Elucidation of bacterial genome complexity using next-generation sequencing

详细信息    查看全文

• 作者：Jungkon Kim (12)
  Sooin Lee (1)
  HyeonSeok Shin (12)
  Sun Chang Kim (123)
  Byung-Kwan Cho (123) bcho@kaist.ac.kr
• 关键词：genome &#8211 ; transcriptome &#8211 ; interactome &#8211 ; nextgeneration sequencing &#8211 ; systems biology &#8211 ; synthetic biology
• 刊名：Biotechnology and Bioprocess Engineering
• 出版年：2012
• 出版时间：October 2012
• 年：2012
• 卷：17
• 期：5
• 页码：887-899
• 全文大小：382.3 KB
• 参考文献：1. Sanger, F., S. Nicklen, and A. R. Coulson (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74: 5463–5467.
  2. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bult, J.-F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. Fitzhugh, C. Fields, J. D. Gocyne, J. Scott, R. Shirley, L.-I. Liu, A. Glodek, J. M. Kelley, J. F. Weidman, C. A. Phillips, T. Spriggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Nguyen, D. M. Saudek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. M. Geoghagen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, and J. C. Venter (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496–512.
  3. Lander, E. S., L. M. Linton, B. Birren, C. Nusbaum, M. C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J. P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J. C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R. H. Waterston, R. K. Wilson, L. W. Hillier, J. D. McPherson, M. A. Marra, E. R. Mardis, L. A. Fulton, A. T. Chinwalla, K. H. Pepin, W. R. Gish, S. L. Chissoe, M. C. Wendl, K. D. Delehaunty, T. L. Miner, A. Delehaunty, J. B. Kramer, L. L. Cook, R. S. Fulton, D. L. Johnson, P. J. Minx, S. W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J. F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R. A. Gibbs, D. M. Muzny, S. E. Scherer, J. B. Bouck, E. J. Sodergren, K. C. Worley, C. M. Rives, J. H. Gorrell, M. L. Metzker, S. L. Naylor, R. S. Kucherlapati, D. L. Nelson, G. M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, D. R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H. M. Lee, J. Dubois, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R. W. Davis, N. A. Federspiel, A. P. Abola, M. J. Proctor, R. M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D. R. Cox, M. V. Olson, R. Kaul, N. Shimizu, K. Kawasaki, S. Minoshima, G. A. Evans, M. Athanasiou, R. Schultz, B. A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W. R. McCombie, M. de la Bastide, N. Dedhia, H. Blocker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J. A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D. G. Brown, C. B. Burge, L. Cerutti, H. C. Chen, D. Church, M. Clamp, R. R. Copley, T. Doerks, S. R. Eddy, E. E. Eichler, T. S. Furey, J. Galagan, J. G. Gilbert, C. Harmon, Y. Hayashizaki, D. Haussler, H. Hermjakob, K. Hokamp, W. Jang, L. S. Johnson, T. A. Jones, S. Kasif, A. Kaspryzk, S. Kennedy, W. J. Kent, P. Kitts, E. V. Koonin, I. Korf, D. Kulp, D. Lancet, T. M. Lowe, A. McLysaght, T. Mikkelsen, J. V. Moran, N. Mulder, V. J. Pollara, C. P. Ponting, G. Schuler, J. Schultz, G. Slater, A. F. Smit, E. Stupka, J. Szustakowski, D. Thierry-Mieg, J. Thierry-Mieg, L. Wagner, J. Wallis, R. Wheeler, A. Williams, Y. I. Wolf, K. H. Wolfe, S. P. Yang, R. F. Yeh, F. Collins, M. S. Guyer, J. Peterson, A. Felsenfeld, K. A. Wetterstrand, A. Patrinos, M. J. Morgan, P. de Jong, J. J. Catanese, K. Osoegawa, H. Shizuya, S. Choi, and Y. J. Chen (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921.
