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Journal of Bacteriology, May 2007, p. 3680-3681, Vol. 189, No. 9
0021-9193/07/$08.00+0     doi:10.1128/JB.00241-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

The Complete Genome Sequence of Bacillus thuringiensis Al Hakam{triangledown}

Jean F. Challacombe,1,3* Michael R. Altherr,3 Gary Xie,1,3 Smriti S. Bhotika,1,3,§ Nancy Brown,3 David Bruce,1,3 Connie S. Campbell,1,3 Mary L. Campbell,1,3 Jin Chen,1,3,{dagger} Olga Chertkov,1,3 Cathy Cleland,6 Mira Dimitrijevic,1,3 Norman A. Doggett,3 John J. Fawcett,1,3 Tijana Glavina,2,4 Lynne A. Goodwin,1,3 Lance D. Green,1,3 Cliff S. Han,1,3 Karen K. Hill,3 Penny Hitchcock,6,{ddagger} Paul J. Jackson,3,5 Paul Keim,7 Avinash Ramesh Kewalramani,1,3 Jon Longmire,3 Susan Lucas,2,5 Stephanie Malfatti,2,5 Diego Martinez,1,3 Kim McMurry,1,3 Linda J. Meincke,1,3 Monica Misra,1,3 Bernice L. Moseman,1,3 Mark Mundt,8 A. Christine Munk,1,3 Richard T. Okinaka,3 B. Parson-Quintana,1,3 Lee Philip Reilly,1,3 Paul Richardson,2,4 Donna L. Robinson,1,3 Elizabeth Saunders,1,3 Roxanne Tapia,1,3 Judith G. Tesmer,1,3 Nina Thayer,1,3 Linda S. Thompson,1,3 Hope Tice,2,4 Lawrence O. Ticknor,6 Patti L. Wills,1,3 Paul Gilna,1,3, and Thomas S. Brettin1,3

DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, New Mexico 87545,1 DOE Joint Genome Institute, Production Genome Facility, Walnut Creek, California 94598,2 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico 87545,3 Lawrence Berkeley National Laboratory, Berkeley, California 94720,4 Lawrence Livermore National Laboratory, Livermore, California 94550,5 Los Alamos National Laboratory, Decision Applications Division, Los Alamos, New Mexico 87545,6 Northern Arizona University, Department of Biological Sciences, Flagstaff, Arizona 86011-5640,7 Los Alamos National Laboratory, W Division, Los Alamos, New Mexico 875458

Received 13 February 2007/ Accepted 19 February 2007


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ABSTRACT
 
Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003).


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INTRODUCTION
 
The Bacillus thuringiensis Al Hakam genome was sequenced at the Joint Genome Institute using plasmid and fosmid DNA libraries. Draft assemblies were based on 246,217 total reads. All libraries provided 23-fold coverage of the genome. The Phred/Phrap/Consed software package was used for sequence assembly and quality assessment. After shotgun sequencing, reads were assembled with parallel phrap (High Performance Software, LLC). Possible misassemblies were corrected by transposon bombing (Epicenter Biotechnologies) of bridging clones. Gaps between contigs were closed by editing in Consed, by custom primer walks, or by PCR amplification. The complete genome of B. thuringiensis Al Hakam achieves an average of 24-fold sequence coverage per base with an error rate of less than 1 in 100,000. The sequences comprising the B. thuringiensis Al Hakam genome can be accessed using the GenBank accession numbers CP000485 and CP000486.

Gene predictions were obtained and annotation was performed as described previously (1). The 5.31-Mb genome of B. thuringiensis Al Hakam contains two replicons: a circular chromosome (5.26 Mb) encoding a predicted 4,969 open reading frames (ORFs), and the pALH1 circular phage, which contains 62 predicted ORFs. The G+C content of the chromosome is 35%, while that of the phage is 36%. The B. thuringiensis Al Hakam genome encodes 105 tRNAs and 13 rRNA operons and contains at least 21 pseudogenes. There were no additional plasmids identified in the assembly Blast searches against the B. thuringiensis Al Hakam genome using known insecticidal genes (cry, cyt, and vip) as queries revealed no chromosome-encoded (or phage-encoded) ORFs with significant similarity. Therefore, we conclude that this genome contains no homologues of the known cry, cyt, or vip genes. However, if they were present originally, it is possible that the plasmid(s) encoding these genes was lost during culture.

Previous AFLP analyses have shown that B. thuringiensis Al Hakam is phylogenetically more closely related to B. anthracis and other "Branch F" Bacillus isolates than to many of the commercially important B. thuringiensis isolates (2). The B. thuringiensis Al Hakam genome provides new sequence data that can be used to further study the evolutionary relationships among B. cereus group organisms.


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ACKNOWLEDGMENTS
 
We acknowledge the Intelligence Technology Innovation Center and the DOE Chemical and Biological Non-Proliferation Program for funding the sequencing and analysis of this genome.


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FOOTNOTES
 
* Corresponding author. Mailing address: Department of Energy Joint Genome Institute, Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545. Phone: (505) 665-1485. Fax: (505) 665-3024. E-mail: jchalla{at}lanl.gov Back

{triangledown} Published ahead of print on 2 March 2007. Back

§ Present address: University of Florida, Gainesville, FL 32611. Back

{dagger} Present address: Advanced Biomedical Computing Center, NCI-Frederick, Frederick, MD 21702. Back

{ddagger} Present address: The Center for Biosecurity of UPMC, The Pier IV Building, 621 E. Pratt Street, Suite 210, Baltimore, MD 21202. Back

Present address: University of California, San Diego, La Jolla, CA 92093. Back


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REFERENCES
 
    1
  1. Han, C. S., G. Xie, J. F. Challacombe, M. R. Altherr, S. S. Bhotika, D. Bruce, C. S. Campbell, M. L. Campbell, J. Chen, O. Chertkov, C. Cleland, M. Dimitrijevic, N. A. Doggett, J. J. Fawcett, T. Glavina, L. A. Goodwin, K. K. Hill, P. Hitchcock, P. J. Jackson, P. Keim, A. R. Kewalramani, J. Longmire, S. Lucas, S. Malfatti, K. McMurry, L. J. Meincke, M. Misra, B. L. Moseman, M. Mundt, A. C. Munk, R. T. Okinaka, B. Parson-Quintana, L. P. Reilly, P. Richardson, D. L. Robinson, E. Rubin, E. Saunders, R. Tapia, J. G. Tesmer, N. Thayer, L. S. Thompson, H. Tice, L. O. Ticknor, P. L. Wills, T. S. Brettin, and P. Gilna. 2006. The pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis. J. Bacteriol. 188:3382-3390.[Abstract/Free Full Text]
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  2. Hoffmaster, A. R., K. K. Hill, J. E. Gee, C. K. Marston, B. K. De, T. Popovic, D. Sue, P. P. Wilkins, S. B. Avashia, R. Drumgoole, C. H. Helma, L. O. Ticknor, R. T. Okinaka, and P. J. Jackson. 2006. Characterization of Bacillus cereus isolates associated with fatal pneumonias: strains are closely related to Bacillus anthracis and harbor B. anthracis virulence genes. J. Clin. Microbiol. 44:3352-3360.[Abstract/Free Full Text]

Journal of Bacteriology, May 2007, p. 3680-3681, Vol. 189, No. 9
0021-9193/07/$08.00+0     doi:10.1128/JB.00241-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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