Aplikasi DNA Barcoding Menggunakan Marka CO1 (Cytochrome Oxidase I) dan CytB (Cytochrome-B) Untuk Autentikasi Produk Ikan Patin (Pangasius sp.) di Kawasan Surabaya

Aulia, Wina Intan Nur (2024) Aplikasi DNA Barcoding Menggunakan Marka CO1 (Cytochrome Oxidase I) dan CytB (Cytochrome-B) Untuk Autentikasi Produk Ikan Patin (Pangasius sp.) di Kawasan Surabaya. Other thesis, Institut Teknologi Sepuluh Nopember.

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Abstract

DNA Barcoding adalah teknik identifikasi secara molekuler yang diyakini paling praktis dan akurat untuk sampel produk olahan yang bentuknya tidak lagi utuh karena akan menyulitkan jika diidentifikasi dengan karakter morfologi. Meskipun dianggap memiliki banyak keunggulan dibandingkan teknik konvensional, beberapa kelemahan ditemukan pada identifikasi dengan metode DNA diantaranya database sekuen yang masih terbatas. Keberhasilan identifikasi dengan metode DNA sangat ditentukan oleh keutuhan fragmen DNA target dan penggunaan primer PCR yang sesuai. Jenis marka molekuler yang sering digunakan untuk identifikasi spesies ikan juga beragam seperti Cytochrome Oxidase 1 (CO1) dan Cytochrome b (CytB). Ikan patin (Pangasius sp.) dan produk olahannya diyakini memiliki nilai ekonomis yang lebih tinggi dibandingkan jenis ikan lainnya karena tekstur dan citarasanya, sehingga ada kemungkinan pemalsuan terhadap produk filet patin tersebut untuk tujuan ekonomis. Tujuan dari penelitian ini yaitu untuk mengidentifikasi status genetik dari spesies ikan patin (Pangasius sp.) yang dipasarkan di kawasan Surabaya berdasarkan sekuens gen CO1 dan CytB serta mengevaluasi pohon filogenetiknya. Dalam penelitian ini, dilakukan ekstraksi DNA dari dua puluh sampel ikan patin pangasius (yaitu ikan segar dan fillet frozen) dilakukan PCR kemudian disekuensing. Selain itu, uji in silico (yaitu PCR dan RFLP PCR) dilakukan untuk mencari perbedaan genetik ikan patin. Hasil penelitian ini menunjukkan bahwa CO1 menghasilkan profil hasil RFLP yang lebih baik dibandingkan CytB berdasarkan uji in silico dengan menggunakan enzim restriksi tertentu (yaitu: HinFI, NlaIII, TaqI dan BsaXI). Selain itu, kinerja CytB lebih baik pada pengujian PCR dibandingkan dengan CO1, namun kurang akurat untuk menentukan intraspesies Pangasidae menggunakan analisis Neighbor-Joining (NJ) dengan parameter Kimura 2. Hasil in vitro menunjukkan bahwa beberapa spesies patin yang dipasarkan di kawasan Surabaya teridentifikasi sebagai spesies Pangasius pangasius dan Pangasius hypophthalmus.
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DNA Barcoding is a molecular identification technique considered the most practical and accurate for processed product samples that are no longer intact, as morphological characteristics would be difficult for species identification. Even though it is considered to have many advantages compared to conventional techniques, some limitations are found in DNAbased method, including a limited sequence database. The success of identification using the DNA method is highly depended on the integrity of the target DNA fragment, and the use of appropriate PCR primers. Various molecular markers are often used for fish species identification by DNA Barcoding method, such as Cytochrome Oxidase 1 (CO1) and Cytochrome b (CytB). In Indonesia pangasius catfish (Pangasius sp.) is typically marketed as fresh fish and frozen fish fillets. Certain types of pangasius catfish filets are believed to have higher economic value than other types of the catfish because of their texture and taste, leading to potential fraud for economic purposes. The aim of this study is to identify the genetic status of the pangasius catfish (Pangasius sp.) marketed in the Surabaya area based on the use of CO1 and CytB as genetic marker for sequencing, and to explore the RFLP method as alternative of sequencing. In this study, we extracted the DNA of twenty pangasius catfish samples (i.e., fresh fish and fRozen fillets), and amplified the CO1 and CytB gene for sequencing. In addition, the in silico assay (i.e., PCR and RFLP PCR) were performed to evaluate the potential of the genetic marker in DNA Barcoding of pangasius catfish. The findings of this study show that CO1 produce a better profile of RFLP result than CytB based on in silico assay utilizing certain restriction enzymes (i.e., HinFI, NlaIII, TaqI and BsaXI). Additionally, the CytB is better performed in the PCR assay compared to CO1, but less accurate to determine intraspecies of some Pangasius species based on result of the Neighbor-Joining (NJ) Tree analysis using Kimura 2 parameters. In vitro results show that several catfish species marketed in the Surabaya area are identified as Pangasius pangasius and Pangasius hypophthalmus.

Item Type:	Thesis (Other)
Uncontrolled Keywords:	Pangasius sp., DNA Barcoding, Cytochrome Oxidase 1 (CO1), Cytochrome b (Cytb), In Silico, PCR RLFP.
Subjects:	Q Science > QH Biology > QH426 Genetics
Divisions:	Faculty of Science and Data Analytics (SCIENTICS) > Biology > 46201-(S1) Undergraduate Thesis
Depositing User:	Wina Intan Nur Aulia
Date Deposited:	13 Aug 2024 03:59
Last Modified:	13 Aug 2024 03:59
URI:	http://repository.its.ac.id/id/eprint/115205

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