Bacillus thuringiensis is an insect pathogen that is widelyused as a biopesticide (3). Here we report the finished, annotated genomesequence of B. thuringiensis Al Hakam, which was collected in Iraq by theUnited Nations Special Commission (2)

Altherr, Michael R.

Bhotika, Smriti S.

Brettin, Thomas S.

Brown, Nancy

Bruce, David

Campbell, Connie S.

Campbell, Mary L.

Challacombe, Jean F.

Chen, Jin

Chertkov, Olga

Cleland, Cathy

Dimitrijevic, Mira

Doggett, Norman A.

Fawcett, John J.

Gilna, Paul

Glavina, Tijana

Goodwin, Lynne A.

Green, Lance D.

Han, Cliff S.

Hill, Karen K.

Hitchcock, Penny

Jackson, Paul J.

Keim, Paul

Kewalramani, Avinash Ramesh

Longmire, Jon

Lucas, Susan

Malfatti, Stephanie

Martinez, Diego

McMurry, Kim

Meincke, Linda J.

Misra, Monica

Moseman, Bernice L.

Mundt, Mark

Munk, A. Christine

Okinaka, Richard T.

Parson-Quintana, B.

Reilly, LeePhilip

Richardson, Paul

Robinson, Donna L.

Rubin, Eddy

Saunders, Elizabeth

Tapia, Roxanne

Tesmer, Judith G.

Thayer, Nina

Thompson, Linda S.

Tice, Hope

Ticknor, Lawrence O.

Wills, Patti L.

Xie, Gary

PubMed

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (3).  Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was  collected in Iraq by the United Nations Special Commission (2)

Reilly, Lee Philip

eScholarship - University of California

Lawrence Berkeley National LaboratoryLawrence Berkeley National LaboratoryTitleThe Complete Genome Sequence of Bacillus thuringiensis Al HakamPermalinkhttps://escholarship.org/uc/item/80j857pfAuthorsChallacombe, Jean F.Altherr, Michael R.Xie, Garyet al.Publication Date2008-05-29 Peer reviewedeScholarship.org Powered by the California Digital LibraryUniversity of California LBNL-62928  Prepr int  Title  The Complete Genome Sequence of Bacillus thuringiensis Al Hakam Author(s),  Jean F. Challacombe,             Michael R. Altherr, et al  Division  Genomics   Journal Name Journal of Bacteriology    May 2007    Vol. 189, No. 9    P. 3680-3681   The Complete Genome Sequence of Bacillus thuringiensis Al Hakam   Jean F. Challacombe*§¶, Michael R. Altherr¶, Gary Xie§¶,  Smriti S. Bhotika§¶•, Nancy Brown¶, David Bruce§¶, Connie S. Campbell§¶, Mary L. Campbell§¶, Jin Chen§¶+, Olga Chertkov§¶, Cathy Clelandψ, Mira Dimitrijevic§¶, Norman A. Doggett¶, John J. Fawcett§¶, Tijana Glavina‡#, Lynne A. Goodwin§¶, Lance D. Green§¶, Cliff S. Han§¶, Karen K. Hill¶, Penny Hitchcockψ , Paul J. Jackson¶Φ, Paul Keim&, Avinash Ramesh Kewalramani§¶, Jon Longmire¶, Susan Lucas‡Φ, Stephanie Malfatti‡Φ, Diego Martinez§¶,Kim McMurry§¶, Linda J. Meincke§¶, Monica Misra§¶, Bernice L. Moseman§¶, Mark Mundtθ, A. Christine Munk§¶, Richard T. Okinaka¶, B. Parson-Quintana§¶, Lee Philip Reilly§¶, Paul Richardson‡#, Donna L. Robinson§¶, Eddy Rubin‡#, Elizabeth Saunders§¶, Roxanne Tapia§¶, Judith G. Tesmer§¶, Nina Thayer§¶, Linda S. Thompson§¶, Hope Tice‡#, Lawrence O. Ticknorψ, Patti L. Wills§¶, Paul Gilna§¶=, Thomas S. Brettin§¶. §DOE Joint Genome Institute Los Alamos National Laboratory, Los Alamos, NM 87545. ‡DOE Joint Genome Institute Production Genome Facility, Walnut Creek, CA 94598. ¶Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545. #Lawrence Berkeley National Laboratory, Berkeley, CA 94720. ΦLawrence Livermore National Laboratory, Livermore, CA 94550. ψLos Alamos National Laboratory Decision Applications Division, Los Alamos, NM 87545. & Northern Arizona University Department of Biological Sciences, Flagstaff AZ 86011-5640. θLos Alamos National Laboratory, W Division, Los Alamos, NM 87545. + Presently at the National Cancer Institute. Presently at The Center for Biosecurity of UPMC, The Pier IV Building, 621 E. Pratt Street, Suite 210, Baltimore, Maryland 21202. •Presently at the University of Florida, Gainesville, FL 32611. =Presently at the University of California, San Diego, La Jolla, CA 92093   Abstract Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (3). Here we report the finished, annotated genome sequence of B.  thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (2).  Methods, Results and Discussion The Bacillus  thuringiensis Al Hakam genome was sequenced at the Joint Genome Institute (JGI) using plasmid and fosmid DNA libraries. Draft assemblies were based on 246217 total reads. All libraries provided 23x coverage of the genome. The Phred/Phrap/Consed software package (http://www.phrap.com) was used for sequence assembly and quality assessment. After shotgun sequencing, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected by transposon bombing (Epicentre 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 4969 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, 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 chromosomally (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 a member of the B. cereus group that is of intermediate relatedness (in terms of sequence identity) to B. anthracis (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.   This program is supported by the U.S. Department of Energy under contract no. W-7405-ENG-36.  This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231 and Los Alamos National Laboratory under contract No. DE-AC52-06NA25396.   References  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. 2. Radnedge, L., P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen. 2003. Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl Environ Microbiol 69:2755-64. 3. Schnepf, E., N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean. 1998. Bacillus thuringiensis and its pesticidal crystal proteins. Microbiology and Molecular Biology Reviews 62:775-806.   

