Seminar Evi Alfiah Taukhid G34062381anitanet.staff.ipb.ac.id/wp-content/plugins/as-pdf... · lebar...
Transcript of Seminar Evi Alfiah Taukhid G34062381anitanet.staff.ipb.ac.id/wp-content/plugins/as-pdf... · lebar...
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Seminar Evi Alfiah Taukhid G34062381
Evi Alfiah Taukhid, Achmad Farajallah dan Arif Wibowo. 2011. KarakterisasiGenom Mitokondria Gen Cyt b pada Ikan Belida Anggota FamiliNotopteridae. Diseminarkan tanggal 2011. Departemen Biologi FMIPA IPB
PENDAHULUAN
Latar Belakang
Ikan belida merupakan ikan tawar anggota genus Chitala, Famili Notopteridae. Ikanbelida atau yang dikenal sebagai ikan pipih mempunyai bentuk pipih dengan mulutlebar dan kepala kecil. Penyebaran alami ikan ini adalah di Sumatera, Jawa, danKalimantan sampai ke semenanjung Malaysia dan Thailand (Permatsari 2009). DiSumatera Selatan, ikan belida digunakan sebagai maskot yang sering dijadikanbahan pembuatan makanan khas. Hal ini karena daging ikan belida berseratlembut, renyah, dan tidak amis. Selain sebagai bahan makanan, ikan belida seringkali dijadikan sebagai ikan hias karena mempunyai bentuk kepala dan variasi warnayang menarik, dan juga mudah dipelihara (Wibowo et al. 2006).
Pada saat ini, diduga populasi ikan belida di alam kondisinya menurun akibatkerusakan habitat dan pemanenan berlebih. Conservation Assessment andManagement Plan (CAMP) mengkategorikan Chitala sp. sebagai spesies langka(Sarkar et al. 2008). Sebagai salah satu penggerak ekonomi masyarakat yangberbasis sumber daya alam, maka berbagai upaya untuk mempelajari populasinyaharus dilakukan. Salah satu upaya yang bisa dilakukan adalah dengan melakukankarakterisasi genom mitokondria sebagai dasar aplikasi lanjutan yang terkaitdengan populasi belida.
Genom mitokondria vertebrata berbentuk sirkular yang terdiri dari 13 gen penyandiprotein, 2 gen penyandi rRNA, 22 gen penyandi tRNA, dan satu ruas tidakmenyandikan yang dikenal sebagai d-loop atau ruas pengontrol (control region).Selain itu, genom mitokondria bersifat non-rekombinasi atau diwariskan secarauniparental. Beberapa gen genom mitokondria seringkali digunakan untuk
page 1 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mempelajari berbagai fenomena populasi, baik intraspesies maupun interspesies(Solihin 1994).
Tujuan
Tujuan penelitian ini adalah menganalisis runutan nukleotida gen cyt b dalamgenom mitokondria ikan belida sebagai dasar mempelajari populasi dan posisifilogenetiknya.
BAHAN DAN METODE
Bahan
Sampel yang digunakan pada penelitian ini adalah 12 sampel darah dan/atau siripikan belida yang diambil dari Sungai Mahakam Kalimantan dan Indragiri Riau.Sampel tersebut merupakan koleksi Bapak Arif Wibowo SP. M.Si dari Balai RisetPerikanan Perairan Umum, Palembang.
Ekstraksi dan Isolasi DNA
Isolasi DNA dilakukan dari darah dan/atau sirip dilakukan menggunakan GenomicDNA mini kit for fresh blood (Geneaid) yang dimodifikasi. Modifikasi dilakukan untukmelisis sel-sel darah dan jaringan yang sudah diawetkan dalam alkohol. Sel-seldarah yang disimpan dalam alkohol 70% dicuci dengan air destilata dua kalikemudian disuspensikan dalam bufer STE (NaCl 1M, Tris-HCL 10mM, EDTA 0.1mM,pH 8.0) hingga volume 350µl. Sedangkan potongan sirip dihancurkan menggunakangunting dalam bufer STE. Sel-sel darah dan sirip dilisis dengan SDS 1% danproteinase K 0.125 mg/ml pada suhu 55oC selama 1 jam sambil dikocok pelan.Metode ekstraksi DNA selanjutnya mengikuti petunjuk Genomic DNA mini kit for
page 2 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
fresh blood (Geneaid).
Amplifikasi dan Visualisasi Fragmen DNA
Amplifikasi gen cyt b genom mitokondria menggunakan pasangan primer W8 danW7 berdasarkan Lavoue´ S dan Sullivana (2004). Pasangan primer ini mengapitruas gen cyt b mulai dari basa ke-14359 hingga 15594 dengan panjang 1236 ntdibandingkan ke genom mitokondria Chitala lopis (GeneBank Accession numberAP008922). Komposisi reaksi PCR dilakukan dengan volume akhir 50 µl terdiri atassampel DNA 5 µl, DW steril 16 µl, primer masing-masing 2 µl dan Taq ready mix 25µl. Reaksi PCR dilakukan menggunakan mesin thermocycler BIOER dengan kondisitahap pradenaturasi 95°C selama 10 menit, tahap berikutnya terdiri dari 35 siklusdari denaturasi 94°C selama satu menit, penempelan primer 42°C selama satumenit dan pemanjangan 72°C selama 1.5 menit. Dan tahap terakhir adalahpemanjangan akhir 72°C selama 7 menit.
Produk PCR diuji menggunakan elektroforesis gel poliakrilamid 6% yang dilanjutkandengan pewarnaan sensitif perak (Tegelstorm 1986).
Perunutan Produk PCR
Produk PCR di atas gel poliakrilamid yang berukuran sesuai dengan desain primerdipilih untuk dimurnikan dengan metode agarose-gel-cutting yang diikuti dengan spin-coloumn DNA extaraction from gel. Produk PCR yang sudah dimurnikandijadikan cetakan dalam PCR for sequencing menggunakan pasangan primer yangsama dengan ampilfikasi awal.
