using different primers, i.e. DRP1 and DRP3 by FF2d-FR1d and DRP2 and DRP4 by LCO1490-HCO2198 primers. The success of amplification marked by the presence of 710 bp (LCO1490-HCO2198) and 707 bp (FF2d-FR1d) bands, which were indicated by those bands were located close to the standard 750 bp DNA ladder. Key words: Snake, Amplification, COI gene, Primers, PC

Analisis Sekuens dan Filogenetik Beberapa Tumbuhan Syzygium (Myrtaceae) di Sulawesi Utara Berdasarkan Gen Matk

Syzygium (Myrtaceae) merupakan tumbuhan yang memiliki banyak manfaat di bidang ekonomi dan kesehatan. Informasi dan publikasi mengenai klasifikasi tumbuhan Syzygium masih sedikit. Pengelompokkan beberapa jenis tumbuhan dalam genus ini masih ditemui masalah, antara lain tumpang tindihnya nama Syzygium dengan Eugenia dan beberapa tumbuhan belum diketahui posisinya dalam klasifikasi. Penelitian ini bertujuan untuk menganalisis variasi sekuens gen matK dan mengkonstruksi pohon filogenetik pada beberapa tumbuhan Syzygium di Sulawesi Utara, yaitu pakoba, jamblang dan bombongan. Analisis variasi sekuens menunjukkan adanya perbedaan satu nukleotida antara tumbuhan pakoba dan jamblang, serta perbedaan 5-6 nukleotida antara bombongan dengan jamblang dan pakoba. Selain itu, variasi juga ditunjukan antara sekuens sampel tumbuhan Syzygium dengan sekuens kerabat yang diperoleh dari basis data GenBank yaitu adanya perbedaan 2-3 nukleotida dengan spesies kerabat terdekat dan perbedaan 5-6 nukleotida dengan spesies kerabat terjauh. Hasil perhitungan jarak genetik menggunakan Kimura-2-parameter menunjukkan nilai jarak interspesies kecil, yaitu 0.000-0.011

Identification of Potential Diesel Oil-degrading Bacteria Isolated From Manado Sea Port Based on 16s Rrna Gene

Petroleum contamination and its derivate in ecosystem are considered as environmental threat all over the world. Some microorganisms exhibit potential to degrade hydrocarbon in contaminated environments. This study aims at identifying potential diesel oil-degrading bacteria grown on artificial media. Bacteria isolated from Manado Sea port were grown in nutrient agar containing artificial diesel oil plus salt water and diesel oil only, respectively. The growing bacteria were isolated and each of them was grown separately to obtain pure isolate. Three bacterial isolates namely AO2, OA3 and OA4 were identified using 16S rRNA gene as Pseudomonas aeroginosa, Klebsiella oxytoca, and Citrobacter sp, respectively