Donacidae memiliki keragaman yang tinggi pada aspek morfologi termasuk variasi bentuk dan pola warna. Variasi yang tinggi seringkali menyebabkan kesalahan dalam identifikasi morfologi, sehingga diperlukan identifikasi secara molekuler. Kajian secara molekuler diperlukan untuk keakuratan identifikasi suatu spesies dan mendukung hasil identifikasi secara morfologi. Penelitian ini bertujuan untuk menganalisis karakter morfologi dan molekuler Donax incarnatus yang terdapat di Pantai Badur, Madura berdasarkan gen COI. Metode penelitian meliputi pengambilan sampel, identifikasi sampel secara morfologi, isolasi DNA, amplifikasi gen COI dengan PCR, elektroforesis dan sekuensing. Karakterisasi morfologi dilakukan dengan pengamatan kualitatif dan kuantitatif. Hasil sekuensing dianalisis dengan software bioinformatika. Hasil penelitian menunjukkan terdapat tiga variasi morfologi pada D. incarnatus yaitu warna eksterior cangkang ungu kehitaman, warna eksterior cangkang oranye kekuningan dan warna eksterior cangkang putih. Karakterisasi molekuler menunjukkan bahwa nilai similaritas D. incarnatus variasi D1, D2 dan D3 sebesar 96,06-99,61%. Hasil alignment seluruh sampel dengan spesies acuan dan outgroup diperoleh 5 variasi basa nukleotida. Nilai rata-rata jarak genetik di antara individu D. incarnatus sebesar 0,89%. Hasil rekonstruksi pohon filogenetik D. incarnatus metode Neighbor-Joining dan Maximum Likelihood adalah terbagi menjadi 3 cluster, yang mana spesies D. incarnatus berasal dari Thailand dan sampel penelitian D. incarnatus berasal dari Pantai Badur, Madura berada pada satu cluster yang sama.
Kata kunci: DNA barcode, molecular phylogenic, Cytochrome C Oxidase I
Donacidae has a high diversity in morphological aspects including variations in shape and color patterns. The variations often causes errors in morphological identification, therefore molecular identification is required. Molecular studies are needed for the accuracy of identification of a species and to support morphological identification results. This study aimed to analyze the morphological and molecular characters of Donax incarnatus found in Badur Beach, Madura based on the COI gene. Research methods included sampling, morphological identification of samples, DNA isolation, COI gene amplification by PCR, electrophoresis and sequencing. Morphological characterization was carried out by qualitative and quantitative observations. Sequencing results were analyzed with bioinformatics software. The results showed that there were three morphological variations in D. incarnatus, namely the exterior color of the purple-black shell, the exterior color of the yellowish orange shell and the exterior color of the white shell. Molecular characterization showed that the similarity value of D. incarnatus with variations D1, D2 and D3 was 96.06-99.61%. Alignment results of all samples with reference species and outgroups obtained 5 variations of nucleotide bases. The average value of genetic distance among D. incarnatus individuals was 0.89%. The results of the reconstruction of the D. incarnatus phylogenetic tree using the Neighbor-Joining and Maximum Likelihood methods were divided into 3 clusters, in which the D. incarnatus species came from Thailand and the research sample D. incarnatus came from Badur Beach, Madura, in the same cluster.
Keywords: DNA barcode, molecular phylogenic, Cytochrome C Oxidase I