  4. Venter, J. C., M. D. Adams, E. W. Myers, P. W. Li, R. J. Mural, G. G. Sutton, H. O. Smith, M. Yandell, C. A. Evans, R. A. Holt, J. D. Gocayne, P. Amanatides, R. M. Ballew, D. H. Huson, J. R. Wortman, Q. Zhang, C. D. Kodira, X. H. Zheng, L. Chen, M. Skupski, G. Subramanian, P. D. Thomas, J. Zhang, G. L. Gabor Miklos, C. Nelson, S. Broder, A. G. Clark, J. Nadeau, V. A. McKusick, N. Zinder, A. J. Levine, R. J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A. E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T. J. Heiman, M. E. Higgins, R. R. Ji, Z. Ke, K. A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G. V. Merkulov, N. Milshina, H. M. Moore, A. K. Naik, V. A. Narayan, B. Neelam, D. Nusskern, D. B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, C. Yan, A. Yao, J. Ye, M. Zhan, W. Zhang, H. Zhang, Q. Zhao, L. Zheng, F. Zhong, W. Zhong, S. Zhu, S. Zhao, D. Gilbert, S. Baumhueter, G. Spier, C. Carter, A. Cravchik, T. Woodage, F. Ali, H. An, A. Awe, D. Baldwin, H. Baden, M. Barnstead, I. Barrow, K. Beeson, D. Busam, A. Carver, A. Center, M. L. Cheng, L. Curry, S. Danaher, L. Davenport, R. Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, N. Garg, A. Gluecksmann, B. Hart, J. Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, J. Johnson, F. Kalush, L. Kline, S. Koduru, A. Love, F. Mann, D. May, S. McCawley, T. McIntosh, I. McMullen, M. Moy, L. Moy, B. Murphy, K. Nelson, C. Pfannkoch, E. Pratts, V. Puri, H. Qureshi, M. Reardon, R. Rodriguez, Y. H. Rogers, D. Romblad, B. Ruhfel, R. Scott, C. Sitter, M. Smallwood, E. Stewart, R. Strong, E. Suh, R. Thomas, N. N. Tint, S. Tse, C. Vech, G. Wang, J. Wetter, S. Williams, M. Williams, S. Windsor, E. Winn-Deen, K. Wolfe, J. Zaveri, K. Zaveri, J. F. Abril, R. Guigo, M. J. Campbell, K. V. Sjolander, B. Karlak, A. Kejariwal, H. Mi, B. Lazareva, T. Hatton, A. Narechania, K. Diemer, A. Muruganujan, N. Guo, S. Sato, V. Bafna, S. Istrail, R. Lippert, R. Schwartz, B. Walenz, S. Yooseph, D. Allen, A. Basu, J. Baxendale, L. Blick, M. Caminha, J. Carnes-Stine, P. Caulk, Y. H. Chiang, M. Coyne, C. Dahlke, A. Mays, M. Dombroski, M. Donnelly, D. Ely, S. Esparham, C. Fosler, H. Gire, S. Glanowski, K. Glasser, A. Glodek, M. Gorokhov, K. Graham, B. Gropman, M. Harris, J. Heil, S. Henderson, J. Hoover, D. Jennings, C. Jordan, J. Jordan, J. Kasha, L. Kagan, C. Kraft, A. Levitsky, M. Lewis, X. Liu, J. Lopez, D. Ma, W. Majoros, J. McDaniel, S. Murphy, M. Newman, T. Nguyen, N. Nguyen, M. Nodell, S. Pan, J. Peck, M. Peterson, W. Rowe, R. Sanders, J. Scott, M. Simpson, T. Smith, A. Sprague, T. Stockwell, R. Turner, E. Venter, M. Wang, M. Wen, D. Wu, M. Wu, A. Xia, A. Zandieh, and X. Zhu (2001) The sequence of the human genome. Science 291: 1304–1351.
  5. Mardis, E. R. (2008) Next-generation DNA sequencing meth ods. Annu. Rev. Genomics Hum. Genet. 9: 387–402.
  6. Shendure, J. and H. Ji (2008) Next-generation DNA sequencing. Nat. Biotechnol. 26: 1135–1145.
  7. Metzker, M. L. (2010) Sequencing technologies — the next generation. Nat. Rev. Genet. 11: 31–46.
  8. MacLean, D., J. D. Jones, and D. J. Studholme (2009) Application of ‘next-generation’ sequencing technologies to microbial genetics. Nat. Rev. Microbiol. 7: 287–296.
  9. Margulies, M., M. Egholm, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka, M. S. Braverman, Y. J. Chen, Z. Chen, S. B. Dewell, L. Du, J. M. Fierro, X. V. Gomes, B. C. Godwin, W. He, S. Helgesen, C. H. Ho, G. P. Irzyk, S. C. Jando, M. L. Alenquer, T. P. Jarvie, K. B. Jirage, J. B. Kim, J. R. Knight, J. R. Lanza, J. H. Leamon, S. M. Lefkowitz, M. Lei, J. Li, K. L. Lohman, H. Lu, V. B. Makhijani, K. E. McDade, M. P. McKenna, E. W. Myers, E. Nickerson, J. R. Nobile, R. Plant, B. P. Puc, M. T. Ronan, G. T. Roth, G. J. Sarkis, J. F. Simons, J. W. Simpson, M. Srinivasan, K. R. Tartaro, A. Tomasz, K. A. Vogt, G. A. Volkmer, S. H. Wang, Y. Wang, M. P. Weiner, P. Yu, R. F. Begley, and J. M. Rothberg (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376–380.