English

The Complete Genome Sequence of Bacillus thuringiensis Al Hakam

UNT (University of North Texas) Digital Library

 LBNL-62928  Prepr int  Title  The Complete Genome Sequence of Bacillus thuringiensis Al Hakam Author(s),  Jean F. Challacombe,             Michael R. Altherr, et al  Division  Genomics   Journal Name Journal of Bacteriology    May 2007    Vol. 189, No. 9    P. 3680-3681   The Complete Genome Sequence of Bacillus thuringiensis Al Hakam   Jean F. Challacombe*§¶, Michael R. Altherr¶, Gary Xie§¶,  Smriti S. Bhotika§¶•, Nancy Brown¶, David Bruce§¶, Connie S. Campbell§¶, Mary L. Campbell§¶, Jin Chen§¶+, Olga Chertkov§¶, Cathy Clelandψ, Mira Dimitrijevic§¶, Norman A. Doggett¶, John J. Fawcett§¶, Tijana Glavina‡#, Lynne A. Goodwin§¶, Lance D. Green§¶, Cliff S. Han§¶, Karen K. Hill¶, Penny Hitchcockψ , Paul J. Jackson¶Φ, Paul Keim&, Avinash Ramesh Kewalramani§¶, Jon Longmire¶, Susan Lucas‡Φ, Stephanie Malfatti‡Φ, Diego Martinez§¶,Kim McMurry§¶, Linda J. Meincke§¶, Monica Misra§¶, Bernice L. Moseman§¶, Mark Mundtθ, A. Christine Munk§¶, Richard T. Okinaka¶, B. Parson-Quintana§¶, Lee Philip Reilly§¶, Paul Richardson‡#, Donna L. Robinson§¶, Eddy Rubin‡#, Elizabeth Saunders§¶, Roxanne Tapia§¶, Judith G. Tesmer§¶, Nina Thayer§¶, Linda S. Thompson§¶, Hope Tice‡#, Lawrence O. Ticknorψ, Patti L. Wills§¶, Paul Gilna§¶=, Thomas S. Brettin§¶. §DOE Joint Genome Institute Los Alamos National Laboratory, Los Alamos, NM 87545. ‡DOE Joint Genome Institute Production Genome Facility, Walnut Creek, CA 94598. ¶Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545. #Lawrence Berkeley National Laboratory, Berkeley, CA 94720. ΦLawrence Livermore National Laboratory, Livermore, CA 94550. ψLos Alamos National Laboratory Decision Applications Division, Los Alamos, NM 87545. & Northern Arizona University Department of Biological Sciences, Flagstaff AZ 86011-5640. θLos Alamos National Laboratory, W Division, Los Alamos, NM 87545. + Presently at the National Cancer Institute.  Presently at The Center for Biosecurity of UPMC, The Pier IV Building, 621 E. Pratt Street, Suite 210, Baltimore, Maryland 21202. •Presently at the University of Florida, Gainesville, FL 32611. =Presently at the University of California, San Diego, La Jolla, CA 92093   Abstract Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (3). Here we report the finished, annotated genome sequence of B.  thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (2).  Methods, Results and Discussion The Bacillus  thuringiensis Al Hakam genome was sequenced at the Joint Genome Institute (JGI) using plasmid and fosmid DNA libraries. Draft assemblies were based on 246217 total reads. All libraries provided 23x coverage of the genome. The Phred/Phrap/Consed software package (http://www.phrap.com) was used for sequence assembly and quality assessment. After shotgun sequencing, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected by transposon bombing (Epicentre 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 4969 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, 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 chromosomally (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 a member of the B. cereus group that is of intermediate relatedness (in terms of sequence identity) to B. anthracis (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.   This program is supported by the U.S. Department of Energy under contract no. W-7405-ENG-36.  This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231 and Los Alamos National Laboratory under contract No. DE-AC52-06NA25396.   References  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. 2. Radnedge, L., P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen. 2003. Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl Environ Microbiol 69:2755-64. 3. Schnepf, E., N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean. 1998. Bacillus thuringiensis and its pesticidal crystal proteins. Microbiology and Molecular Biology Reviews 62:775-806.   

The Complete Genome Sequence of Bacillus thuringiensis AlHakam

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The Complete Genome Sequence of Bacillus thuringiensis AlHakam

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