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Bottom-up genome assembly using the Bacillus subtilis genome vector


We established a protocol to construct complete recombinant genomes from their small contiguous DNA pieces and obtained the genomes of mouse mitochondrion and rice chloroplast using a B. subtilis genome (BGM) vector. This method allows the design of any recombinant genomes, valuable not only for fundamental research in systems biology and synthetic biology but also for various applications in the life sciences.

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Figure 1: Domino cloning and BReT retrieval.
Figure 2: Complete mouse mitochondrial genome and rice chloroplast genome DNA in the BGM vector.


  1. Itaya, M., Tsuge, K., Koizumi, M. & Fujita, K. Proc. Natl. Acad. Sci. USA 102, 15971–15976 (2005).

    Article  CAS  Google Scholar 

  2. Lartigue, C. et al. Science 317, 632–638 (2007).

    Article  CAS  Google Scholar 

  3. Tian, J. et al. Nature 432, 1050–1054 (2004).

    Article  CAS  Google Scholar 

  4. Itaya, M. et al. J. Biochem. 134, 513–519 (2003).

    Article  CAS  Google Scholar 

  5. Yoon, Y.G. & Koob, M. Nucleic Acids Res. 31, 1407–1415 (2003).

    Article  CAS  Google Scholar 

  6. Yonemura, I. et al. Gene 391, 171–177 (2007).

    Article  CAS  Google Scholar 

  7. Bibb, M.J., Van Etten, R.A., Wright, C.T., Walberg, M.W. & Clayton, D.A. Cell 26, 167–180 (1981).

    Article  CAS  Google Scholar 

  8. Itaya, M. Mol. Gen. Genet. 248, 9–16 (1995).

    Article  CAS  Google Scholar 

  9. Tang, J. et al. Plant Physiol. 135, 412–420 (2004).

    Article  CAS  Google Scholar 

  10. Tsuge, K. & Itaya, M. J. Bacteriol. 183, 5453–5456 (2001).

    Article  CAS  Google Scholar 

  11. Tsuge, K., Matsui, K. & Itaya, M. Nucleic Acids Res. 31, e133 (2003).

    Article  Google Scholar 

  12. Tomita, S., Tsuge, K., Kikuchi, Y. & Itaya, M. Appl. Environ. Microbiol. 70, 2508–2513 (2004).

    Article  CAS  Google Scholar 

  13. Kaneko, S., Akioka, M., Tsuge, K. & Itaya, M. J. Mol. Biol. 349, 1036–1044 (2005).

    Article  CAS  Google Scholar 

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We thank Y. Tozawa, S. Kaneko, I. Yonemura and M. Ikeuchi for helpful discussions. We appreciate the technical help given by Y. Sakuma, and the crude rice DNA samples provided by S. Kosugi and H. Yanagawa (Institute for Advanced Biosciences, Keio Univ.).

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Correspondence to Mitsuhiro Itaya.

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Supplementary Tables 1–2, Supplementary Figures 1–5, Supplementary Methods (PDF 3026 kb)

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Itaya, M., Fujita, K., Kuroki, A. et al. Bottom-up genome assembly using the Bacillus subtilis genome vector. Nat Methods 5, 41–43 (2008).

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