  10. Bentley, D. R., S. Balasubramanian, H. P. Swerdlow, G. P. Smith, J. Milton, C. G. Brown, K. P. Hall, D. J. Evers, C. L. Barnes, H. R. Bignell, J. M. Boutell, J. Bryant, R. J. Carter, R. Keira Cheetham, A. J. Cox, D. J. Ellis, M. R. Flatbush, N. A. Gormley, S. J. Humphray, L. J. Irving, M. S. Karbelashvili, S. M. Kirk, H. Li, X. Liu, K. S. Maisinger, L. J. Murray, B. Obradovic, T. Ost, M. L. Parkinson, M. R. Pratt, I. M. Rasolonjatovo, M. T. Reed, R. Rigatti, C. Rodighiero, M. T. Ross, A. Sabot, S. V. Sankar, A. Scally, G. P. Schroth, M. E. Smith, V. P. Smith, A. Spiridou, P. E. Torrance, S. S. Tzonev, E. H. Vermaas, K. Walter, X. Wu, L. Zhang, M. D. Alam, C. Anastasi, I. C. Aniebo, D. M. Bailey, I. R. Bancarz, S. Banerjee, S. G. Barbour, P. A. Baybayan, V. A. Benoit, K. F. Benson, C. Bevis, P. J. Black, A. Boodhun, J. S. Brennan, J. A. Bridgham, R. C. Brown, A. A. Brown, D. H. Buermann, A. A. Bundu, J. C. Burrows, N. P. Carter, N. Castillo, E. C. M. Chiara, S. Chang, R. Neil Cooley, N. R. Crake, O. O. Dada, K. D. Diakoumakos, B. Dominguez-Fernandez, D. J. Earnshaw, U. C. Egbujor, D. W. Elmore, S. S. Etchin, M. R. Ewan, M. Fedurco, L. J. Fraser, K. V. Fuentes Fajardo, W. Scott Furey, D. George, K. J. Gietzen, C. P. Goddard, G. S. Golda, P. A. Granieri, D. E. Green, D. L. Gustafson, N. F. Hansen, K. Harnish, C. D. Haudenschild, N. I. Heyer, M. M. Hims, J. T. Ho, A. M. Horgan, K. Hoschler, S. Hurwitz, D. V. Ivanov, M. Q. Johnson, T. James, T. A. Huw Jones, G. D. Kang, T. H. Kerelska, A. D. Kersey, I. Khrebtukova, A. P. Kindwall, Z. Kingsbury, P. I. Kokko-Gonzales, A. Kumar, M. A. Laurent, C. T. Lawley, S. E. Lee, X. Lee, A. K. Liao, J. A. Loch, M. Lok, S. Luo, R. M. Mammen, J. W. Martin, P. G. McCauley, P. McNitt, P. Mehta, K. W. Moon, J. W. Mullens, T. Newington, Z. Ning, B. Ling Ng, S. M. Novo, M. J. O’Neill, M. A. Osborne, A. Osnowski, O. Ostadan, L. L. Paraschos, L. Pickering, A. C. Pike, D. Chris Pinkard, D. P. Pliskin, J. Podhasky, V. J. Quijano, C. Raczy, V. H. Rae, S. R. Rawlings, A. Chiva Rodriguez, P. M. Roe, J. Rogers, M. C. Rogert Bacigalupo, N. Romanov, A. Romieu, R. K. Roth, N. J. Rourke, S. T. Ruediger, E. Rusman, R. M. Sanches-Kuiper, M. R. Schenker, J. M. Seoane, R. J. Shaw, M. K. Shiver, S. W. Short, N. L. Sizto, J. P. Sluis, M. A. Smith, J. Ernest Sohna Sohna, E. J. Spence, K. Stevens, N. Sutton, L. Szajkowski, C. L. Tregidgo, G. Turcatti, S. Vandevondele, Y. Verhovsky, S. M. Virk, S. Wakelin, G. C. Walcott, J. Wang, G. J. Worsley, J. Yan, L. Yau, M. Zuerlein, J. C. Mullikin, M. E. Hurles, N. J. McCooke, J. S. West, F. L. Oaks, P. L. Lundberg, D. Klenerman, R. Durbin, and A. J. Smith (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53–59.
  11. Shendure, J., G. J. Porreca, N. B. Reppas, X. Lin, J. P. McCutcheon, A. M. Rosenbaum, M. D. Wang, K. Zhang, R. D. Mitra, and G. M. Church (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728–1732.
  12. Harris, T. D., P. R. Buzby, H. Babcock, E. Beer, J. Bowers, I. Braslavsky, M. Causey, J. Colonell, J. Dimeo, J. W. Efcavitch, E. Giladi, J. Gill, J. Healy, M. Jarosz, D. Lapen, K. Moulton, S. R. Quake, K. Steinmann, E. Thayer, A. Tyurina, R. Ward, H. Weiss, and Z. Xie (2008) Single-molecule DNA sequencing of a viral genome. Science 320: 106–9.
  13. Eid, J., A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, A. Bibillo, K. Bjornson, B. Chaudhuri, F. Christians, R. Cicero, S. Clark, R. Dalal, A. Dewinter, J. Dixon, M. Foquet, A. Gaertner, P. Hardenbol, C. Heiner, K. Hester, D. Holden, G. Kearns, X. Kong, R. Kuse, Y. Lacroix, S. Lin, P. Lundquist, C. Ma, P. Marks, M. Maxham, D. Murphy, I. Park, T. Pham, M. Phillips, J. Roy, R. Sebra, G. Shen, J. Sorenson, A. Tomaney, K. Travers, M. Trulson, J. Vieceli, J. Wegener, D. Wu, A. Yang, D. Zaccarin, P. Zhao, F. Zhong, J. Korlach, and S. Turner (2009) Real-time DNA sequencing from single polymerase molecules. Science 323: 133–138.