Analisis DNA
Hasil perunutan nukleotida yang diperoleh kemudian diedit secara manualberdasarkan kromatogram mesin perunut DNA. Runutan nukleotida yang telahdiedit kemudian saling disejajarkan menggunakan program Clustal W yang
page 3 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
tertanam dalam MEGA 4.0 (Kumar et al. 2008) dengan melibatkan beberaparunutan gen cyt b anggota famili Notopteridae, yaitu Chitala lopis (AP008922) dan Notopterus notopterus (AP008924). Hasil pensejajaran kemudian diedit ulangsecara manual berdasarkan triplet kodon.
Deskripsi perbandingan runutan nukelotida dan analisis filogeni dilakukanmenggunakan MEGA 4.0 (Kumar et al. 2008) berdasarkan model subtitusi Kimura-2-parameter. Analisis kekerabatan antar sampel menggunakan metode neighbourjoining (NJ) dengan bootstrap 1000x.
HASIL DAN PEMBAHASAN
Amplifikasi dan Visualisasi Fragmen DNA
Amplifikasi gen cyt b dengan menggunakan pasangan primer W8-W7 selalumenghasilkan amplikon yang tidak spesifik (unspecific PCR products). Hal inidisebabkan oleh spesifisitas penempelan primer berkisar antara 66% - 86%terhadap runutan nukleotida genom mitokondria pada beberapa spesiespembanding. Multiband amplicon ini mungkin disebabkan oleh spesifisitas primeryang rendah terhadap runutan mtDNA genus Notopterus. Walaupun begitu, ukuranamplikon yang sesuai dengan desain primer kemudian dipotong setelah dipisahkanmenggunakan metode gel extraction-spin coloumn.
Dari 12 sampel, ada tujuh sampel (KCO001, KCO005, TU02, TU06, TU07, PP03, danKALTIM02) yang menunjukkan adanya amplikon target ukuran, yaitu dengan ukuransekitar 1200 bp. Lima sampel sisanya (PB34, PB02, KCO02, TP04, dan KALBAR03)tidak menghasilkan amplikon yang sesuai dengan target ukuran atau intensitasamplikon yang muncul di atas gel poliakrilamid terlalu tipis.
page 4 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Perunutan Produk PCR
Perunutan nukleotida pada enam sampel yang berasal dari dua lokasi, yaituKCO001 dan KCO005 dari Sungai Indragiri, Riau; TU02, TU06, TU07, dan KALTIM02dari Sungai Mahakam, Kalimantan menunjukkan homologi yang tinggi denganspesies pembanding. Sedangkan satu sampel (PP03) tidak menghasilkankromatogram runutan DNA yang baik. Setelah diedit, panjang runutan DNA yangsaling homolog untuk setiap sampel adalah 650 nt dan diperoleh rata-ratakomposisi nukleotida dari enam sampel tersebut ialah A = 30.7%; T = 25.9%; G =12.8%; C = 30.5%. Dari 650 nt, sebanyak 497 nt sama pada semua sampel.Sedangkan dari 153 nt yang berbeda, terdiri dari 102 nt mengalami substitusihanya pada satu sampel, dan 51 nt berbeda minimal pada dua sampel.
Analisis Filogeni
Jarak genetik antar populasi lokal spesies yang diperoleh dari Sungai Mahakam danIndragiri yang dibandingkan dengan spesies lainnya yang diperoleh dari genebankbiasanya ditentukan untuk populasi hewan tertentu pada daerah geografi yangterpisah. Dua hal yang diperlukan dalam menentukan jarak genetik adalahkesamaan genetik dan nilai jarak genetik. Jarak genetik antar sampel dibandingkandengan sampel spesies yang telah ada di genebank beserta standar error yangdiperoleh berdasarkan model subtitusi K2P dengan bootstrap 1000x (Tabel)menghasilkan nilai rata-rata sebesar 0.089 dengan kesamaan genetik tertinggisebesar 0.168 pada Notopterus notopterus (India) dengan KCO001, serta jarakgenetik terendah sebesar 0.000 pada TU02 dengan KALTIM02.
Tabel. Jarak genetik antar sampel (di bawah diagonal) dan standar error (di atasdiagonal) berdasarkan model subtitusi K2P dengan bootstrap 1000x.
No Sampel 1 2 3 4 5 6 7 81 KALTIM02 0.01
40.009
0.000
0.002
0.004
0.014
0.015
2 KCO001 0.105
0.014
0.014
0.014
0.015
0.015
0.018
page 5 / 308page 5 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
3
page 6 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
KCO005
page 7 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.0
page 8 / 308
0.11 0.00 0.00 0.00 0.01 0.01
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
45
page 9 / 308
2 9 9 9 4 6
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
4
page 10 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TU02
page 11 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.000
page 12 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.105
page 13 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.045
page 14 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 15 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.002
page 16 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.004
page 17 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.014
page 18 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.015
page 19 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
5
page 20 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TU06
page 21 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.002
page 22 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.107
page 23 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.047
page 24 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.002
page 25 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 26 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.004
page 27 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.014
page 28 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.015
page 29 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
6
page 30 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TU07
page 31 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.009
page 32 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.116
page 33 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.053
page 34 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.009
page 35 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.011
page 36 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 37 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.015
page 38 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.016
page 39 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
7
page 40 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
C. lopis
page 41 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.109
page 42 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.116
page 43 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.113
page 44 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.109
page 45 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.111
page 46 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.114
page 47 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 48 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.017
page 49 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
8
page 50 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Notopterus(India)
page 51 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.139
page 52 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.168
page 53 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.143
page 54 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.139
page 55 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.141
page 56 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.151
page 57 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.161
page 58 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TopologipohonfilogenimenggunakanmetodeNJdenganbootstrap1000x,mengelompokkanstrukturpopulasiyangdigambarkanolehmtDNAinisetidaknya
page 59 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
membagipopulasiikanbelidayangberasaldariSungaiMahakamdanIndragirisertaspesieslainyangberasaldarigenebankmenjadiduakelompok(Gambar 2).Kelompok Iterdiri
page 60 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
darisemuasampel(KALTIM02,TU02,TU06,TU07,KCO001,danKCO005),sertasatuspesiesdarigenebank,yaitu C.lopis.Kelompok IIadalah Notopterusnotopterus(India).
