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2550-1232 E-ISSN: 2550-0929 JURNAL p-ISSN: 2550-1232 e-ISSN: 2550-0929 JURNAL SUMBERDAYA AKUATIK INDOPASIFIK Berkala Ilmiah Penelitian Perikanan dan Kelautan Volume 1, Nomor 2, November 2017 Foto © Foto Taufik B. Pramono Diterbitkan oleh: FAKULTAS PERIKANAN DAN ILMU KELAUTAN UNIVERSITAS PAPUA MANOKWARI JURNAL SUMBERDAYA AKUATIK INDOPASIFIK Berkala Ilmiah Penelitian Perikanan dan Kelautan Volume 1, Nomor 1, Mei 2017 Jurnal Sumberdaya Akuatik Indopasifik adalah berkala ilmiah hasil penelitian dan telaah pustaka bidang perikanan dan kelautan, diterbitkan oleh Fakultas Perikanan dan Ilmu Kelautan (FPIK) – Universitas Papua (UNIPA). Terbit pertama kali pada bulan Mei 2017 dalam versi cetak dan online. Jurnal ini diterbitkan 2 (dua) kali setahun pada bulan Mei dan November. Redaksi menerima sumbangan artikel dengan ketentuan seperti yang tercantum pada halaman akhir. PENGELOLA JURNAL Penanggung Jawab Dekan Fakultas Perikanan dan Ilmu Kelautan - UNIPA Editor Utama Dr. A. Hamid A. Toha, M.Si Editor Pelaksana Simon P.O. Leatemia, S.Pi, M.Si Tresia S. Tururaja, S.Ik., M.Si Nurhani Widiastuti, S.Pi., M.Si Dandy Saleki, S.Ik, M.Si Muhammad Dailami, S.Si, M.Si Layout Editor Muhammad Ilham Azhar, S.Ik Arnoldus Ananta Samudra, S.Pi Alamat Redaksi Gedung Fakultas Perikanan dan Ilmu Kelautan (FPIK) – UNIPA Jl. Gunung Salju Amban, Kampus UNIPA Manokwari 98314 Telp (0986) 211675, 212165; Fax (0986) 211675 e-mail : [email protected] website : http://ejournalfpikunipa.ac.id Informasi berlangganan, korespondensi dan pengiriman artikel dapat menghubungi redaksi ke alamat di atas. Print ISSN : 2550-1232 Elektronik ISSN : 2550-0929 JURNAL SUMBERDAYA AKUATIK INDOPASIFIK Berkala Ilmiah Penelitian Perikanan dan Kelautan Volume 1, Nomor 1, November 2017 DAFTAR ISI Identifikasi Ikan Genus Mystus Dengan Pendekatan Genetik Taufik B. Pramono, Diana Arfiati, Maheno S. Widodo, Uun 123 – 132 Yanuhar Kelimpahan Fitoplankton Dan Perannya Sebagai Sumber Makanan Ikan Di Teluk Pabean, Jawa Barat 133 - 144 A. Andriani, A. Damar, MF Rahardjo, C.P. H. Simanjuntak, A. Asriansyah, R.M. Aditriawan Hambur Balik Akustik Permukaan Substrat Dasar Perairan Menggunakan Echosounder Bim Tunggal 145 - 152 Baigo Hamuna, Lisiard Dimara, Sri Pujiyati, Nyoman Metta N. Natih Kontribusi Pendapatan Kelompok Usaha Perempuan Pesisir Dalam Pengolahan Hasil Perikanan Di Manokwari 153 - 164 Selvi Tebaiy, Juliana Leiwakabessy, Eddy T Wambrauw Komposisi Jenis Dan Tingkat Trofik (Trophic Level) Hasil Tangkapan Bagan Di Perairan Desa Ohoililir, Kabupaten 165 - 174 Maluku Tenggara E. Almohdar, F. N. J Souisa Karakter Danau Laut Balbullol Di Misool Raja Ampat 175 - 186 Gandi Y.S. Purba, Eko Haryono, Sunarto Pola Sebaran Plankton Secara Horizontal Di Perairan Desa Ohoililir, Kabupaten Maluku Tenggara 187 - 192 Fabian N.J. Souisa, Erna Almohdar Pramono et.al: Identifikasi Ikan Genus Mystus p-ISSN 2550-1232 e-ISSN 2550-0929 IDENTIFIKASI IKAN GENUS MYSTUS DENGAN PENDEKATAN GENETIK Identification Of Mystus Fish With Genetic Approach Taufik B. Pramono1,2, Diana Arfiati2, Maheno S. Widodo2, Uun Yanuhar2 1 PS Budidaya Perairan, FPIK, Unsoed, Purwokerto, 53123, Indonesia 2 Program PascaSarjana, FPIK, UB, Malang, 