  14. Rothberg, J. M., W. Hinz, T. M. Rearick, J. Schultz, W. Mileski, M. Davey, J. H. Leamon, K. Johnson, M. J. Milgrew, M. Edwards, J. Hoon, J. F. Simons, D. Marran, J. W. Myers, J. F. Davidson, A. Branting, J. R. Nobile, B. P. Puc, D. Light, T. A. Clark, M. Huber, J. T. Branciforte, I. B. Stoner, S. E. Cawley, M. Lyons, Y. Fu, N. Homer, M. Sedova, X. Miao, B. Reed, J. Sabina, E. Feierstein, M. Schorn, M. Alanjary, E. Dimalanta, D. Dressman, R. Kasinskas, T. Sokolsky, J. A. Fidanza, E. Namsaraev, K. J. McKernan, A. Williams, G. T. Roth, and J. Bustillo (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348–352.
  15. Pagani, I., K. Liolios, J. Jansson, I. M. Chen, T. Smirnova, B. Nosrat, V. M. Markowitz, and N. C. Kyrpides (2012) The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 40: 571–579.
  16. Cho, B. K., K. Zengler, Y. Qiu, Y. S. Park, E. M. Knight, C. L. Barrett, Y. Gao, and B. O. Palsson (2009) The transcription unit architecture of the Escherichia coli genome. Nat. Biotechnol. 27: 1043–1049.
  17. Motamedian, E. and F. Naeimpoor (2011) Prediction of proton exchange and bacterial growth on various substrates using constraint-based modeling approach. Biotechnol. Bioproc. Eng. 16: 875–884.
  18. Choudhary, M., J. M. Yoon, R. Gonzalez, and J. V. Shanks (2011) Re-examination of metabolic fluxes in Escherichia coli during anaerobic fermentation of glucose using 13C labeling experiments and 2-dimensional nuclear magnetic resonance (NMR) spectroscopy. Biotechnol. Bioproc. Eng. 16: 419–437.
  19. Tenaillon, O., A. Rodriguez-Verdugo, R. L. Gaut, P. McDonald, A. F. Bennett, A. D. Long, and B. S. Gaut (2012) The molecular diversity of adaptive convergence. Science 335: 457–461.
  20. Petrosino, J. F., S. Highlander, R. A. Luna, R. A. Gibbs, and J. Versalovic (2009) Metagenomic pyrosequencing and microbial identification. Clin. Chem. 55: 856–866.
  21. Wang, Z., M. Gerstein, and M. Snyder (2009) RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 10: 57–63.
  22. Wold, B. and R. M. Myers (2008) Sequence census methods for functional genomics. Nat. Methods 5: 19–21.
  23. Ronaghi, M., M. Uhl茅n, and P. Nyr茅n (1998) A sequencing method based on real-time pyrophosphate. Science 281: 363–365.
  24. Fedurco, M., A. Romieu, S. Williams, I. Lawrence, and G. Turcatti (2006) BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies. Nucleic Acids Res. 34: 22.
  25. Valouev, A., J. Ichikawa, T. Tonthat, J. Stuart, S. Ranade, H. Peckham, K. Zeng, J. A. Malek, G. Costa, K. McKernan, A. Sidow, A. Fire, and S. M. Johnson (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 18: 1051–1063.
  26. Glenn, T. C. (2011) Field guide to next-generation DNA sequencers. Mol. Ecol. Resour. 11: 759–769.
  27. Cho, B. K., B. Palsson, and K. Zengler (2011) Deciphering the regulatory codes in bacterial genomes. Biotechnol. J. 6: 1052–1063.
  28. Dohm, J. C., C. Lottaz, T. Borodina, and H. Himmelbauer (2007) SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 17: 1697–1706.
  29. Tom, J. (2006) Whole genome assembly using paired end reads in E. coli, B. licheniformis, and S. cerevisiae, Roche.
  30. Conrad, T. M., A. R. Joyce, M. K. Applebee, C. L. Barrett, B. Xie, Y. Gao, and B. O. Palsson (2009) Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing shortterm laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol. 10: 118.
  31. Grunenwald, H., B. Baas, N. Caruccio, and F. Syed (2010) Rapid, high-throughput library preparation for next-generation sequencing. Nat. Methods 7.
  32. Carter, A. T., B. M. Pearson, L. C. Crossman, N. Drou, D. Heavens, D. Baker, M. Febrer, M. Caccamo, K. A. Grant, and M. W. Peck (2011) Complete genome sequence of the proteolytic Clostridium botulinum type A5 (B3botulinum M. Pearson, J. Bacteriol. 193: 2351–2352.
  33. Bao, G., R. Wang, Y. Zhu, H. Dong, S. Mao, Y. Zhang, Z. Chen, Y. Li, and Y. Ma (2011) Complete genome sequence of Clostridium acetobutylicum DSM 1731, a solvent-producing strain with multireplicon genome architecture. J. Bacteriol. 193: 5007–5008.
