Identifikasi dan Analisis Filogentik Kerang Kima (Genus Tridacna) dari Pulau Kur Menggunakan DNA Barcoding
Abstract
Abstrak
Peran penting kerang Kima secara ekologis sebagai salah satu spesies kunci dalam ekosistem terumbu karang menyebabkan biota laut ini mengalami tekanan antropogenik di sebagian besar wilayah di Indo-Pasifik, termasuk Indonesia. Penelitian ini bertujuan untuk mengidentifikasi spesies Kima genus Tridacna asal Pulau Kur menggunakan markea gen COI dan menganalisis hubungan filogenetiknya. Sampel jaringan Kima diekstrak menggunakan kit ekstraksi komersial. Primer universal (LCO1490; HCO2198) dan primer spesifik Kima (LCO: 5’-GGG TGA TAA TTC GAA CAG AA-3’; RCO: 5’-TAG TTA AAG CCC CAG CTA AA-3’) digunakan untuk mengamplifikasi DNA target. Analisis data dilakukan terhadap 26 sekuen Kima asal Pulau Kur dengan panjang fragmen 479 bp menggunakan software MEGA6 meliputi analisis jarak genetik dan pohon filogenetik. Hasil analisis homologi menggunakan BLASTn mendapatkan empat jenis Kima, yaitu Tridacna maxima, T. crocea, T. noae, dan T. squamosa dengan similaritas 99–100%. Hasil penelitian menunjukkan bahwa jarak genetik dalam spesies sangat rendah berkisar 0,0000–0,0103 sedangkan jarak genetik antar spesies berkisar antara 0,0112–0,1729. Hasil konstruksi pohon filogenetik kerang Kima menunjukkan adanya dua klad utama yang kohesif dan jelas terpisah, yaitu kelompok Tridacna yang monofiletik dan Hippopus hippopus. Berdasarkan hasil penelitian, teknik DNA Barcoding sangat efektif untuk identifikasi dan mengkonfirmasi fenomena cryptic spesies.
Abstract
The role of the giant clam as the key and ecologically important species in coral reef ecosystem has led them to experience anthropogenic pressure in the most of Indo-pacific region including Indonesia. This research aimed to identify the species of giant clam Tridacna from Kur Island, Southeast Maluku by using COI gene marker and to analyze their phylogenetic relationship. The tissue sample of giant clam was extracted with a commercial extraction kit. Universal primer (LCO1490; HCO2198) and specific primer for giant clam (LCO: 5’-GGG TGA TAA TTC GAA CAG AA-3’; RCO: 5’-TAG TT AAG CCC CAG CTA AA-3’) was used to amplify DNA target. Twenty-six sequences from Kur Island with 479 bp fragment length were analyzed by using MEGA6 software. Homological analysis on BLASTn found four species i.e Tridacna maxima, T. crocea, T. noae, and T. squamosa with 99–100% similarity. The result also showed that genetic distance value intraspecies was very low ranging from 0.000 to 0.0105, while genetic distance inter-species ranged from 0.0112 to 0.1729. Reconstruction of phylogenetic tree of giant clam revealed two main group that cohesive and clearly separated i.e Tridacna group which monophyletic and Hippopus hippopuxs. Based on the result, the DNA barcoding technique was effective for identification and confirmation of the occurrence of cryptic species phenomenon.
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DOI: https://doi.org/10.15408/kauniyah.v15i1.17631 Abstract - 0 PDF - 0
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