page 61 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Titiknenekmoyang(anchestralnode) menunjukkanbahwakekerabatankeenamsampelberasaldarisatunenekmoyang/indukkandengan C.lopis,dengannilaikeragaman1%.Hal
page 62 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
inidisebabkanolehpolapenyebaranikanbelidasangatberkaitaneratdenganarus.Sebagaipredatorairtawar,ikanbelidahidup dihabitatsungaidandaerahyangseringtergena
page 63 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ngbanjir.Hidupnyadidataranrendahdenganketinggiantidaklebihdari30mdpl(Widyastuti1993).DitegaskanpulaolehSjafei etal.(1989)bahwaikaninimerupakancontoh
page 64 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ikanyangberdistribusididataranrendah.Faktor-faktoryangmempengaruhidistribusiikanairtawaradalahfaktorfisikyangmeliputisuhu,derajatfluktuasiair,gradien,urutanaliran,dan
page 65 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
turbiditas;faktorkimiayangmeliputioksigenterlarut,pH,senyawanitrogen,klorinitas,salinitas,danBOD;sertafaktorbiologiyangmeliputihubunganpredatordanmangsa,kompetis
page 66 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
i,dansimbiosis.
Gambar 1. Hasilrekonstruksipohonfilogenipengelompokkanenamsam
page 67 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
peldanduaspesies darigenebank.
SIMPULANDANSARAN
KeragamangenetikdanhubunganfilogeniberdasarkangencytbmtDNApada
page 68 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
enamsampelyangberasaldariSungaiMahakam,KalimantandanIndragiri,Riauyangdibandingkandenganduasampeldarigenebank,beradadalamkelompokyangsamadengan
page 69 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
cytbmtDNAdari Chitalalopis.
DibutuhkanpenelitianlebihlanjutdenganmenggunakanruasgenpadamtDNAselaingencytbdanpengambilansampeldariberb
page 70 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
agaipopulasiyangberbedadariSungaiMahakamdanIndragiriuntukmembuktikankekerabatanantarasampeldengan C.lopis
DAFTARPUST
page 71 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
AKA
Kumar S,Dudley J,NeiM,TamuraK.2008.MEGA: Abiologist-centricsoftwareforevolutionaryanalysisofDNAandproteinsequences.BriefingsinBioinformatics9:29
page 72 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
9-306.
Lavoue´S,SullivanaJP.2004.Simultaneousanalysisoffivemolecularmarkersprovidesawell-supportedphylogenetichypothesis forthelivingbony-tonguefishe
page 73 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
s(Osteoglossomorpha:Teleostei).MolecularPhylogeneticsandEvolution 33(2004)171–185.
PermatsariHP.2009.Faunaidentitasikanbelida. http://indopedia.gunadar
page 74 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ma.ac.id/content/88/5942/id/ikan-belida-notopterus-chitala-hb.html [9September2010].
SarkarUK,NegiRS,DeepakPK,LakraWS,PaulSK.2008.Biologicalparametersofthe
page 75 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
endangeredfish Chitalachitala (Osteoglossiformes:Notopteridae)fromsomeIndianrivers. FisheriesResearch90(2008)170–177.
Sjafei S,RahardjoMF,AffandiR,Brodjo M.
page 76 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
1989.SistematikaIkan.DepartemenPendidikandanKebudayaan,DirektoratJendralPendidikanTinggi,PusatAntarUniversitasIlmuHayat,InstitutPertanianBogor.
page 77 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
SolihinDD.1994.PeranDNAmitokondria(mtDNA)dalamstudikeragamangenetikdanbiologipopulasipadahewan. JHayati1:1-4.
Tegelstrom H.1986.Mitochondrial
page 78 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
DNAinnaturalpopulations:animproveroutineforthe
screening ofgeneticvariationbased onsensitivesilverstaining. Elecytrophoresis 7:226-229.
WibowoA,
page 79 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
SunarnoMTD,MakmurS,Subagja,MuflikhahN.2006.IkanBelida (Chitalalopis)PotensinyaSebagaiIkanHiasUnggulandanBerbagaiHambatanPengembangannya.Palembang:Balai
page 80 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
RisetPerikananPerairanUmum.
WidyastutiYE.1993.Flora-FaunaMaskotNasionaldanPropinsi.PenebarSwadaya:Jakarta.
EviAlfiahTaukhid,AchmadFara
page 81 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
jallahdanArifWibowo.2011. KarakterisasiGenomMitokondriaGenCytbpadaIkanBelidaAnggotaFamiliNotopteridae.Diseminarkantanggal2011.Departemen
page 82 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
BiologiFMIPAIPB
PENDAHULUAN
LatarBelakang
Ikanbelidamerupakanikantawaranggotagenus Chitala, Famili
page 83 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Notopteridae.Ikanbelidaatauyangdikenalsebagaiikanpipihmempunyaibentukpipihdenganmulutlebardankepalakecil.Penyebaranalamiikaniniadalah diSumatera,Jawa,dan
page 84 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
KalimantansampaikesemenanjungMalaysiadanThailand(Permatsari2009).DiSumateraSelatan,ikanbelidadigunakansebagaimaskotyangseringdijadikanbahanpembuatan
page 85 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
makanankhas. Halinikarenadagingikanbelidaberseratlembut,renyah,dantidakamis.Selainsebagaibahanmakanan,ikanbelidaseringkalidijadikansebagaiikanhiaskare
page 86 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
namempunyaibentukkepaladanvariasiwarnayangmenarik,danjugamudahdipelihara(Wibowo et al.2006).
Padasaatini,didugapopulasiikanbelida dialamkondisinya
page 87 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
menurunakibatkerusakanhabitatdanpemanenanberlebih.ConservationAssessmentandManagementPlan(CAMP)mengkategorikan Chitalasp.sebagaispesieslangka(Sarkar etal.
page 88 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
2008).Sebagaisalahsatupenggerakekonomimasyarakatyangberbasissumberdayaalam,makaberbagaiupayauntukmempelajaripopulasinyaharusdilakukan.Salahsatuupay
page 89 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ayangbisadilakukanadalahdenganmelakukankarakterisasigenommitokondriasebagaidasaraplikasilanjutanyangterkaitdenganpopulasibelida.