  34. Oh, S., H. Roh, H.-J. Ko, S. Kim, K. H. Kim, S. E. Lee, I. S. Chang, S. Kim, and I.-G. Choi (2011) Complete genome sequencing of Lactobacillus acidophilus 30SC, isolated from swine intestine. J. Bacteriol. 193: 2882–2883.
  35. Sun, Z., X. Chen, J. Wang, W. Zhao, Y. Shao, Z. Guo, X. Zhang, Z. Zhou, T. Sun, L. Wang, H. Meng, H. Zhang, and W. Chen (2011) Complete genome sequence of Lactobacillus delbrueckii subsp. bulgaricus strain ND02. J. Bacteriol. 193: 3426–3427.
  36. Wegmann, U., K. Overweg, N. Horn, A. Goesmann, A. Narbad, M. J. Gasson, and C. Shearman (2009) Complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry. J. Bacteriol. 191: 7142–7143.
  37. Wang, Y., C. Chen, L. Ai, F. Zhou, Z. Zhou, L. Wang, H. Zhang, W. Chen, and B. Guo (2011) Complete genome sequence of the probiotic Lactobacillus plantarum ST-III. J. Bacteriol. 193: 313–314.
  38. Siezen, R. J., J. Bayjanov, B. Renckens, M. Wels, S. A. F. T. van Hijum, D. Molenaar, and J. E. T. van Hylckama Vlieg (2010) Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium. J. Bacteriol. 192: 2649–2650.
  39. Comas, I., S. Borrell, A. Roetzer, G. Rose, B. Malla, M. Kato-Maeda, J. Galagan, S. Niemann, and S. Gagneux (2012) Wholegenome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes. Nat. Genet. 44: 106–110.
  40. Hernandez, D., P. Francois, L. Farinelli, M. Osteras, and J. Schrenzel (2008) De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. Genome Res. 18: 802–809.
  41. Nishito, Y., Y. Osana, T. Hachiya, K. Popendorf, A. Toyoda, A. Fujiyama, M. Itaya, and Y. Sakakibara (2010) Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data. BMC Genet. 11: 243.
  42. Tajima, N., S. Sato, F. Maruyama, T. Kaneko, N. V. Sasaki, K. Kurokawa, H. Ohta, Y. Kanesaki, H. Yoshikawa, S. Tabata, M. Ikeuchi, and N. Sato (2011) Genomic structure of the cyanobacterium Synechocystis sp. PCC 6803 strain GT-S. DNA Res. 18: 393–399.
  43. Warren, R. L., G. G. Sutton, S. J. M. Jones, and R. A. Holt (2007) Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23: 500–501.
  44. Miller, J. R., S. Koren, and G. Sutton (2010) Assembly algorithms for next-generation sequencing data. Genomics 95: 315–327.
  45. Zhang, J., R. Chiodini, A. Badr, and G. Zhang (2011) The impact of next-generation sequencing on genomics. J. Genet. Genomics 38: 95–109.
  46. Minty, J. J., A. A. Lesnefsky, F. Lin, Y. Chen, T. A. Zaroff, A. B. Veloso, B. Xie, C. A. McConnell, R. J. Ward, D. R. Schwartz, J. M. Rouillard, Y. Gao, E. Gulari, and X. N. Lin (2011) Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. Microb. Cell Fact. 10: 18.
  47. Chistoserdova, L. (2010) Recent progress and new challenges in metagenomics for biotechnology. Biotechnol. Lett. 32: 1351–1359.
  48. Qin, J., R. Li, J. Raes, M. Arumugam, K. S. Burgdorf, C. Manichanh, T. Nielsen, N. Pons, F. Levenez, T. Yamada, D. R. Mende, J. Li, J. Xu, S. Li, D. Li, J. Cao, B. Wang, H. Liang, H. Zheng, Y. Xie, J. Tap, P. Lepage, M. Bertalan, J. M. Batto, T. Hansen, D. Le Paslier, A. Linneberg, H. B. Nielsen, E. Pelletier, P. Renault, T. Sicheritz-Ponten, K. Turner, H. Zhu, C. Yu, M. Jian, Y. Zhou, Y. Li, X. Zhang, N. Qin, H. Yang, J. Wang, S. Brunak, J. Dore, F. Guarner, K. Kristiansen, O. Pedersen, J. Parkhill, J. Weissenbach, P. Bork, and S. D. Ehrlich (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59–65.
  49. Valles, S. M., D. H. Oi, F. Yu, X. X. Tan, and E. A. Buss (2012) Metatranscriptomics and pyrosequencing facilitate discovery of potential viral natural enemies of the invasive Caribbean crazy ant, Nylanderia pubens. PLoS One 7: e31828.
  50. Murakawa, G. J., C. Kwan, J. Yamashita, and D. P. Nierlich (1991) Transcription and decay of the lac messenger: Role of an intergenic terminator. J. Bacteriol. 173: 28–36.
