珊瑚礁生態系是地球上擁有高生物歧異度的生態系，有「海中的熱帶雨林」之稱，珊瑚礁中所孕育的生物種類，超過陸地上所有物種的總和；近年來全球的珊瑚礁劣化的情況非常嚴重，除了溫室效應造成珊瑚礁白化死亡外，更發現藍綠藻(Cyanobacteria)與海綿Terpios hoshinota共生後，大量覆蓋於珊瑚礁上，造成珊瑚礁死亡，俗稱「珊瑚黑死病」；本研究為了對於藍綠藻GI1有基因階段的了解，本文利用生物資訊中的基因體序列分析技術對藍綠藻GI1進行全新全基因組序列組裝(de novo assembly)，得到藍綠藻GI1的基因體大小大約為7Mb，再透過全基因組序列進一步利用MEGA 5.05對於藍綠藻GI1分析於藍綠藻中的親緣關係，並可以提供後人研究藍綠藻第二目時有一個全基因組參考序列(Whole genome reference sequence)，對藍綠藻進行更深入的研究。

The ecosystem of the coral reef is the highest biodiversity system on the earth, it's also named 'tropical rain forest of the ocean'.In react years, the situation of the coral reef is getting worse, excepting to the green house effect that cause the death of the coral reef, there is a new research, that mutualism between Terpios hoshinota and Cyanobacteria will cover the coral reef and cause it lack of photosynthesis, called black disease of the coral reef and it has become the disaster of the world. According to researches to this disease, it has found that GI1 is the specie promoted the Terpios hoshinota to invade coral reef. Therefore, the understanding of the GI1 genome is getting more important to assistance the research for it. We sequence whole genome of GI1 by next-generation de novo sequencing method and the de novo assembly to build the whole genome. With the contigs by the velvet assembler , we can further analysis the phylogenetic of GI1. We use MEGA 5.5 to accomplish the phylogenetic tree and it can be a reference for Cyanobacteria type II research in the future. Furthermore, the genome of GI1 assembled in this paper is the first reference of Cyanobacteria type II that can do a further research in the future.

[1] Z. Wang, et al., "De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)," BMC Genomics, vol. 11, p. 726, 2010.
[2] S. F. Altschul, et al., "Basic local alignment search tool," Journal of molecular biology, vol. 215, pp. 403-410, 1990.
[3] M. G. Giglio, et al., "Applying the Gene Ontology in microbial annotation," Trends in Microbiology, vol. 17, pp. 262-268, 2009.
[4] T. D. Harris, et al., "Single-molecule DNA sequencing of a viral genome," Science, vol. 320, pp. 106-9, Apr 4 2008.
[5] W. Ye, et al., "Molecular phylogenetics and the evolution of host plant associations in the nematode genus Fergusobia (Tylenchida: Fergusobiinae)," Mol Phylogenet Evol, vol. 45, pp. 123-41, Oct 2007.
[6] M. Shumway, et al., "Archiving next generation sequencing data," Nucleic Acids Res, vol. 38, pp. D870-1, Jan 2010.
[7] R. Leinonen, et al., "The sequence read archive," Nucleic Acids Res, vol. 39, pp. D19-21, Jan 2011.
[8] E. R. Mardis, "Next-Generation DNA Sequencing Methods," Annual Review of Genomics and Human Genetics, vol. 9, pp. 387-402, 2008.
[9] T. Sasaki, et al., "The genome sequence and structure of rice chromosome 1," NATURE, vol. 420, pp. 312-316, 2002.
[10] S. Huang, et al., "The genome of the cucumber, Cucumis sativus L," Nature genetics, vol. 41, pp. 1275-1281, 2009.
[11] J. Wang, et al., "The diploid genome sequence of an Asian individual," NATURE, vol. 456, pp. 60-65, 2008.
[12] R. Li, et al., "The sequence and de novo assembly of the giant panda genome," NATURE, vol. 463, pp. 311-317, 2009.
[13] N. Siva, "1000 Genomes project," Nature biotechnology, vol. 26, pp. 256-256, 2008.
[14] A. Tomitani, "The evolutionary diversification of cyanobacteria: Molecular-phylogenetic and paleontological perspectives," Proceedings of the National Academy of Sciences, vol. 103, pp. 5442-5447, 2006.