Genommitokondriavert
page 90 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ebrataberbentuksirkularyangterdiridari13genpenyandiprotein,2genpenyandirRNA,22genpenyanditRNA,dansaturuastidakmenyandikanyangdikenalsebagai d-loopatauruas
page 91 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
pengontrol (controlregion).Selainitu,genommitokondriabersifatnon-rekombinasiataudiwariskansecarauniparental.Beberapagengenommitokondriaseringkalidigunakanuntuk
page 92 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mempelajariberbagaifenomenapopulasi,baikintraspesiesmaupuninterspesies(Solihin1994).
Tujuan
Tujuanpenelitian iniadalahmenganalisis
page 93 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
runutannukleotidagencytbdalamgenommitokondriaikanbelidasebagaidasarmempelajaripopulasidanposisifilogenetiknya.
BAHANDAN
page 94 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
METODE
Bahan
Sampelyangdigunakanpadapenelitian iniadalah12sampeldarahdan/atausiripikanbelidayangdiambildariSungaiMahakamKali
page 95 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mantandanIndragiriRiau.SampeltersebutmerupakankoleksiBapakArifWibowoSP.M.SidariBalaiRisetPerikananPerairanUmum,Palembang.
Ekstra
page 96 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ksidanIsolasiDNA
IsolasiDNAdilakukandaridarahdan/atausiripdilakukanmenggunakan GenomicDNAminikitforfreshblood(Geneaid) yangdimodifikasi.Modifikasi
page 97 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
dilakukanuntukmelisissel-seldarahdanjaringanyangsudahdiawetkandalamalkohol.Sel-seldarahyangdisimpandalamalkohol70%dicucidenganairdestilataduakalikem
page 98 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
udiandisuspensikandalambuferSTE(NaCl 1M,Tris-HCL10mM,EDTA0.1mM,pH8.0)hinggavolume350µl.Sedangkanpotongansiripdihancurkanmenggunakanguntingdala
page 99 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mbuferSTE.Sel-seldarahdansiripdilisisdenganSDS1%danproteinase K0.125mg/mlpadasuhu55oCselama1jamsambildikocokpelan.MetodeekstraksiDNAselanjutnya
page 100 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mengikutipetunjuk GenomicDNAminikitforfreshblood(Geneaid).
AmplifikasidanVisualisasiFragmenDNA
Amplifikasi
page 101 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
gencytbgenommitokondriamenggunakanpasanganprimerW8danW7berdasarkanLavoue´SdanSullivana (2004).Pasanganprimerinimengapitruasgencytbmul
page 102 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
aidaribasake-14359hingga15594denganpanjang1236 ntdibandingkankegenommitokondria Chitalalopis(GeneBankAccessionnumberAP008922).KomposisireaksiPCR
page 103 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
dilakukandenganvolumeakhir 50µlterdiriatassampelDNA5 µl,DWsteril 16µl,primermasing-masing 2µldan Taqreadymix 25µl.ReaksiPCRdilakukanmenggunakanmesin ther
page 104 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mocyclerBIOERdengankondisitahappradenaturasi95°Cselama10menit,tahapberikutnyaterdiridari35siklusdaridenaturasi94°Cselamasatumenit,penempelanprimer42°C
page 105 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
selamasatumenitdanpemanjangan72°Cselama1.5menit.Dantahapterakhiradalahpemanjanganakhir72°Cselama7menit.
ProdukPCRdiujimenggunakan
page 106 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
elektroforesisgelpoliakrilamid6%yangdilanjutkandenganpewarnaansensitifperak(Tegelstorm1986).
PerunutanProdukPCR
Produk PCRdiatasgel
page 107 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
poliakrilamidyangberukuransesuaidengandesainprimerdipilihuntukdimurnikandenganmetode agarose-gel-cuttingyangdiikutidengan spin-coloumnDNAextaractionfromgel.Prod
page 108 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ukPCRyangsudahdimurnikandijadikancetakandalam PCRforsequencingmenggunakanpasanganprimeryangsamadenganampilfikasiawal.
Ana
page 109 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
lisisDNA
HasilperunutannukleotidayangdiperolehkemudiandieditsecaramanualberdasarkankromatogrammesinperunutDNA.Runutannukleotida
page 110 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
yangtelahdieditkemudiansalingdisejajarkanmenggunakanprogramClustalWyangtertanamdalamMEGA4.0 (Kumar etal. 2008)denganmelibatkanbeberaparunutan
page 111 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
gencytbanggotafamiliNotopteridae,yaitu Chitalalopis(AP008922)dan Notopterusnotopterus(AP008924).Hasilpensejajarankemudiandieditulangsecaramanualberdasarkan
page 112 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
tripletkodon.
DeskripsiperbandinganrunutannukelotidadananalisisfilogenidilakukanmenggunakanMEGA4.0(Kumar et al.2008)berdasarkanmodelsubtitusi
page 113 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Kimura-2-parameter. Analisiskekerabatanantarsampelmenggunakanmetode neighbourjoining (NJ)dengan bootstrap1000x.
HAS
page 114 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ILDANPEMBAHASAN
AmplifikasidanVisualisasiFragmenDNA
Amplifikasigencytbdenganmenggunakanpasanga
page 115 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
nprimerW8-W7selalumenghasilkanamplikonyangtidakspesifik (unspecificPCRproducts).Halinidisebabkanolehspesifisitaspenempelanprimerberkisarantara66%-86%terh
page 116 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
adaprunutannukleotidagenommitokondriapadabeberapaspesiespembanding. Multibandampliconinimungkindisebabkanolehspesifisitasprimeryangrendahterhadap
page 117 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
runutanmtDNAgenus Notopterus.Walaupunbegitu,ukuranamplikonyangsesuaidengandesainprimerkemudiandipotongsetelahdipisahkanmenggunakanmetode gelextractio
page 118 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
n-spincoloumn.
Dari12sampel,adatujuhsampel(KCO001,KCO005,TU02,TU06,TU07,PP03,danKALTIM02)yangmenunjukkanadanyaamplikontargetukuran,
page 119 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
yaitudenganukuransekitar1200bp.Limasampelsisanya(PB34,PB02,KCO02,TP04,danKALBAR03)tidakmenghasilkanamplikonyangsesuaidengantargetukuranatauinte
page 120 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
nsitasamplikonyangmunculdiatasgelpoliakrilamidterlalutipis.