  51. Sorek, R. and P. Cossart (2010) Prokaryotic transcriptomics: A new view on regulation, physiology and pathogenicity. Nat. Rev. Genet. 11: 9–16.
  52. Makita, Y., M. Nakao, N. Ogasawara, and K. Nakai (2004) DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32: 75–77.
  53. de Smit, M. H. and J. van Duin (1990) Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis. Proc. Natl. Acad. Sci. USA 87: 7668–7672.
  54. Laursen, B. S., H. P. S酶rensen, K. K. Mortensen, and H. U. Sperling-Petersen (2005) Initiation of protein synthesis in bacteria. Microbiol. Mol. Biol. R. 69: 101–123.
  55. Bendtsen, K. M., J. Erd玫ssy, Z. Csiszovszki, S. L. Svenningsen, K. Sneppen, S. Krishna, and S. Semsey (2011) Direct and indirect effects in the regulation of overlapping promoters. Nucleic Acids Res. 39: 6879–6885.
  56. Lasa, I., A. Toledo-Arana, A. Dobin, M. Villanueva, I. R. de los Mozos, M. Vergara-Irigaray, V. Segura, D. Fagegaltier, J. R. Penad茅s, J. Valle, C. Solano, and T. R. Gingeras (2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proc. Natl. Acad. Sci. USA 108: 20172–20177.
  57. Casades煤s, J. and D. Low (2006) Epigenetic gene regulation in the bacterial world. Microbiol. Mol. Biol. R. 70: 830–856.
  58. Levin, J. Z., M. Yassour, X. Adiconis, C. Nusbaum, D. A. Thompson, N. Friedman, A. Gnirke, and A. Regev (2010) Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat. Methods 7: 709–715.
  59. Gertz, J., K. E. Varley, N. S. Davis, B. J. Baas, I. Y. Goryshin, R. Vaidyanathan, S. Kuersten, and R. M. Myers (2012) Transposase mediated construction of RNA-seq libraries. Genome Res. 22: 134–141.
  60. Pease, J. and R. Sooknanan (2012) A rapid, directional RNAseq library preparation workflow for Illumina庐 sequencing. Nat. Methods: i–ii.
  61. Lamm, A. T., M. R. Stadler, H. Zhang, J. I. Gent, and A. Z. Fire (2011) Multimodal RNA-seq using single-strand, doublestrand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome. Genome Res. 21: 265–275.
  62. Flicek, P., and E. Birney (2009) Sense from sequence reads: methods for alignment and assembly. Nat. Methods 6: 6–12.
  63. Li, H., J. Ruan, and R. Durbin (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18: 1851–1858.
  64. Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10: 25.
  65. Li, H. and R. Durbin (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760.
  66. Li, R., Y. Li, K. Kristiansen, and J. Wang (2008) SOAP: Short oligonucleotide alignment program. Bioinformatics 24: 713–714.
  67. Simpson, J. T., K. Wong, S. D. Jackman, J. E. Schein, S. J. Jones, and I. Birol (2009) ABySS: A parallel assembler for short read sequence data. Genome Res. 19: 1117–1123.
  68. Maccallum, I., D. Przybylski, S. Gnerre, J. Burton, I. Shlyakhter, A. Gnirke, J. Malek, K. McKernan, S. Ranade, T. P. Shea, L. Williams, S. Young, C. Nusbaum, and D. B. Jaffe (2009) ALLPATHS 2: Small genomes assembled accurately and with high continuity from short paired reads. Genome Biol. 10: 103.
  69. Zerbino, D. R. and E. Birney (2008) Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18: 821–829.
  70. Nicol, J. W., G. A. Helt, S. G. Blanchard, Jr., A. Raja, and A. E. Loraine (2009) The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets. Bioinformatics 25: 2730–2731.
  71. Carver, T., M. Berriman, A. Tivey, C. Patel, U. Bohme, B. G. Barrell, J. Parkhill, and M. A. Rajandream (2008) Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24: 2672–2676.
  72. Wang, L., Z. Feng, X. Wang, and X. Zhang (2010) DEGseq: An R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26: 136–138.
  73. Robinson, M. D., D. J. McCarthy, and G. K. Smyth (2010) edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140.
  74. Anders, S., and W. Huber (2010) Differential expression analysis for sequence count data. Genome Biol. 11: 106.
  75. Langmead, B., K. D. Hansen, and J. T. Leek (2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol. 11: 83.
  76. Nagalakshmi, U., Z. Wang, K. Waern, C. Shou, D. Raha, M. Gerstein, and M. Snyder (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344–1349.
  77. Dornenburg, J. E., A. M. Devita, M. J. Palumbo, and J. T. Wade (2010) Widespread Antisense transcription in Escherichia coli. MBio 1: 00024–00010.
  78. Toledo-Arana, A., O. Dussurget, G. Nikitas, N. Sesto, H. Guet-Revillet, D. Balestrino, E. Loh, J. Gripenland, T. Tiensuu, K. Vaitkevicius, M. Barthelemy, M. Vergassola, M. A. Nahori, G. Soubigou, B. Regnault, J. Y. Coppee, M. Lecuit, J. Johansson, and P. Cossart (2009) The Listeria transcriptional landscape from saprophytism to virulence. Nature 459: 950–956.
