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All Journal Bioma : Berkala Ilmiah Biologi Indonesian Journal of Biotechnology
Christina Retna Handayani, Christina Retna
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Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Education Immunology & microbiology Materials Science & Nanotechnology

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Cloning and Sequence Analysis of Capsid Protein Gene of Iridovirus Indonesian Isolates ., Murwantoko; Handayani, Christina Retna; Pratiwi, Rarastoeti
Indonesian Journal of Biotechnology Vol 14, No 1 (2009)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (131.285 KB)

Abstract

Iridovirus was known as agents that caused serious systemic disease in freshwater and marine fishes. The mortality up to 100% of orange-spotted grouper (Epinephelus coioides) due to iridovirus infection has been reported in Indonesia. The gene encoding capsid protein of iridovirus is supposed to be conserved and has the potency for the development of control methods. The objectives of this study are to clone the gene encoding capsid protein iridovirus and to analyze their sequences. The   spleen tissues of orange-spotted grouper were collected and extracted their DNA. The DNA fragment of capsid protein of iridovirus genes were amplified by PCR using designed primers with the extraction DNA as templates. The amplified DNA fragments were cloned in pBSKSII and sequenced.  The genes encoding capsid protein of iridovirus from Jepara and Bali were successfully amplified and cloned. The Jepara clone (IJP03) contained complete open reading frame (ORF) of the gene composed by 1362 bp nucleotides which encoded 453 amino acids. Those Jepara and Bali (IGD01) clones shared 99.8% similarity in nucleotide level and 99.4% at amino acid level. Based on those sequences, Indonesian iridovirus was belonged to genus Megalocystivirus and shared 99,6-99,9% similarity on nucleotide level with DGIV, ISKNV, MCIV, and ALIV
Karakterisasi Genetik Fragmen Gen Penyandi RNA Polimerase Infectious Myonecrosis Virus (IMNV) yang Menginfeksi Udang Vannamei (Litopenaeus vannamei Boone.) dari Lampung, Gresik dan Pontianak Sudjito, Yason Lukman; Handayani, Christina Retna; Kusumaningrum, Hermin Pancasakti; Budiharjo, Anto
Bioma : Berkala Ilmiah Biologi Vol. 16, No.1, Tahun 2014
Publisher : Departemen Biologi, Fakultas Sains dan Matematika, Universitas Diponegoro

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (178.652 KB) | DOI: 10.14710/bioma.16.1.18-25

Abstract

A massive death of vannamei shrimp (Litopenaeus vannamei Boone.) due to Infectious Myonecrosis Virus (IMNV) infection has occurred in Indonesia recently and still cannot be eradicated efficiently. The fast reproduction of IMNV depends on the RdRp gene that encodes for RNA polymerase. Genetic characterization of IMNV RdRp gene from Indonesia is important in order to compare with other IMNV to find out genetic variation as a base for combating this virus. IMNV-infected vannamei were taken from major aquaculture region in Indonesia (Lampung, Gresik and Pontianak). RNA polymerase coding genes (12 and 13 region) from infected vannamei were amplified using RT-PCR with appropriate primer. Amplification products were sequenced and the results were analyzed using BioEdit 7.1.3.0, ClustalW2, CLC free workbench 6.6.2. and ClustalX programs. Results showed that homology value of IMNV RdRp gene  from Lampung and Gresik were 98,04-9958% compared with IMNV from Brazil (Acc. No. AY570982). Amino acid analysis revealed homology value of IMNV RdRp gene  from Lampung  and Gresik were 100% and 99.04% compared with IMNV from Brasil. IMNV RdRp gene  from Pontianak cannot be analysed due to low quality of RNA.   Key words: vannamei, IMNV, RdRp, genetic characterization
Co-Authors Anto Budiharjo Hermin Pancasakti Kusumaningrum Murwantoko . Rarastoeti Pratiwi Yason Lukman Sudjito, Yason Lukman