PerunutanProdukPCR
Perunutannukleotidapadaenamsam
page 121 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
pelyangberasaldaridualokasi,yaituKCO001danKCO005dariSungaiIndragiri,Riau;TU02,TU06,TU07,danKALTIM02dariSungaiMahakam,Kalimantanmenunjukkanhom
page 122 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ologiyangtinggidenganspesiespembanding.Sedangkansatusampel(PP03)tidakmenghasilkankromatogramrunutanDNAyangbaik.Setelahdiedit,panjangrunutanDNAyangsaling
page 123 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
homologuntuksetiapsampeladalah650ntdandiperolehrata-ratakomposisinukleotidadarienamsampeltersebutialahA =30.7%; T=25.9%; G=12.8%; C=30.5%.Dari650
page 124 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
nt,sebanyak497ntsamapadasemuasampel.Sedangkandari153ntyangberbeda,terdiridari102ntmengalamisubstitusihanyapadasatusampel,dan51ntberbedamini
page 125 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
malpadaduasampel.
AnalisisFilogeni
JarakgenetikantarpopulasilokalspesiesyangdiperolehdariSungaiMahakamdanIndragiriyang
page 126 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
dibandingkandenganspesieslainnyayangdiperolehdarigenebankbiasanyaditentukanuntukpopulasihewantertentupadadaerahgeografiyangterpisah.Duahalyangdiperlukandala
page 127 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mmenentukanjarakgenetikadalahkesamaangenetikdannilaijarakgenetik.Jarakgenetikantarsampeldibandingkandengansampelspesiesyangtelahadadigenebank
page 128 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
besertastandarerroryangdiperolehberdasarkanmodelsubtitusiK2Pdenganbootstrap1000x(Tabel)menghasilkannilairata-ratasebesar0.089dengankesamaangenetiktertinggisebe
page 129 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
sar0.168pada Notopterusnotopterus(India)denganKCO001,sertajarakgenetikterendahsebesar0.000padaTU02denganKALTIM02.
Tabel. Jarak
page 130 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
genetikantarsampel(dibawahdiagonal)danstandarerror(diatasdiagonal) berdasarkanmodelsubtitusiK2Pdenganbootstrap1000x.
No Sampel 1 2 3 4 5 6 7 81 KALTIM02 0.01
40.009
0.000
0.002
0.004
0.014
0.015
2 KCO001 0.105
0.014
0.014
0.014
0.015
0.015
0.018
3 KCO005 0.045
0.112
0.009
0.009
0.009
0.014
0.016
4 TU02 0.000
0.105
0.045
0.002
0.004
0.014
0.015
page 131 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 132 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
5
page 133 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TU06
page 134 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.002
page 135 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.107
page 136 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.047
page 137 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.002
page 138 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 139 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.004
page 140 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.014
page 141 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.015
page 142 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
6
page 143 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TU07
page 144 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.009
page 145 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.116
page 146 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.053
page 147 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.009
page 148 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.011
page 149 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 150 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.015
page 151 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.016
page 152 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
7
page 153 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
C. lopis
page 154 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.109
page 155 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.116
page 156 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.113
page 157 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.109
page 158 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.111
page 159 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.114
page 160 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 161 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.017
page 162 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
8
page 163 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Notopterus(India)
page 164 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.139
page 165 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.168
page 166 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.143
page 167 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.139
page 168 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.141
page 169 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.151
page 170 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.161
page 171 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TopologipohonfilogenimenggunakanmetodeNJdenganbootstrap1000x,mengelompokkanstrukturpopulasiyangdigambarkanolehmtDNAinisetidaknya
page 172 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
membagipopulasiikanbelidayangberasaldariSungaiMahakamdanIndragirisertaspesieslainyangberasaldarigenebankmenjadiduakelompok(Gambar 2).Kelompok Iterdiri
page 173 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
darisemuasampel(KALTIM02,TU02,TU06,TU07,KCO001,danKCO005),sertasatuspesiesdarigenebank,yaitu C.lopis.Kelompok IIadalah Notopterusnotopterus(India).
page 174 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Titiknenekmoyang(anchestralnode) menunjukkanbahwakekerabatankeenamsampelberasaldarisatunenekmoyang/indukkandengan C.lopis,dengannilaikeragaman1%.Hal
page 175 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
inidisebabkanolehpolapenyebaranikanbelidasangatberkaitaneratdenganarus.Sebagaipredatorairtawar,ikanbelidahidup dihabitatsungaidandaerahyangseringtergena
page 176 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ngbanjir.Hidupnyadidataranrendahdenganketinggiantidaklebihdari30mdpl(Widyastuti1993).DitegaskanpulaolehSjafei etal.(1989)bahwaikaninimerupakancontoh
page 177 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ikanyangberdistribusididataranrendah.Faktor-faktoryangmempengaruhidistribusiikanairtawaradalahfaktorfisikyangmeliputisuhu,derajatfluktuasiair,gradien,urutanaliran,dan
page 178 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
turbiditas;faktorkimiayangmeliputioksigenterlarut,pH,senyawanitrogen,klorinitas,salinitas,danBOD;sertafaktorbiologiyangmeliputihubunganpredatordanmangsa,kompetis
page 179 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
i,dansimbiosis.
Gambar 1. Hasilrekonstruksipohonfilogenipengelompokkanenamsam
page 180 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
peldanduaspesies darigenebank.
SIMPULANDANSARAN
KeragamangenetikdanhubunganfilogeniberdasarkangencytbmtDNApada
page 181 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
enamsampelyangberasaldariSungaiMahakam,KalimantandanIndragiri,Riauyangdibandingkandenganduasampeldarigenebank,beradadalamkelompokyangsamadengan
page 182 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
cytbmtDNAdari Chitalalopis.
DibutuhkanpenelitianlebihlanjutdenganmenggunakanruasgenpadamtDNAselaingencytbdanpengambilansampeldariberb
page 183 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
agaipopulasiyangberbedadariSungaiMahakamdanIndragiriuntukmembuktikankekerabatanantarasampeldengan C.lopis
DAFTARPUST
page 184 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
AKA
Kumar S,Dudley J,NeiM,TamuraK.2008.MEGA: Abiologist-centricsoftwareforevolutionaryanalysisofDNAandproteinsequences.BriefingsinBioinformatics9:29
page 185 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
9-306.
