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研究生：	陳冠勳 Santanumurti, Muhammad Browijoyo
論文名稱：	鑑定台灣南部地域石斑魚樣本感染之虹彩病毒株的基因序列分析 Genetic Variation and Geographic Distribution of Iridovirus in Southern Taiwan
指導教授：	洪健睿 Hong, Jiann-Ruey
學位類別：	碩士 Master
系所名稱：	生物科學與科技學院 - 生物科技研究所 Institute of Biotechnology
論文出版年：	2017
畢業學年度：	105
語文別：	英文
論文頁數：	81
中文關鍵詞：	大細胞病毒、ISKNV 、MCP 、DdDP 、ATPase 、台灣
外文關鍵詞：	Megalocytivirus, ISKNV, MCP, DdDP, ATPase, Taiwan
相關次數：	點閱：73 下載：2
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台灣是石斑魚的第二大生產國。但在孵化和集約水產養殖，疾病的問題是不可避免的。大規模感染台灣水產養殖的病原體是來自鳶尾病毒的流感病毒和巨大細胞病毒。幾項研究已經開展檢測台灣傳播何種巨大細胞病毒。不幸的是，襲擊台灣的巨大細胞病毒株不清楚。本研究的目的是找出什麼樣的巨大細胞病毒主要感染台灣南部。分析地區包括白沙倫，茄萣與林圓等三地。根據MCP（Major Capsid Protein)，DdDP （DNA dependent DNA Polymerase）和ATPase（Adenosine Triphosphatase）的PCR來分析不同之病魚樣本，分析基因包括有來進行序列檢測。根據PCR方法的結果台灣南部是被虹膜病毒科的巨噬細胞病感染了從結果我們可以得出結論， ISKNV是通過PCR，根據 MCP，DdDP和ATPase檢測的巨噬細胞病毒株。可以得出結論，ISKNV是在台灣南部傳播的主要巨大細胞病毒株。通過了解其特點，這項研究有助於了解台灣南部的虹膜病毒分佈，防止其蔓延。

關鍵字：大細胞病毒，ISKNV，MCP，DdDP，ATPase，台灣

Taiwan is the second largest producers of groupers. However, in grouper hatchery and intensive culture, the problem of disease is unavoidable. The pathogens that massively infects Taiwan’s grouper culture are ranavirus and megalocytivirus from Iridoviridae family. Several studies were already conducted to detect what kind of iridovirus strain that spread in Taiwan. Unfortunately, the viral strain that attacked Taiwan was still unclear. This study purpose was to find out iridovirus strain mostly infecting the south places of Taiwan, including Baisha, Linyuan and Jieting. Open reading frame encoding the MCP (Major Capsid Protein), DdDP (DNA dependent DNA Polymerase) and ATPase (Adenosine Triphosphatase) were sequenced to determine the viral strain. The results indicated that megalocytivirus was the iridoviridae family that infected the south of Taiwan by using PCR method. Further analysis was conducted according to MCP, DdDP and ATPase to find out megalocytivirus strain. Even though there were insertion and deletion in nucleotides, it could be concluded that megalocytivirus strain that spread in the south of Taiwan was ISKNV-like virus. This research was hopefully useful for understanding iridovirus distribution in the south of Taiwan and preventing its spread.

Keywords : Megalocytivirus, ISKNV, MCP, DdDP, ATPase, Taiwan

Chinese Abstract (中文摘要)	     I
Abstract	    II
Acknowledgments	  VI
Table of Contents	 VII
Contents of Tables	  IX
Contents of Figures	    X
Abbreviation List	 XII
1. Research Background	     1
	1-1 Taiwan aquaculture	     1 
	1-2 Grouper fish	     2
	1-3 Iridovirus	     3
	1-4 Genetic diversity	     4
	1-5 Research objectives	     5
2. Materials and Methods	     6
	2-1 Materials	     6
	2-2 Methodology	     6
	2-2-1 DNA isolation	     6
	2-2-2 PCR (Polymerase Chain Reaction)	     6
	2-2-3 Purification	     7
	2-2-4 Sequencing analysis	     7
	2-2-5 Phylogenetic tree analysis	     8
3. Results	     9
	3-1 Ranavirus distribution in southern Taiwan	     9
	3-2 Megalocytivirus distribution in southern Taiwan	     9
	3-3 Phylogenetic tree of samples	   14 
4. Discussion	   16
References	   19
Tables	   27
Figures	   32