  79. Georg, J., B. Voss, I. Scholz, J. Mitschke, A. Wilde, and W. R. Hess (2009) Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol. Syst. Biol. 5: 305.
  80. Liu, J. M., J. Livny, M. S. Lawrence, M. D. Kimball, M. K. Waldor, and A. Camilli (2009) Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing. Nucleic Acids Res. 37: 46.
  81. Sittka, A., S. Lucchini, K. Papenfort, C. M. Sharma, K. Rolle, T. T. Binnewies, J. C. Hinton, and J. Vogel (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet. 4: e1000163.
  82. Rasmussen, S., H. B. Nielsen, and H. Jarmer (2009) The transcriptionally active regions in the genome of Bacillus subtilis. Mol. Microbiol. 73: 1043–1057.
  83. Guell, M., V. van Noort, E. Yus, W. H. Chen, J. Leigh-Bell, K. Michalodimitrakis, T. Yamada, M. Arumugam, T. Doerks, S. Kuhner, M. Rode, M. Suyama, S. Schmidt, A. C. Gavin, P. Bork, and L. Serrano (2009) Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268–1271.
  84. Wurtzel, O., R. Sapra, F. Chen, Y. Zhu, B. A. Simmons, and R. Sorek (2010) A single-base resolution map of an archaeal transcriptome. Genome Res. 20: 133–141.
  85. Qiu, Y., B. K. Cho, Y. S. Park, D. Lovley, B. Palsson, and K. Zengler (2010) Structural and operational complexity of the Geobacter sulfurreducens genome. Genome Res. 20: 1304–1311.
  86. Guell, M., E. Yus, M. Lluch-Senar, and L. Serrano (2011) Bacterial transcriptomics: what is beyond the RNA horiz-ome? Nat. Rev. Microbiol. 9: 658–669.
  87. Sharma, C. M., S. Hoffmann, F. Darfeuille, J. Reignier, S. Findeiss, A. Sittka, S. Chabas, K. Reiche, J. Hackermuller, R. Reinhardt, P. F. Stadler, and J. Vogel (2010) The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 464: 250–255.
  88. Albrecht, M., C. M. Sharma, M. T. Dittrich, T. Muller, R. Reinhardt, J. Vogel, and T. Rudel (2011) The transcriptional landscape of Chlamydia pneumoniae. Genome Biol. 12: 98.
  89. Mitschke, J., J. Georg, I. Scholz, C. M. Sharma, D. Dienst, J. Bantscheff, B. Vo脽, C. Steglich, A. Wilde, J. Vogel, and W. R. Hess (2011) An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc. Natl. Acad. Sci. USA 108: 2124–2129.
  90. J盲ger, D., C. M. Sharma, J. Thomsen, C. Ehlers, J. Vogel, and R. A. Schmitz (2009) Deep sequencing analysis of the Methanosarcina mazei G枚1 transcriptome in response to nitrogen availability. Proc. Natl. Acad. Sci. USA 106: 21878–21882.
  91. Schmidtke, C., S. Findeiss, C. M. Sharma, J. Kuhfuss, S. Hoffmann, J. Vogel, P. F. Stadler, and U. Bonas (2012) Genomewide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res. 40: 2020–2031.
  92. Filiatrault, M. J., P. V. Stodghill, C. R. Myers, P. A. Bronstein, B. G. Butcher, H. Lam, G. Grills, P. Schweitzer, W. Wang, D. J. Schneider, and S. W. Cartinhour (2011) Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One 6: e29335.
  93. Irnov, I., C. M. Sharma, J. Vogel, and W. C. Winkler (2010) Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res. 38: 6637–6651.
  94. Fuchs, R. T., F. J. Grundy, and T. M. Henkin (2006) The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase. Nat. Struct. Mol. Biol. 13: 226–233.
  95. O’Donnell, S. M. and G. R. Janssen (2002) Leaderless mRNAs bind 70S ribosomes more strongly than 30S ribosomal subunits in Escherichia coli. J. Bacteriol. 184: 6730–6733.
  96. Perkins, T. T., R. A. Kingsley, M. C. Fookes, P. P. Gardner, K. D. James, L. Yu, S. A. Assefa, M. He, N. J. Croucher, D. J. Pickard, D. J. Maskell, J. Parkhill, J. Choudhary, N. R. Thomson, and G. Dougan (2009) A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella Typhi. PLoS Genet. 5: e1000569.
  97. Waters, L. S. and G. Storz (2009) Regulatory RNAs in bacteria. Cell 136: 615–628.
  98. Yoder-Himes, D. R., P. S. Chain, Y. Zhu, O. Wurtzel, E. M. Rubin, J. M. Tiedje, and R. Sorek (2009) Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc. Natl. Acad. Sci. USA 106: 3976–3981.