Lavoue´S,SullivanaJP.2004.Simultaneousanalysisoffivemolecularmarkersprovidesawell-supportedphylogenetichypothesis forthelivingbony-tonguefishe
page 186 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
s(Osteoglossomorpha:Teleostei).MolecularPhylogeneticsandEvolution 33(2004)171–185.
PermatsariHP.2009.Faunaidentitasikanbelida. http://indopedia.gunadar
page 187 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ma.ac.id/content/88/5942/id/ikan-belida-notopterus-chitala-hb.html [9September2010].
SarkarUK,NegiRS,DeepakPK,LakraWS,PaulSK.2008.Biologicalparametersofthe
page 188 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
endangeredfish Chitalachitala (Osteoglossiformes:Notopteridae)fromsomeIndianrivers. FisheriesResearch90(2008)170–177.
Sjafei S,RahardjoMF,AffandiR,Brodjo M.
page 189 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
1989.SistematikaIkan.DepartemenPendidikandanKebudayaan,DirektoratJendralPendidikanTinggi,PusatAntarUniversitasIlmuHayat,InstitutPertanianBogor.
page 190 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
SolihinDD.1994.PeranDNAmitokondria(mtDNA)dalamstudikeragamangenetikdanbiologipopulasipadahewan. JHayati1:1-4.
Tegelstrom H.1986.Mitochondrial
page 191 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
DNAinnaturalpopulations:animproveroutineforthe
screening ofgeneticvariationbased onsensitivesilverstaining. Elecytrophoresis 7:226-229.
WibowoA,
page 192 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
SunarnoMTD,MakmurS,Subagja,MuflikhahN.2006.IkanBelida (Chitalalopis)PotensinyaSebagaiIkanHiasUnggulandanBerbagaiHambatanPengembangannya.Palembang:Balai
page 193 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
RisetPerikananPerairanUmum.
WidyastutiYE.1993.Flora-FaunaMaskotNasionaldanPropinsi.PenebarSwadaya:Jakarta.
EviAlfiahTaukhid,AchmadFara
page 194 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
jallahdanArifWibowo.2011. KarakterisasiGenomMitokondriaGenCytbpadaIkanBelidaAnggotaFamiliNotopteridae.Diseminarkantanggal2011.Departemen
page 195 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
BiologiFMIPAIPB
PENDAHULUAN
LatarBelakang
Ikanbelidamerupakanikantawaranggotagenus Chitala, Famili
page 196 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Notopteridae.Ikanbelidaatauyangdikenalsebagaiikanpipihmempunyaibentukpipihdenganmulutlebardankepalakecil.Penyebaranalamiikaniniadalah diSumatera,Jawa,dan
page 197 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
KalimantansampaikesemenanjungMalaysiadanThailand(Permatsari2009).DiSumateraSelatan,ikanbelidadigunakansebagaimaskotyangseringdijadikanbahanpembuatan
page 198 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
makanankhas. Halinikarenadagingikanbelidaberseratlembut,renyah,dantidakamis.Selainsebagaibahanmakanan,ikanbelidaseringkalidijadikansebagaiikanhiaskare
page 199 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
namempunyaibentukkepaladanvariasiwarnayangmenarik,danjugamudahdipelihara(Wibowo et al.2006).
Padasaatini,didugapopulasiikanbelida dialamkondisinya
page 200 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
menurunakibatkerusakanhabitatdanpemanenanberlebih.ConservationAssessmentandManagementPlan(CAMP)mengkategorikan Chitalasp.sebagaispesieslangka(Sarkar etal.
page 201 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
2008).Sebagaisalahsatupenggerakekonomimasyarakatyangberbasissumberdayaalam,makaberbagaiupayauntukmempelajaripopulasinyaharusdilakukan.Salahsatuupay
page 202 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ayangbisadilakukanadalahdenganmelakukankarakterisasigenommitokondriasebagaidasaraplikasilanjutanyangterkaitdenganpopulasibelida.
Genommitokondriavert
page 203 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ebrataberbentuksirkularyangterdiridari13genpenyandiprotein,2genpenyandirRNA,22genpenyanditRNA,dansaturuastidakmenyandikanyangdikenalsebagai d-loopatauruas
page 204 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
pengontrol (controlregion).Selainitu,genommitokondriabersifatnon-rekombinasiataudiwariskansecarauniparental.Beberapagengenommitokondriaseringkalidigunakanuntuk
page 205 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mempelajariberbagaifenomenapopulasi,baikintraspesiesmaupuninterspesies(Solihin1994).
Tujuan
Tujuanpenelitian iniadalahmenganalisis
page 206 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
runutannukleotidagencytbdalamgenommitokondriaikanbelidasebagaidasarmempelajaripopulasidanposisifilogenetiknya.
BAHANDAN
page 207 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
METODE
Bahan
Sampelyangdigunakanpadapenelitian iniadalah12sampeldarahdan/atausiripikanbelidayangdiambildariSungaiMahakamKali
page 208 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mantandanIndragiriRiau.SampeltersebutmerupakankoleksiBapakArifWibowoSP.M.SidariBalaiRisetPerikananPerairanUmum,Palembang.
Ekstra
page 209 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ksidanIsolasiDNA
IsolasiDNAdilakukandaridarahdan/atausiripdilakukanmenggunakan GenomicDNAminikitforfreshblood(Geneaid) yangdimodifikasi.Modifikasi
page 210 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
dilakukanuntukmelisissel-seldarahdanjaringanyangsudahdiawetkandalamalkohol.Sel-seldarahyangdisimpandalamalkohol70%dicucidenganairdestilataduakalikem
page 211 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
udiandisuspensikandalambuferSTE(NaCl 1M,Tris-HCL10mM,EDTA0.1mM,pH8.0)hinggavolume350µl.Sedangkanpotongansiripdihancurkanmenggunakanguntingdala
page 212 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mbuferSTE.Sel-seldarahdansiripdilisisdenganSDS1%danproteinase K0.125mg/mlpadasuhu55oCselama1jamsambildikocokpelan.MetodeekstraksiDNAselanjutnya
page 213 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mengikutipetunjuk GenomicDNAminikitforfreshblood(Geneaid).