[15] L. T. Tan, "Bioactive natural products from marine cyanobacteria for drug discovery," Phytochemistry, vol. 68, pp. 954-979, 2007.
[16] G. Plucer-Rosario, "The effect of substratum on the growth of Terpios,an encrusting sponge which kills corals," Coral Reefs, vol. 5, p. 197~200, 1987.
[17] S. Gao, et al., "Chemical and Biological Studies of Nakiterpiosin and Nakiterpiosinone," J. AM. CHEM. SOC., vol. 132, p. 371~383, 2009.
[18] P. G. Bryan, "Growth rate, toxicity, and distribution of the encrusting spong Terpios sp in Guam, mariana Islands," Micronesica, vol. 9, p. 237~242, 1973.
[19] B. E. Schirrmeister, et al., "The origin of multicellularity in cyanobacteria," BMC Evolutionary Biology, vol. 11, p. 45, 2011.
[20] J. D. Watson and F. H. G. Crick, "Molecular Structure of Nucleic Acids," Nature, vol. 171, pp. 964-967, 1953.
[21] F. Sanger, et al., "Nucleotide sequence of bacteriophage phi X174 DNA," NATURE, vol. 265, pp. 687-95, Feb 24 1977.
[22] R. Dulbecco, "A turning point in cancer research: sequencing the human genome," Science, vol. 231, pp. 1055-6, Mar 7 1986.
[23] F. S. Collins, "The Human Genome Project: Lessons from Large-Scale Biology," Science, vol. 300, pp. 286-290, 2003.
[24] K. A. Frenkel, "The human genome project and informatics," Communications of the ACM, vol. 34, pp. 40-51, 1991.
[25] E. W. Myers, et al., "On the sequencing and assembly of the human genome," Proc Natl Acad Sci U S A, vol. 99, pp. 4145-6, Apr 2 2002.
[26] R. A. Holt and S. J. M. Jones, "The new paradigm of flow cell sequencing," Genome Research, vol. 18, p. 839, 2008.
[27] M. L. Metzker, "Sequencing technologies- the next generation," Nature Reviews Genetics, vol. 11, pp. 31-46, 2009.
[28] K. L. Nielsen, "Low-Cost-Medium Throughput Sanger Dideoxy Sequencing," METHODS IN MOLECULAR BIOLOGY-CLIFTON THEN TOTOWA-, vol. 387, p. 71, 2008.
[29] S. A. Soper, et al., "Sanger DNA-sequencing reactions performed in a solid-phase nanoreactor directly coupled to capillary gel electrophoresis," Analytical chemistry, vol. 70, pp. 4036-4043, 1998.
[30] S. Anderson, "Shotgun DNA sequencing using cloned DNase I-generated fragments," Nucleic Acids Res, vol. 9, pp. 3015-27, Jul 10 1981.
[31] J. Messing, et al., "A system for shotgun DNA sequencing," Nucleic Acids Res, vol. 9, pp. 309-21, Jan 24 1981.
[32] S. Tommasi, et al., "Innovative technology for cancer risk analysis," Ann Oncol, vol. 22 Suppl 1, pp. i37-43, Jan 2011.
[33] M. Ronaghi, et al., "Real-time DNA sequencing using detection of pyrophosphate release," Analytical Biochemistry, vol. 242, pp. 84-89, Nov 1 1996.
[34] M. Kircher and J. Kelso, "High-throughput DNA sequencing--concepts and limitations," Bioessays, vol. 32, pp. 524-36, Jun 2010.
[35] W. J. Ansorge, "Next-generation DNA sequencing techniques," N Biotechnol, vol. 25, pp. 195-203, Apr 2009.
[36] G. Turcatti, et al., "A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis," Nucleic Acids Research, vol. 36, pp. -, Mar 2008.
[37] M. Fedurco, et al., "BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies," Nucleic Acids Research, vol. 34, pp. -, 2006.
[38] C. Adessi, et al., "Solid phase DNA amplification: characterisation of primer attachment and amplification mechanisms," Nucleic Acids Res, vol. 28, p. E87, Oct 15 2000.