Contents of Tables
Table 1. 	PCR primers used for gene amplification	   28
Table 2. 	Percentage   similarities  of  the  nucleotide  sequence  of  the  MCP   between   the 
	megalocytiviruses isolated from Baisha, Linyuan and Jieting with  references	   29
Table 3. 	Percentage   similarities  of  the  nucleotide  sequence  of  the  ATPase between the    
	megalocytiviruses isolated from Baisha, Linyuan and Jieting with references	   30
Table 4.	Percentage   similarities  of  the  nucleotide  sequence  of  the  DdDP  between  the
	megalocytiviruses isolated from Baisha, Linyuan and Jieting with references	   31


Contents of Figures
Figure 1. 	Agarose  gel  showing  PCR  product  of  MCP of ranavirus  isolated from Baisha, 
	Linyuan and Jieting	   33
Figure 2.	Agarose  gel  showing  PCR  product  of  MCP  of  megalocytivirus  isolated from 
	Baisha, Linyuan and Jieting	   34
Figure 3.	Sequence alignment of MCP isolated from Baisha	   35
Figure 4.	Sequence alignment of MCP isolated from Linyuan	   36
Figure 5.	Sequence alignment of MCP isolated from Jieting	   37
Figure 6.	Comparison of the nucleotide sequence of the MCP between the    megalocytiviruses isolated in Baisha, Linyuan and Jieting with references	   38
Figure 7.	Agarose gel showing PCR product of megalocytivirus ATPase from Baisha, Linyuan and Jieting	   50
Figure 8.	Sequence alignment of ATPase isolated from Baisha	   51
Figure 9.	Sequence alignment of ATPase isolated from Linyuan	   52
Figure 10.	Sequence alignment of ATPase isolated from Jieting	   53
Figure 11.	Comparison    of    the    nucleotide    sequence    of    the    ATPase  between  the 
	megalocytiviruses isolated in Baisha, Linyuan and Jieting with references	   54
Figure 12.	Agarose gel showing PCR product of megalocytivirus DdDP from Baisha, Linyuan and Jieting	   66
Figure 13.	Sequence alignment of DdDP isolated from Baisha	   67
Figure 14.	Sequence alignment of DdDP isolated from Linyuan	   68
Figure 15.	Sequence alignment of DdDP isolated from Jieting	   69
Figure 16.	Comparison    of    the    nucleotide    sequence   of    the    DdDP    between   the  
	megalocytiviruses isolated in Baisha, Linyuan and Jieting with references	   70
Figure 17.	Phylogenetic tree of megalocytivirus based on ATPase	   76
Figure 18.	Phylogenetic tree of megalocytivirus based on MCP	   77
Figure 19. 	Phylogenetic tree of megalocytivirus based on DdDP	   78
Figure 20. 	Phylogenetic tree of ISKNV based on MCP	   79
Figure 21. 	Phylogenetic tree of ISKNV based on ATPase	   80
Figure 22. 	Phylogenetic tree of ISKNV based on DdDP	   81
                                    

Afero, F., Miao, S. and Perez, A. A. Economic analysis of tiger grouper Epinephelus fuscoguttatus and humpback grouper Cromileptes altivelis commercial cage culture in Indonesia. Aquaculture International 18, 725-739, 2010.

Ahn, B. I., Liao, P. A., and Kim, H. Impacts of the cross-straits economic cooperation framework agreement on the grouper fish markets in Taiwan and mainland China: A stochastic simulation analysis. China Agricultural Economic Review 6, 574-597, 2014.

Amos, W., and Harwood, J. Factors affecting levels of genetic diversity in natural populations. Philosophical Transactions Royal Society of London Series B Biological Sciences 353, 177-186, 1998.

Barrett, R. D., and Schluter, D. Adaptation from standing genetic variation. Trends in Ecology and Evolution 23, 38-44, 2008.

Béné, C., Barange, M., Subasinghe, R., Pinstrup-Andersen, P., Merino, G., Hemre, G. I., and Williams, M., 2015. Feeding 9 billion by 2050–Putting fish back on the menu. Food Security 7, 261-274, 2015.

Benjamin, C. Y., Shinn, P. Y., Rebecca, H. C., and Pai, P. L. The Current status of grouper culture operations and cost analysis of the industry in Taiwan. Jacobs Journal of Aquaculture and Research 1, 14, 2015.

Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Molecular Biology and Evolution 17, 540-552, 2000.

Chao, C. B., Chen, C. Y., Lai, Y. Y., Lin, C. S., and Huang, H. T. Histological, ultrastructural, and in situ hybridization study on enlarged cells in grouper Epinephelus hybrids infected by grouper iridovirus in Taiwan (TGIV). Diseases of Aquatic Organisms 58, 127-142, 2004.

Chao, C. B., Yang, S. C., Tsai, H. Y., Chen, C. Y., Lin, C. S. and Huang, H. T. A nested PCR for the detection of grouper iridovirus in Taiwan (TGIV) in cultured hybrid grouper, giant seaperch, and largemouth bass. Journal of Aquatic Animal Health 14, 104-113, 2002.

Chen, C. L., and Qiu, G. H. The long and bumpy journey: Taiwan׳ s aquaculture development and
management. Marine Policy 48, 152-161, 2014.

Chen, M. H., Hung, S. W., Chang, C. H., Chen, P. Y., Lin, C. C., Hsu, T. H., Cheng, C. F., Lin, S. L., Tu, C. Y., Tsang, C. L., and Lin, Y. H. Red sea bream iridovirus infection in marble goby (Bleeker, Oxyeleotrismarmoratus) in Taiwan. African Journal of Microbiology Research 7, 1009-1014, 2013.

Chen, S. C., Chuang, C. T., Hu, S. H., and Nan, F. H. Competitiveness and supply chain management study on Taiwan grouper industry. Supply Chain Management and Information Systems 4, 536-541, 2006.

Chevenet, F., Brun, C., Bañuls, A. L., Jacq, B., and Christen, R. TreeDyn: towards dynamic graphics and annotations for analyses of trees. Biomed Central Bioinformatics 7, 439, 2006.

Chinchar, V. G., Hick, P., Ince, I. A., Jancovich, J. K., Marschang, R., Qin, Q., Subramaniam, K., Waltzek, T. B., Whittington, R., Williams, T., and Zhang, Q. Y. ICTV Virus Taxonomy Profile: Iridoviridae. Journal of General Virology 98, 890-891, 2017.

Chiu, C. H., Cheng, C. H., Cave, W. R., Guu, Y. K., and Cheng, W. Dietary administration of the probiotic, Saccharomyces cerevisiae P13, enhanced the growth, innate immune responses, and disease resistance of the grouper, Epinephelus coioides. Fish and Shellfish Immunology 29, 1053-1059, 2010.

Chou, H. Y., Hsu, C. C., and Peng, T. Y. Isolation and characterization of a pathogenic iridovirus from cultured grouper (Epinephelus sp.) in Taiwan. Fish Pathology 33, 201-206, 1998.

De Silva, S. S., and Turchini, G. M. Towards understanding the impacts of the pet food industry on
world fish and seafood supplies. Journal of Agricultural and Environmental Ethics 21, 459-467, 2008.

Dereeper, A., Audic, S., Claverie, J. M., and Blanc, G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. Biomed Central Evolutionary Biology 10, 8, 2010.

Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32, 1792-1797, 2004.

Evensen, Ø., and Leong, J. A. C. DNA vaccines against viral diseases of farmed fish. Fish and Shellfish Immunology 35, 1751-1758, 2013.

Excoffier, L. Patterns of DNA sequence diversity and genetic structure after a range expansion: lessons from the infinite‐island model. Molecular Ecology 13, 853-864, 2004.

Fabinyi, M. Historical, cultural and social perspectives on luxury seafood consumption in China. Environmental Conservation 39, 83-92, 2012

Fu, X., Li, N., Liu, L., Lin, Q., Wang, F., Lai, Y., Jiang, H., Pan, H., Shi, C., and Wu, S. Genotype
and host range analysis of infectious spleen and kidney necrosis virus (ISKNV). Virus Genes 42, 97-109, 2011.

Goldburg, R. and Naylor, R. Future seascapes, fishing, and fish farming. Frontiers in Ecology and the Environment 3, 21-28, 2005.

Gudding, R., and Van Muiswinkel, W. B. A history of fish vaccination: science-based disease prevention in aquaculture. Fish and Shellfish Immunology 35, 1683-1688, 2013.

Guindon, S., and Gascuel, O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52, 696-704, 2003.

