Kajian Keragaman Genetik Gen Cytochrome Oxidase Subunit 1 (COX1) Ikan Tenggiri (Scomberomorus sp.) Asal Cilacap, Rembang, dan Ambon
Mentari Nabila Anindhita, Prof. Dr. drh. Rini Widayanti, M.P.
2023 | Skripsi | KEDOKTERAN HEWAN
Ikan tenggiri merupakan salah satu spesies ikan yang
termasuk ke dalam golongan ikan pelagis terbesar yang tersebar di berbagai
daerah Indonesia. Ikan ini merupakan bagian dari
famili Scombridae
yang memiliki 15 genus dan 51 spesies. Daerah persebaran ikan tenggiri
di Indonesia meliputi seluruh perairan Sumatera, perairan Jawa, Nusa Tenggara,
Kalimantan, Sulawesi, Ambon, dan Papua. Keberadaan ikan tenggiri di beberapa perairan Indonesia tersebut
tentunya menimbulkan pertanyaan apakah terdapat perbedaan di antara ikan-ikan
tersebut. Oleh karena itu, perlu dilakukan kajian genetik menggunakan analisis
DNA untuk mengetahui keragaman genetiknya.
Terdapat sembilan sampel ikan tenggiri yang berasal
dari Cilacap (C1, C2, dan C3), Rembang (R1, R2, dan R3), Ambon (M1, M2, dan
M3). Sampel isolasi yang digunakan sebagai template untuk proses amplifikasi gen Cytochrome Oxidase I menggunakan primer forward (COISCOMAF)
dan primer reverse (COISCOMAR). Hasil produk PCR sebesar 1673 bp selanjutnya
dilakukan sekuensing DNA. Hasil sekuensing gen COX1 selanjutnya dianalisis
keragaman genetic dan filogenetiknya bersama spesies lain dari Genbank
menggunakan program MEGA XI.
Hasil
analisis menunjukkan bahwa gen COX1 terdiri dari 1252 nukleotida yang menyandi
417 asam amino. Analisis filogram berdasarkan sekuen nukleotida dan sekuen asam
amino gen COX1 menunjukkan bahwa sampel ikan tenggiri asal Rembang dan Ambon
berkerabat dekat dengan jarak genetik 0% - 0,8%. Ikan tenggiri asal Cilacap dan
Rembang berkerabat dekat dengan ikan Scomberomorus niphonius didukung dengan jarak genetic 11,1% - 11,9%. Gen COX1 dapat dijadikan
penanda genetik pada sampel ikan tenggiri asal Cilacap dengan ikan tenggiri
asal Rembang dan Ambon.
Mackerel
fish is one of the fish species that belongs to the largest pelagic fish group
which is spread in various regions of Indonesia. This fish is part of the
Scombridae family which has 15 genera and 51 species. The distribution area of
mackerel in Indonesia covers the waters region of
Sumatra, Java, Nusa Tenggara, Kalimantan, Sulawesi, Ambon and Papua. The
existence of mackerel in several Indonesian waters certainly raises the
question, whether there any
differences between these fish. Therefore, it is necessary to carry out genetic
studies using DNA analysis to determine genetic diversity.
There
were nine samples of mackerel from Cilacap (C1, C2, and C3), Rembang (R1, R2,
and R3), Ambon (M1, M2, and M3). The isolation sample obtained was then used as
a template for the amplification process using the PCR method. The isolation
results will be amplified for Cytochrome
Oxidase I gene using a forward and a reverse primer. The results of the PCR
product were 1673 bp, then DNA sequencing was carried out. The results of the
COX1 gene sequencing were then analyzed for the genetic
and phylogenetic diversity together with eight (8)
species from Genbank using the MEGA XI program.
The
results of data analysis showed that the COX1
gene consists of 1252 nucleotides which encode 417 amino acids. Phylogram
analysis based on nucleotide sequences and amino acid sequences of the COX1 gene described that mackerel
samples from Rembang and Ambon were closely related with a genetic distance of
0% - 0.8%. Mackerel fish from Cilacap, Rembang and Ambon closely related to
Scomberomorus niphonius supported by a genetic distance of 11.1% - 11.9%. The
COX1 gene can be used as a genetic marker in samples of
mackerel from Cilacap and mackerel from Rembang and Ambon with a total
difference of nine amino acids.
Kata Kunci : ikan tenggiri, gen COX1, Scomberomorus sp., PCR, sekuensing