65145, Indonesia *Korespondensi : [email protected] ABSTRAK Ikan-ikan dari Famili Bagridae di Indonesia mencapai 60 jenis dan salah satunya dari genus Msytus. Metode yang digunakan untuk identifikasi ikan yang sangat cepat dan akurat sangat diperlukan. DNA barcoding adalah teknik identifikasi baru dengan pendekatan molekular. Gen CO1 diamplifikasi dan produk PCR disekuensing serta dianalisis dengan menggunakan software bioinformatika. Pengeditan hasil sekuensing dan penentuan komposisi nukleotida dianalisis dengan software Mega5. Urutan DNA disejajarkan dengan ClustalW vers. 1.4. Sekuens dibandingkan dengan data GenBank menggunakan BLAST (Basic Local Aligment Search Tools) dan BOLDSystems. Pohon filogenetik dibuat dengan menggunakan metode Neighbor_Joining. Salah satu contoh identifikasi ikan dari genus Mystus yang telah dikonfirmasi adalah Mystus nigriceps menjadi Mystus singaringan. Kata Kunci : Identifikasi, Mystus, DNA barcode ABSTRACT The fish of the Bagridae Family in Indonesia reach until 60 species and one of them is from the genus Msytus. The method is used for fast and accurate species identification was needed. DNA barcoding was a new identification method with molecularly approach. The CO1 gene was amplified and PCR products were sequenced and analyzed using bioinformatics software. Editing of sequencing results and determining the nucleotide composition were analyzed with Mega5 software. The DNA sequence was aligned with ClustalW vers. 1.4. Sequences are compared with GenBank data using BLAST (Basic Local Aligment Search Tools) and BOLDSystems. Phylogenetic tree was made using Neighbor_Joining method. One example of the identification of fish from the confirmed Mystus genus is Mystus nigriceps being the Mystus singaringan. Keywords : Identification, Mystus, DNA Barcoding PENDAHULUAN hanya ditemukan di Sundaland (Hubert Ikan air tawar di Indonesia yang et.al., 2015). telah diidentifikasi sekitar 1218 spesies Ikan-ikan famili Bagridae juga dari 84 famili termasuk 1172 spesies asli ditemukan di DAS Serayu Jawa Tengah. dari 79 famili dan 630 spesies bersifat Setijanto et.al. (1999) melaporkan bahwa endemik. Ikan dari Famili Bagridae terdapat tiga spesies ikan famili Bagridae teridentifikasi sebanyak 60 spesies. di Sungai Serayu dan Mengaji yaitu Uniknya, ikan dari Famili Bagridae tidak Mystus gulio, mystus microcanthus dan ditemukan daerah Wallacea dan Sahul, Mystus nigriceps. Putro (2003) dan Pramono (2010) di Sungai Klawing yang ©Jurnal Sumberdaya Akuatik Indopasifik, Vol. 1 No. 2 November 2017, www.ejournalfpikunipa.ac.id 123 Pramono et.al: Identifikasi Ikan Genus Mystus p-ISSN 2550-1232 e-ISSN 2550-0929 masih merupakan DAS Serayu, masing- Ekstraksi DNA, PCR, dan masing mendapatkan spesies ikan famili Sekuensing Bagridae lain yaitu ikan Baceman Ekstraksi DNA genom dari (Mystus nemurus) dan yaitu ikan Seng- sampel menggunakan metode Quick garingan (Mystus nigriceps). Penamaan DNA Tissue/Insect Miniprep Kit (Zymo spesies-spesies ikan dari Famili Bagridae Research). Gen CO1 diamplifikasi meng- yang telah ditemukan dan diteliti di DAS gunakan pasangan primer universal Serayu tersebut berdasarkan karakter LCO1490: 5’-ggtcaacaaatcataaagatattgg- morfologi yang mengacu pada Kotellat 3’ dan HCO2198: 5’-taaacttcagggtgacca et.al. (1993). aaaaatca-3’ (Folmer et.al., 1994). Kom- Penamaan dan determinasi spesies posisi reaksi PCR (25µl), yaitu 12,5 µl yang benar sangat penting untuk mela- PCR Buffer (2x), 0,5 µl primer forward kukan kajian bioekologi dan kajian lain- (10 pmol/µl), 0,5 µl primer reverse (10 nya. Seiring dengan perkembangan bio- pmol/µl), KOD FX Neo (1.0U/µl), 1 µl logi molekuler, telah ditemukan metode template DNA, dan 5 µl ddH O. baru untuk identifikasi spesies berbasis 2 Amplifikasi dilakukan dalam mesin DNA yang dikenal dengan DNA Bar- Toyobo KOD FX Neo Catalog No KFX- coding (Floyd, et.al., 2002; Hebert et.al., 201. 2003a; ). DNA barcoding membe-rikan Reaksi Polimerase Chain Reaction kecepatan dan keakuratan dalam identi- (PCR) dilakukan dalam 35 siklus dengan fikasi spesies dengan fokus analisis pada parameter pre denaturasi awal suhu segmen kecil dari mtDNA (Muchlisin 95oC/3 menit, denaturasi 98oC/10 detik, et.al., 2013; Karim et.al., 2015). DNA annealing 50oC/30 detik, extention 68oC/ barcoding dapat menjadi solusi krisis 1 menit. Hasil PCR divi-sualisasi de- taksonomi (Meier et.al., 2006). ngan elektroforesis gel agarosa 1% (b/v), Penamaan spesies dari ikan Famili dimurnikan meng-gunakan Shrimp Bagridae utamanya ikan Seng-garingan Alkaline Phosphotase (Amersham Bio- (Mystus nigriceps) yang telah diteliti sciences Corporation, Arlington Heights, sebelumnya perlu diperjelas dengan Illinois, USA) dan Exonuclease (Amer- pendekatan genetik menggunakan meto- sham) (SAP/EXO). Sekuensing 2 arah de DNA Barcoding. (bi-directional) dila-kukan oleh First Penelitian ini bertujuan untuk Base CO (Malaysia) menggunakan Big mengkon-firmasi penamaan spesies ikan Dye© terminator v3.1 cycle sequencing dari genus Mystus utamanya Mystus kit Applied Biosystem. nigriceps secara genetik menggunakan marker gen CO1. Harapannya dapat Analisis Data dijadikan dasar dalam manajemen sumberdaya ikan dan konservasi serta Pengeditan hasil sekuensing dan budidayanya selanjutnya. penentuan komposisi nukleotida diana- lisis dengan software Mega5 (Tamura METODE PENELITIAN et.al., 2011). Urutan DNA disejajarkan dengan ClustalW vers. 1.4 (Thompson et Ikan Uji al., 1997). Sekuens dibandingkan dengan Sejumlah 18 ekor ikan uji data GenBank menggunakan BLAST dikoleksi dari Sungai Klawing Kabu- (Basic Local Aligment Search Tools) paten Purbalingga Provinsi Jawa (Altschul et.al., 1997) dan BOLDSys- Tengah pada Februari 2017 dengan tems (Ratnasingham dan Hebert, 2007). bantuan nelayan setempat. Untuk Pohon filogenetik dibuat dengan meng- keperluan idetinfikasi spesies diambil gunakan metode Neighbor Joining sebuah jaringan sirip ekor (caudal fin) (Saitou dan Nei, 1987). dan disimpan dalam larutan etanol 95%. 124 ©Jurnal Sumberdaya Akuatik Indopasifik, Vol. 1 No. 2 November 2017, www.ejournalfpikunipa.ac.id Pramono et.al: Identifikasi Ikan Genus Mystus p-ISSN 2550-1232 e-ISSN 2550-0929 HASIL DAN PEMBAHASAN Homologi untuk menentukan identitas spesies dilakukan analisis Hasil PCR menunjukkan gen BLAST (Gambar 3) dan DNA Barcoding CO1 teramplifikasi dengan panjang 697 menggunakan BOLD system (Gambar bp (Gambar 1). Ukuran panjang ampli- 4). fikasi
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