AmplifikasidanVisualisasiFragmenDNA
Amplifikasi
page 214 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
gencytbgenommitokondriamenggunakanpasanganprimerW8danW7berdasarkanLavoue´SdanSullivana (2004).Pasanganprimerinimengapitruasgencytbmul
page 215 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
aidaribasake-14359hingga15594denganpanjang1236 ntdibandingkankegenommitokondria Chitalalopis(GeneBankAccessionnumberAP008922).KomposisireaksiPCR
page 216 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
dilakukandenganvolumeakhir 50µlterdiriatassampelDNA5 µl,DWsteril 16µl,primermasing-masing 2µldan Taqreadymix 25µl.ReaksiPCRdilakukanmenggunakanmesin ther
page 217 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mocyclerBIOERdengankondisitahappradenaturasi95°Cselama10menit,tahapberikutnyaterdiridari35siklusdaridenaturasi94°Cselamasatumenit,penempelanprimer42°C
page 218 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
selamasatumenitdanpemanjangan72°Cselama1.5menit.Dantahapterakhiradalahpemanjanganakhir72°Cselama7menit.
ProdukPCRdiujimenggunakan
page 219 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
elektroforesisgelpoliakrilamid6%yangdilanjutkandenganpewarnaansensitifperak(Tegelstorm1986).
PerunutanProdukPCR
Produk PCRdiatasgel
page 220 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
poliakrilamidyangberukuransesuaidengandesainprimerdipilihuntukdimurnikandenganmetode agarose-gel-cuttingyangdiikutidengan spin-coloumnDNAextaractionfromgel.Prod
page 221 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ukPCRyangsudahdimurnikandijadikancetakandalam PCRforsequencingmenggunakanpasanganprimeryangsamadenganampilfikasiawal.
Ana
page 222 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
lisisDNA
HasilperunutannukleotidayangdiperolehkemudiandieditsecaramanualberdasarkankromatogrammesinperunutDNA.Runutannukleotida
page 223 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
yangtelahdieditkemudiansalingdisejajarkanmenggunakanprogramClustalWyangtertanamdalamMEGA4.0 (Kumar etal. 2008)denganmelibatkanbeberaparunutan
page 224 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
gencytbanggotafamiliNotopteridae,yaitu Chitalalopis(AP008922)dan Notopterusnotopterus(AP008924).Hasilpensejajarankemudiandieditulangsecaramanualberdasarkan
page 225 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
tripletkodon.
DeskripsiperbandinganrunutannukelotidadananalisisfilogenidilakukanmenggunakanMEGA4.0(Kumar et al.2008)berdasarkanmodelsubtitusi
page 226 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Kimura-2-parameter. Analisiskekerabatanantarsampelmenggunakanmetode neighbourjoining (NJ)dengan bootstrap1000x.
HAS
page 227 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ILDANPEMBAHASAN
AmplifikasidanVisualisasiFragmenDNA
Amplifikasigencytbdenganmenggunakanpasanga
page 228 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
nprimerW8-W7selalumenghasilkanamplikonyangtidakspesifik (unspecificPCRproducts).Halinidisebabkanolehspesifisitaspenempelanprimerberkisarantara66%-86%terh
page 229 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
adaprunutannukleotidagenommitokondriapadabeberapaspesiespembanding. Multibandampliconinimungkindisebabkanolehspesifisitasprimeryangrendahterhadap
page 230 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
runutanmtDNAgenus Notopterus.Walaupunbegitu,ukuranamplikonyangsesuaidengandesainprimerkemudiandipotongsetelahdipisahkanmenggunakanmetode gelextractio
page 231 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
n-spincoloumn.
Dari12sampel,adatujuhsampel(KCO001,KCO005,TU02,TU06,TU07,PP03,danKALTIM02)yangmenunjukkanadanyaamplikontargetukuran,
page 232 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
yaitudenganukuransekitar1200bp.Limasampelsisanya(PB34,PB02,KCO02,TP04,danKALBAR03)tidakmenghasilkanamplikonyangsesuaidengantargetukuranatauinte
page 233 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
nsitasamplikonyangmunculdiatasgelpoliakrilamidterlalutipis.
PerunutanProdukPCR
Perunutannukleotidapadaenamsam
page 234 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
pelyangberasaldaridualokasi,yaituKCO001danKCO005dariSungaiIndragiri,Riau;TU02,TU06,TU07,danKALTIM02dariSungaiMahakam,Kalimantanmenunjukkanhom
page 235 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ologiyangtinggidenganspesiespembanding.Sedangkansatusampel(PP03)tidakmenghasilkankromatogramrunutanDNAyangbaik.Setelahdiedit,panjangrunutanDNAyangsaling
page 236 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
homologuntuksetiapsampeladalah650ntdandiperolehrata-ratakomposisinukleotidadarienamsampeltersebutialahA =30.7%; T=25.9%; G=12.8%; C=30.5%.Dari650
page 237 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
nt,sebanyak497ntsamapadasemuasampel.Sedangkandari153ntyangberbeda,terdiridari102ntmengalamisubstitusihanyapadasatusampel,dan51ntberbedamini
page 238 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
malpadaduasampel.
AnalisisFilogeni
JarakgenetikantarpopulasilokalspesiesyangdiperolehdariSungaiMahakamdanIndragiriyang
page 239 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
dibandingkandenganspesieslainnyayangdiperolehdarigenebankbiasanyaditentukanuntukpopulasihewantertentupadadaerahgeografiyangterpisah.Duahalyangdiperlukandala
page 240 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
mmenentukanjarakgenetikadalahkesamaangenetikdannilaijarakgenetik.Jarakgenetikantarsampeldibandingkandengansampelspesiesyangtelahadadigenebank
page 241 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
besertastandarerroryangdiperolehberdasarkanmodelsubtitusiK2Pdenganbootstrap1000x(Tabel)menghasilkannilairata-ratasebesar0.089dengankesamaangenetiktertinggisebe
page 242 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
sar0.168pada Notopterusnotopterus(India)denganKCO001,sertajarakgenetikterendahsebesar0.000padaTU02denganKALTIM02.
Tabel. Jarak
page 243 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
genetikantarsampel(dibawahdiagonal)danstandarerror(diatasdiagonal) berdasarkanmodelsubtitusiK2Pdenganbootstrap1000x.