[39] E. R. Mardis, "The impact of next-generation sequencing technology on genetics," Trends in Genetics, vol. 24, pp. 133-141, 2008.
[40] W. Zhang, et al., "A practical comparison of de novo genome assembly software tools for next-generation sequencing technologies," PLoS ONE, vol. 6, p. e17915, 2011.
[41] J. R. Miller, et al., "Assembly algorithms for next-generation sequencing data," Genomics, vol. 95, pp. 315-327, 2010.
[42] J. C. Dohm, et al., "SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing," Genome Research, vol. 17, p. 1697, 2007.
[43] R. L. Warren, et al., "Assembling millions of short DNA sequences using SSAKE," Bioinformatics, vol. 23, p. 500, 2007.
[44] D. Hernandez, et al., "De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer," Genome Research, vol. 18, p. 802, 2008.
[45] J. Chen and S. Skiena, "Assembly for double-ended short-read sequencing technologies," Advances in Genome Sequencing Technology and Algorithms, pp. 123-141, 2007.
[46] H. Mohammad and A. Navid, "Crystallizing short-read assemblies around seeds," BMC Bioinformatics, vol. 10.
[47] S. Kumar and M. L. Blaxter, "Comparing de novo assemblers for 454 transcriptome data," BMC Genomics, vol. 11, p. 571, 2010.
[48] D. R. Zerbino and E. Birney, "Velvet: Algorithms for de novo short read assembly using de Bruijn graphs," Genome Research, vol. 18, pp. 821-829, 2008.
[49] D. R. Zerbino, et al., "Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler," PLoS ONE, vol. 4, p. e8407, 2009.
[50] D. R. Zerbino, "Using the Velvet de novo Assembler for Short Read Sequencing Technologies," 2010.
[51] J. Butler, et al., "ALLPATHS: De novo assembly of whole-genome shotgun microreads," Genome Research, vol. 18, pp. 810-820, 2008.
[52] S. Gnerre, et al., "High-quality draft assemblies of mammalian genomes from massively parallel sequence data," Proceedings of the National Academy of Sciences, vol. 108, p. 1513, 2011.
[53] M. C. Schatz, et al., "Assembly of large genomes using second-generation sequencing," Genome Research, vol. 20, pp. 1165-1173, Sep 2010.
[54] J. C. Dohm, et al., "SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing," Genome Research, vol. 17, pp. 1697-1706, 2007.
[55] 林紋如, "黑皮海綿(Terpios hoshinota)在綠島及蘭嶼的分布與生長," 2009.
[56] E. Hirose and A. Murakami, "Microscopic Anatomy and Pigment Characterization of Coral-Encrusting Black Sponge with Cyanobacterial Symbiont,Terpios hoshinota," Zoological Science, vol. 28, pp. 199-205, 2011.
[57] S.-L. Tang, et al., "Bacteria associated with an encrusting sponge (Terpios hoshinota) and the corals partially covered by the sponge," Environmental Microbiology, pp. no-no, 2011.
[58] R. Klaus and M. Kateherine, "Terpios hoshinota,a new cyanobacteriosponge threatening Pacific reefs," Science Marina, vol. 57, p. 395~403, 1993.
[59] N. Saitou and M. Nei, "The neighbor-joining method: a new method for reconstructing phylogenetic trees," Mol Biol Evol, vol. 4, pp. 406-25, Jul 1987.
[60] Wen-Hsiung Li, Molecular Evolution, 1996.
[61] Wen-Hsiung Li and Dan Graur, Fundamentals of Molecular Evolution, 2000.
[62] L. L. Cavalli-Sforza and A. W. Edwards, "Phylogenetic analysis. Models and estimation procedures," Am J Hum Genet, vol. 19, pp. 233-57, May 1967.
[63] W. G. Weisburg, et al., "16S ribosomal DNA amplification for phylogenetic study," J Bacteriol, vol. 173, pp. 697-703, Jan 1991.
[64] C. R. Woese, et al., "Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids," Microbiology and Molecular Biology Reviews, vol. 47, p. 621, 1983.
[65] E. Roberts, et al., "Molecular signatures of ribosomal evolution," Proc Natl Acad Sci U S A, vol. 105, pp. 13953-8, Sep 16 2008.