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Cirrhilabrus cf. ryukyuensis from Cenderawasih Bay and Raja Ampat have different colormorphs with Cirrhilabrus ryukyuensis . This study was conducted to determine the phylogenetic relationship, evolution and genetic diversity of Cirrhilabrus cf . ryukyuensis based on Cytochrome oxidase sub unit 1 (COI) gene. Mitochondrial DNA extracted by using chelex 10%. FISH-BCH and BCL primers were used to amplify COI gene fragment and sequencing. Data analysis conducted by using software Sequencher 4.1 and MEGA 5. COI genes from six samples of C. cf rykyuensis from Cenderawasih Bay and Raja Ampat have total 613 base pairs. The average compositions of nucleotides are T 32.8%, C 26.3%, A 23.2% and G 17.7%. There is six positions of polymorphism that caused by transition. Conversion of nucleotides to amino acid sequence resulted in 204 amino acid with the same sequence. The phylogenetic tree from six sample showed that all in one clade, but different clade from Cirrhilabrus cyanopleura from GenBank Abstrak Cirrhilabrus cf . ryukyuensis asal Teluk Cenderawasih dan Raja Ampat secara morfologi memiliki perbedaan warna dengan Cirrhilabrus ryukyuensis . Penelitian ini bertujuan menentukan hubungan filogenetik, evolusi, dan keragaman genetik  Cirrhilabrus cf . ryukyuensis berdasarkan gen Sitokrom Oksidase sub Unit I (COI). Genom DNA mitokondria diekstrak menggunakan larutan chelex 10%. Primer FISH-BCH dan BCL digunakan untuk mengamplifikasi fragmen Gen COI dan sekuensing. Analisis data dilakukan dengan menggunakan perangkat lunak Sequencher 4.1 dan MEGA 5. Gen COI dari enam sampel C. cf . rykyuensis asal Teluk Cenderawasih dan Raja Ampat, memiliki panjang basa men-capai 613 bp. Komposisi rata-rata nukleotida T 32,8%, C 26,3%, A 23,2% dan G 17,7%. Terdapat enam posisi poli-morfisme yang kesemuanya disebabkan oleh mutasi transition . Hasil penerjemahan nukleotida, diperoleh asam amino dengan panjang 204 asam amino dengan urutan yang sama. Pohon filogenetik menunjukkan keenam sampel berada dalam satu clade yang sama dan berbeda dari clade Cirrhilabrus cyanopleura data Gene Bank.

Genetic analisys of cytochrome oxidase sub unit 1 gene fragment from Cirrhilabrus cf. ryukyuensis (Labridae) from Cenderawasih Bay and Raja Ampat