He, J. G., Wang, S. P., Zeng, K., Huang, Z. J., and Chan, S. M. Systemic disease caused by an iridovirus‐like agent in cultured mandarin fish, Siniperca chuatsi (Basilewsky), in China. Journal of Fish Diseases 23, 219-222, 2000.

He, J. G., Zeng, K., Weng, S. P., and Chan, B. C. Experimental transmission, pathogenicity and physical-chemical properties of infectious spleen and kidney necrosis virus (ISKNV). Aquaculture 204, 11-24, 2002.

Hilbert, B. J., Hayes, J. A., Stone, N. P., Duffy, C. M., Sankaran, B., and Kelch, B. A. Structure and mechanism of the ATPase that powers viral genome packaging. Proceedings of the National Academy of Sciences of the United States of America 112, 3792-3799, 2015.

Huang, S. M., Tu, C., Tseng, C. H., Huang, C. C., Chou, C. C., Kuo, H. C. and Chang, S. K. Genetic analysis of fish iridoviruses isolated in Taiwan during 2001-2009. Archives of Virology 156, 1505-1515, 2011.

Huang, X., Huang, Y., Xu, L., Wei, S., Ouyang, Z., Feng, J., and Qin, Q. Identification and
characterization of a novel lymphocystis disease virus isolates from cultured grouper in China. Journal of Fish Diseases 38, 379-387, 2015.

Jacob, C., McDaniels, T., and Hinch, S. Indigenous culture and adaptation to climate change:
sockeye salmon and the St’át’imc people. Mitigation and Adaptation Strategies for Global Change 15, 859-876, 2010.

Jiang, S. T. The quality control status of cobia, Rachycentron canadum, and grouper, Epinephelus malabaricus, in Taiwan. Journal of the World Aquaculture Society 41, 266-273, 2010.

Jung-Schroers, V., Adamek, M., Wohlsein, P., Wolter, J., Wedekind, H., and Steinhagen, D. First outbreak of an infection with infectious spleen and kidney necrosis virus (ISKNV) in ornamental fish in Germany. Diseases of Aquatic Organisms 119, 239-244, 2016.

Kielley, W. W. Myosin adenosine triphosphatase. The Enzymes 5, 159-168, 1961.

Kurita, J., and Nakajima, K. Megalocytiviruses. Viruses 4, 521-538, 2012.

Lai, Y. S., Murali, S., Ju, H. Y., Wu, M. F., Guo, I. C., Chen, S. C., Fang, K., and Chang, C. Y. Two iridovirus‐susceptible cell lines established from kidney and liver of grouper, Epinephelus awoara (Temminck and Schlegel), and partial characterization of grouper iridovirus. Journal of Fish Diseases 23, 379-388, 2000.

Leu, J. H., Wu, M. H., and Chou, H. Y. A comparative study between ranavirus and megalocytivirus infections in orange-spotted grouper (Epinephelus coioides). Journal of Marine Science and Technology 21, 58-64, 2013.

Liao, I. C., Su, H. M., and Chang, E. Y. Techniques in finfish larviculture in Taiwan. Aquaculture 200, 1-31, 2001.

Liu, C. C., Chen, C. M., Pai, T. W., Chou, H. Y., and Hsu, H. H. Exclusive genomic pathway analysis for groupers infected by different iridovirus. IEEE Xplore Digital Library 9, 508-512, 2015.

Losos, J. B. The princeton guide to evolution. Princeton University Press 10, 3-10, 2014.

Munday, B. L., Kwang, J., and Moody, N. Betanodavirus infections of teleost fish: a review.
Journal of Fish Diseases 25, 127-142, 2002.

Mylonas, C. C., De La Gándara, F., Corriero, A., and Ríos, A. B. Atlantic bluefin tuna (Thunnus thynnus) farming and fattening in the Mediterranean Sea. Reviews in Fisheries Science 18, 266-280, 2010.

Naylor, R. L., Goldburg, R. J., Primavera, J. H., and Kautsky, N. Effect of aquaculture on world fish supplies. Nature 405, 1017, 2000.

Nurhidayu, A., Ina-Salwany, M. Y., Daud, H. M. and Harmin, S. A. Isolation, screening and
characterization of potential probiotics from farmed tiger grouper (Epinephelus fuscoguttatus). African Journal of Microbiology Research 6, 1924-1930, 2012.