  99. Drevinek, P., M. T. Holden, Z. Ge, A. M. Jones, I. Ketchell, R. T. Gill, and E. Mahenthiralingam (2008) Gene expression changes linked to antimicrobial resistance, oxidative stress, iron depletion and retained motility are observed when Burkholderia cenocepacia grows in cystic fibrosis sputum. BMC Infect. Dis. 8: 121.
  100. Passalacqua, K. D., A. Varadarajan, B. D. Ondov, D. T. Okou, M. E. Zwick, and N. H. Bergman (2009) Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191: 3203–3211.
  101. Park, P. J. (2009) ChIP-seq: Advantages and challenges of a maturing technology. Nat. Rev. Genet. 10: 669–680.
  102. Johnson, D. S., A. Mortazavi, R. M. Myers, and B. Wold (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497–502.
  103. Robertson, G., M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao, T. Zeng, G. Euskirchen, B. Bernier, R. Varhol, A. Delaney, N. Thiessen, O. L. Griffith, A. He, M. Marra, M. Snyder, and S. Jones (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4: 651–657.
  104. Cho, B. K., C. L. Barrett, E. M. Knight, Y. S. Park, and B. O. Palsson (2008) Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc. Natl. Acad. Sci. USA 105: 19462–19467.
  105. Cho, B. K., S. Federowicz, Y. S. Park, K. Zengler, and B. O. Palsson (2012) Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat. Chem. Biol. 8: 65–71.
  106. Cho, B. K., S. A. Federowicz, M. Embree, Y. S. Park, D. Kim, and B. O. Palsson (2011) The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res. 39: 6456–6464.
  107. Cho, B. K., E. M. Knight, C. L. Barrett, and B. O. Palsson (2008) Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res. 18: 900–910.
  108. Grainger, D. C., D. Hurd, M. Harrison, J. Holdstock, and S. J. Busby (2005) Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc. Natl. Acad. Sci. USA 102: 17693–17698.
  109. Grainger, D. C., D. Hurd, M. D. Goldberg, and S. J. Busby (2006) Association of nucleoid proteins with coding and noncoding segments of the Escherichia coli genome. Nucleic Acids Res. 34: 4642–4652.
  110. Grainger, D. C., H. Aiba, D. Hurd, D. F. Browning, and S. J. Busby (2007) Transcription factor distribution in Escherichia coli: Studies with FNR protein. Nucleic Acids Res. 35: 269–278.
  111. Wade, J. T., D. C. Roa, D. C. Grainger, D. Hurd, S. J. Busby, K. Struhl, and E. Nudler (2006) Extensive functional overlap between sigma factors in Escherichia coli. Nat. Struct. Mol. Biol. 13: 806–814.
  112. Herring, C. D., M. Raffaelle, T. E. Allen, E. I. Kanin, R. Landick, A. Z. Ansari, and B. O. Palsson (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J. Bacteriol. 187: 6166–6174.
  113. Wade, J. T., N. B. Reppas, G. M. Church, and K. Struhl (2005) Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 19: 2619–2630.
  114. Alper, H., K. Miyaoku, and G. Stephanopoulos (2005) Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat. Biotechnol. 23: 612–616.
  115. Dye, C., S. Scheele, P. Dolin, V. Pathania, and M. C. Raviglione (1999) Consensus statement. Global burden of tuberculosis: Estimated incidence, prevalence, and mortality by country. WHO global surveillance and monitoring project. JAMA 282: 677–686.
  116. Rodrigue, S., J. Brodeur, P. E. Jacques, A. L. Gervais, R. Brzezinski, and L. Gaudreau (2007) Identification of mycobacterial sigma factor binding sites by chromatin immunoprecipitation assays. J. Bacteriol. 189: 1505–1513.
  117. Prieto, A. I., C. Kahramanoglou, R. M. Ali, G. M. Fraser, A. S. Seshasayee, and N. M. Luscombe (2012) Genomic analysis of DNA binding and gene regulation by homologous nucleoidassociated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res. 40: 3524–3537.
  118. Kahramanoglou, C., A. S. Seshasayee, A. I. Prieto, D. Ibberson, S. Schmidt, J. Zimmermann, V. Benes, G. M. Fraser, and N. M. Luscombe (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res. 39: 2073–2091.
• 作者单位：1. Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 305-701 Korea2. Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon, 305-701 Korea3. Intelligent Synthetic Biology Center, Daejeon, 305-701 Korea
• ISSN：1976-3816

文摘

Next-generation sequencing (NGS) technologies generate higher resolution and less noise data that can allow the assembly of bacterial genome sequences. It also enables the characterization and quantification of transcriptomes, and the genome-wide profiling of DNA-protein interactions. With decreasing cost of NGS, such revolutionary advances in technology has become a powerful tool for studying bacterial genome complexity, which in turn will be used to design synthetic genome. This review describes the NGS approaches, the challenges associated with their application and the advances made so far in characterizing bacterial genomes, transcriptomes, and interactomes. We anticipate these high-throughput data to be a resourceful and broadly used for elucidating bacterial cells at the system level and furthermore, for the synthesis of intelligent biological systems for biotechnological purposes.