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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Draft Genome Sequence of a New <italic>Bacillus cereus</italic> Strain tsu1</title><author><name sortKey="Li, Hui" sort="Li, Hui" uniqKey="Li H" first="Hui" last="Li">Hui Li</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Zhou, Suping" sort="Zhou, Suping" uniqKey="Zhou S" first="Suping" last="Zhou">Suping Zhou</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Johnson, Terrance" sort="Johnson, Terrance" uniqKey="Johnson T" first="Terrance" last="Johnson">Terrance Johnson</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Vercruysse, Koen" sort="Vercruysse, Koen" uniqKey="Vercruysse K" first="Koen" last="Vercruysse">Koen Vercruysse</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Ropelewski, Alexander J" sort="Ropelewski, Alexander J" uniqKey="Ropelewski A" first="Alexander J." last="Ropelewski">Alexander J. Ropelewski</name><affiliation><nlm:aff id="aff2">Pittsburgh Supercomputer Center, Pittsburgh, Pennsylvania, USA</nlm:aff></affiliation></author><author><name sortKey="Thannhauser, Theodore W" sort="Thannhauser, Theodore W" uniqKey="Thannhauser T" first="Theodore W." last="Thannhauser">Theodore W. Thannhauser</name><affiliation><nlm:aff id="aff3">R.W. Holley Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA, ARS, Ithaca, New York, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25523768</idno><idno type="pmc">4271158</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271158</idno><idno type="RBID">PMC:4271158</idno><idno type="doi">10.1128/genomeA.01294-14</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000622</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000622</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Draft Genome Sequence of a New <italic>Bacillus cereus</italic> Strain tsu1</title><author><name sortKey="Li, Hui" sort="Li, Hui" uniqKey="Li H" first="Hui" last="Li">Hui Li</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Zhou, Suping" sort="Zhou, Suping" uniqKey="Zhou S" first="Suping" last="Zhou">Suping Zhou</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Johnson, Terrance" sort="Johnson, Terrance" uniqKey="Johnson T" first="Terrance" last="Johnson">Terrance Johnson</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Vercruysse, Koen" sort="Vercruysse, Koen" uniqKey="Vercruysse K" first="Koen" last="Vercruysse">Koen Vercruysse</name><affiliation><nlm:aff id="aff1">College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</nlm:aff></affiliation></author><author><name sortKey="Ropelewski, Alexander J" sort="Ropelewski, Alexander J" uniqKey="Ropelewski A" first="Alexander J." last="Ropelewski">Alexander J. Ropelewski</name><affiliation><nlm:aff id="aff2">Pittsburgh Supercomputer Center, Pittsburgh, Pennsylvania, USA</nlm:aff></affiliation></author><author><name sortKey="Thannhauser, Theodore W" sort="Thannhauser, Theodore W" uniqKey="Thannhauser T" first="Theodore W." last="Thannhauser">Theodore W. Thannhauser</name><affiliation><nlm:aff id="aff3">R.W. Holley Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA, ARS, Ithaca, New York, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Genome Announcements</title><idno type="eISSN">2169-8287</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>This paper reports the draft genome sequence of a new <italic>Bacillus cereus</italic> strain tsu1, isolated on an agar-cellulose plate. The draft genome sequence is 5.81 Mb, revealing 5,673 coding sequences. It contains genes for cellulose-degradation and biosynthesis pathways of polyhydroxybutyrate (PHB) and 8 rRNA genes (5S, 16S, and 23S).</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jakucs, E" uniqKey="Jakucs E">E Jakucs</name></author><author><name sortKey="Varallyay, E" uniqKey="Varallyay E">E Várallyay</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, Y" uniqKey="Yang Y">Y Yang</name></author><author><name sortKey="Zhang, A" uniqKey="Zhang A">A Zhang</name></author><author><name sortKey="Howe, K" uniqKey="Howe K">K Howe</name></author><author><name sortKey="Wilson, Db" uniqKey="Wilson D">DB Wilson</name></author><author><name sortKey="Moser, F" uniqKey="Moser F">F Moser</name></author><author><name sortKey="Irwin, D" uniqKey="Irwin D">D Irwin</name></author><author><name sortKey="Thannhauser, Tw" uniqKey="Thannhauser T">TW Thannhauser</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wei, Yh" uniqKey="Wei Y">YH Wei</name></author><author><name sortKey="Chen, Wc" uniqKey="Chen W">WC Chen</name></author><author><name sortKey="Huang, Ck" uniqKey="Huang C">CK Huang</name></author><author><name sortKey="Wu, Hs" uniqKey="Wu H">HS Wu</name></author><author><name sortKey="Sun, Ym" uniqKey="Sun Y">YM Sun</name></author><author><name sortKey="Lo, Cw" uniqKey="Lo C">CW Lo</name></author><author><name sortKey="Janarthanan, Om" uniqKey="Janarthanan O">OM