No Sampel 1 2 3 4 5 6 7 81 KALTIM02 0.01
40.009
0.000
0.002
0.004
0.014
0.015
2 KCO001 0.105
0.014
0.014
0.014
0.015
0.015
0.018
3 KCO005 0.045
0.112
0.009
0.009
0.009
0.014
0.016
4 TU02 0.000
0.105
0.045
0.002
0.004
0.014
0.015
page 244 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 245 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
5
page 246 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TU06
page 247 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.002
page 248 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.107
page 249 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.047
page 250 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.002
page 251 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 252 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.004
page 253 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.014
page 254 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.015
page 255 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
6
page 256 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TU07
page 257 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.009
page 258 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.116
page 259 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.053
page 260 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.009
page 261 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.011
page 262 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 263 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.015
page 264 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.016
page 265 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
7
page 266 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
C. lopis
page 267 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.109
page 268 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.116
page 269 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.113
page 270 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.109
page 271 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.111
page 272 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.114
page 273 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
page 274 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.017
page 275 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
8
page 276 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Notopterus(India)
page 277 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.139
page 278 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.168
page 279 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.143
page 280 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.139
page 281 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.141
page 282 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.151
page 283 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
0.161
page 284 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
TopologipohonfilogenimenggunakanmetodeNJdenganbootstrap1000x,mengelompokkanstrukturpopulasiyangdigambarkanolehmtDNAinisetidaknya
page 285 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
membagipopulasiikanbelidayangberasaldariSungaiMahakamdanIndragirisertaspesieslainyangberasaldarigenebankmenjadiduakelompok(Gambar 2).Kelompok Iterdiri
page 286 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
darisemuasampel(KALTIM02,TU02,TU06,TU07,KCO001,danKCO005),sertasatuspesiesdarigenebank,yaitu C.lopis.Kelompok IIadalah Notopterusnotopterus(India).
page 287 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
Titiknenekmoyang(anchestralnode) menunjukkanbahwakekerabatankeenamsampelberasaldarisatunenekmoyang/indukkandengan C.lopis,dengannilaikeragaman1%.Hal
page 288 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
inidisebabkanolehpolapenyebaranikanbelidasangatberkaitaneratdenganarus.Sebagaipredatorairtawar,ikanbelidahidup dihabitatsungaidandaerahyangseringtergena
page 289 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ngbanjir.Hidupnyadidataranrendahdenganketinggiantidaklebihdari30mdpl(Widyastuti1993).DitegaskanpulaolehSjafei etal.(1989)bahwaikaninimerupakancontoh
page 290 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ikanyangberdistribusididataranrendah.Faktor-faktoryangmempengaruhidistribusiikanairtawaradalahfaktorfisikyangmeliputisuhu,derajatfluktuasiair,gradien,urutanaliran,dan
page 291 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
turbiditas;faktorkimiayangmeliputioksigenterlarut,pH,senyawanitrogen,klorinitas,salinitas,danBOD;sertafaktorbiologiyangmeliputihubunganpredatordanmangsa,kompetis
page 292 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
i,dansimbiosis.
Gambar 1. Hasilrekonstruksipohonfilogenipengelompokkanenamsam
page 293 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
peldanduaspesies darigenebank.
SIMPULANDANSARAN
KeragamangenetikdanhubunganfilogeniberdasarkangencytbmtDNApada
page 294 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
enamsampelyangberasaldariSungaiMahakam,KalimantandanIndragiri,Riauyangdibandingkandenganduasampeldarigenebank,beradadalamkelompokyangsamadengan
page 295 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
cytbmtDNAdari Chitalalopis.
DibutuhkanpenelitianlebihlanjutdenganmenggunakanruasgenpadamtDNAselaingencytbdanpengambilansampeldariberb
page 296 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
agaipopulasiyangberbedadariSungaiMahakamdanIndragiriuntukmembuktikankekerabatanantarasampeldengan C.lopis
DAFTARPUST
page 297 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
AKA
Kumar S,Dudley J,NeiM,TamuraK.2008.MEGA: Abiologist-centricsoftwareforevolutionaryanalysisofDNAandproteinsequences.BriefingsinBioinformatics9:29
page 298 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
9-306.
Lavoue´S,SullivanaJP.2004.Simultaneousanalysisoffivemolecularmarkersprovidesawell-supportedphylogenetichypothesis forthelivingbony-tonguefishe
page 299 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
s(Osteoglossomorpha:Teleostei).MolecularPhylogeneticsandEvolution 33(2004)171–185.
PermatsariHP.2009.Faunaidentitasikanbelida. http://indopedia.gunadar
page 300 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
ma.ac.id/content/88/5942/id/ikan-belida-notopterus-chitala-hb.html [9September2010].
SarkarUK,NegiRS,DeepakPK,LakraWS,PaulSK.2008.Biologicalparametersofthe
page 301 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
endangeredfish Chitalachitala (Osteoglossiformes:Notopteridae)fromsomeIndianrivers. FisheriesResearch90(2008)170–177.
Sjafei S,RahardjoMF,AffandiR,Brodjo M.
page 302 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
1989.SistematikaIkan.DepartemenPendidikandanKebudayaan,DirektoratJendralPendidikanTinggi,PusatAntarUniversitasIlmuHayat,InstitutPertanianBogor.
page 303 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
SolihinDD.1994.PeranDNAmitokondria(mtDNA)dalamstudikeragamangenetikdanbiologipopulasipadahewan. JHayati1:1-4.
Tegelstrom H.1986.Mitochondrial
page 304 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
DNAinnaturalpopulations:animproveroutineforthe
screening ofgeneticvariationbased onsensitivesilverstaining. Elecytrophoresis 7:226-229.
WibowoA,
page 305 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
SunarnoMTD,MakmurS,Subagja,MuflikhahN.2006.IkanBelida (Chitalalopis)PotensinyaSebagaiIkanHiasUnggulandanBerbagaiHambatanPengembangannya.Palembang:Balai
page 306 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/
RisetPerikananPerairanUmum.
WidyastutiYE.1993.Flora-FaunaMaskotNasionaldanPropinsi.PenebarSwadaya:Jakarta.
page 307 / 308
Achmad Farajallah | Seminar Evi Alfiah Taukhid G34062381Copyright Achmad Farajallah [email protected]://achamad.staff.ipb.ac.id/2011/12/02/seminar-evi-alfiah-taukhid-g34062381/