Reverter, M., Bontemps, N., Lecchini, D., Banaigs, B., and Sasal, P. Use of plant extracts in fish aquaculture as an alternative to chemotherapy: current status and future perspectives. Aquaculture 433, 50-61, 2014.

Rimmer, M. Grouper and snapper aquaculture in Taiwan. Austasia Aquaculture 12, 3-7, 1998.

Sambrook J., Fritsch, E. F., and Maniatis, T. Molecular cloning: a laboratory manual. Cold Spring
Harbor Laboratory Press 2, 54-57, 1989.

Shi, C. Y., Jia, K. T., Yang, B., and Huang, J. Complete genome sequence of a Megalocytivirus (family Iridoviridae) associated with turbot mortality in China. Virology Journal 7, 159, 2010.

Somga, J. R., Somga, S. S., and Reantaso, M. B. Impacts of disease on small-scale grouper culture in the Philippines. FAO Fisheries Technical Paper 406, 207-214, 2002.

Son, V. M., Chang, C. C., Wu, M. C., Guu, Y. K., Chiu, C. H. and Cheng, W. Dietary administration of the probiotic, Lactobacillus plantarum, enhanced the growth, innate immune responses, and disease resistance of the grouper Epinephelus coioides. Fish and Shellfish Immunology 26, 691-698, 2009.

Song, J. Y., Kitamura, S. I., Jung, S. J., Miyadai, T., Tanaka, S., Fukuda, Y., Kim, S. R., and Oh, M. J. Genetic variation and geographic distribution of megalocytiviruses. The Journal of Microbiology 46, 29-33, 2008.

Song, W. J., Qin, Q. W., Qiu, J., Huang, C. H., Wang, F., and Hew, C. L. Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis. Journal of Virology 78, 12576-12590, 2004.

Sudthongkong, C., Miyata, M., and Miyazaki, T. Iridovirus disease in two fresh-water tropical
ornamental fishes: African lampeye and Dwarf Gourami. Diseases of Aquatic Organisms 48 , 163-173, 2002.

Sun, Y. Z., Yang, H. L., Ma, R. L., and Lin, W. Y. Probiotic applications of two dominant gut Bacillus strains with antagonistic activity improved the growth performance and immune responses of grouper Epinephelus coioides. Fish and Shellfish Immunology 29, 803-809, 2010.

Tidona, C. A., Schnitzler, P., Kehm, R., and Darai, G. Is the major capsid protein of iridoviruses a suitable target for the study of viral evolution. Virus Genes 16, 59-66, 1998.

Ting, K. H., Lin, K. L., Jhan, H. T., Huang, T. J., Wang, C. M., and Liu, W. H. Application of a sustainable fisheries development indicator system for Taiwan’s aquaculture industry. Aquaculture 437, 398-407, 2015.

Wang, C. S., Chao, S. Y., Ku, C. C., Wen, C. M., and Shih, H. H. PCR amplification and sequence analysis of the major capsid protein gene of megalocytiviruses isolated in Taiwan. Journal of Fish Diseases 32, 543-550, 2009.

Wang, C. S., and Wen, C. M. Megalocytiviruses. Molecular Detection of Animal Viral Pathogen 1, 825-836, 2016.

Wang, Y. Q., Lü, L., Weng, S. P., Huang, J. N., Chan, S. M. and He, J. G. Molecular epidemiology and phylogenetic analysis of a marine fish infectious spleen and kidney necrosis virus-like (ISKNV-like) virus. Archives of Virology 152, 763-773, 2007.

Wargo, A. R., Kell, A. M., Scott, R. J., Thorgaard, G. H., and Kurath, G. Analysis of host genetic diversity and viral entry as sources of between-host variation in viral load. Virus Research 165, 71-80, 2012.

Whitehead, S. S., Blaney, J. E., Durbin, A. P., and Murphy, B. R. Prospects for a dengue virus vaccine. Nature Reviews Microbiology 5, 518, 2007.

Williams, T., Barbosa-Solomieu, V., and Chinchar, V. G. A decade of advances in research
iridovirus. Advances in Virus Research 65, 174, 2005.

Zhang, M., Xiao, Z. Z., Hu, Y. H., and Sun, L. Characterization of a megalocytivirus from cultured rock bream, Oplegnathus fasciatus (Temminck & Schlege), in China. Aquaculture Research 43, 556-564, 2012.

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