Janarthanan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Karr, Db" uniqKey="Karr D">DB Karr</name></author><author><name sortKey="Waters, Jk" uniqKey="Waters J">JK Waters</name></author><author><name sortKey="Emerich, Dw" uniqKey="Emerich D">DW Emerich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Boetzer, M" uniqKey="Boetzer M">M Boetzer</name></author><author><name sortKey="Henkel, Cv" uniqKey="Henkel C">CV Henkel</name></author><author><name sortKey="Jansen, Hj" uniqKey="Jansen H">HJ Jansen</name></author><author><name sortKey="Butler, D" uniqKey="Butler D">D Butler</name></author><author><name sortKey="Pirovano, W" uniqKey="Pirovano W">W Pirovano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, X" uniqKey="Huang X">X Huang</name></author><author><name sortKey="Madan, A" uniqKey="Madan A">A Madan</name></author></analytic></biblStruct></listBibl></div1></back></TEI><pmc article-type="brief-report"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Announc</journal-id><journal-id journal-id-type="iso-abbrev">Genome Announc</journal-id><journal-id journal-id-type="hwp">ga</journal-id><journal-id journal-id-type="pmc">ga</journal-id><journal-id journal-id-type="publisher-id">GA</journal-id><journal-title-group><journal-title>Genome Announcements</journal-title></journal-title-group><issn pub-type="epub">2169-8287</issn><publisher><publisher-name>American Society for Microbiology</publisher-name><publisher-loc>1752 N St., N.W., Washington, DC</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25523768</article-id><article-id pub-id-type="pmc">4271158</article-id><article-id pub-id-type="publisher-id">genomeA01294-14</article-id><article-id pub-id-type="doi">10.1128/genomeA.01294-14</article-id><article-categories><subj-group subj-group-type="heading"><subject>Prokaryotes</subject></subj-group></article-categories><title-group><article-title>Draft Genome Sequence of a New <italic>Bacillus cereus</italic> Strain tsu1</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Li</surname><given-names>Hui</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Zhou</surname><given-names>Suping</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Johnson</surname><given-names>Terrance</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Vercruysse</surname><given-names>Koen</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ropelewski</surname><given-names>Alexander J.</given-names></name><xref ref-type="aff" rid="aff2"><sup>b</sup></xref></contrib><contrib contrib-type="author"><name><surname>Thannhauser</surname><given-names>Theodore W.</given-names></name><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><aff id="aff1"><label>a</label>College of Agriculture, Human and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA</aff><aff id="aff2"><label>b</label>Pittsburgh Supercomputer Center, Pittsburgh, Pennsylvania, USA</aff><aff id="aff3"><label>c</label>R.W. Holley Center for Agriculture and Health, Plant, Soil and Nutrition Research Unit, USDA, ARS, Ithaca, New York, USA</aff></contrib-group><author-notes><corresp id="cor1">Address correspondence to Suping Zhou, <email>zsuping@tnstate.edu</email>.</corresp></author-notes><pub-date pub-type="epub"><day>18</day><month>12</month><year>2014</year></pub-date><pub-date pub-type="collection"><season>Nov-Dec</season><year>2014</year></pub-date><volume>2</volume><issue>6</issue><elocation-id>e01294-14</elocation-id><history><date date-type="received"><day>31</day><month>10</month><year>2014</year></date><date date-type="accepted"><day>11</day><month>11</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2014 Li et al.</copyright-statement><copyright-year>2014</copyright-year><copyright-holder>Li et al.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 Unported license</ext-link>.</license-p></license></permissions><self-uri xlink:title="pdf" xlink:type="simple" xlink:href="jga006141937001.pdf"></self-uri><abstract><p>This paper reports the draft genome sequence of a new <italic>Bacillus cereus</italic> strain tsu1, isolated on an agar-cellulose plate. The draft genome sequence is 5.81 Mb, revealing 5,673 coding sequences. It contains genes for cellulose-degradation and biosynthesis pathways of polyhydroxybutyrate (PHB) and 8 rRNA genes (5S, 16S, and 23S).</p></abstract><counts><page-count count="1"></page-count></counts><custom-meta-group><custom-meta><meta-name>cover-date</meta-name><meta-value>November/December 2014</meta-value></custom-meta><custom-meta><meta-name>access-type</meta-name><meta-value>free</meta-value></custom-meta></custom-meta-group></article-meta></front><body><sec><title>GENOME ANNOUNCEMENT</title><p><italic>Bacillus cereus</italic> is a widespread bacterium dwelling in soil. Several strains have demonstrated biochemical activities in degrading cellulose and also producing valuable biopolymers. Whole-genome sequencing of these strains will provide significant resources for developing sustainable bioenergy and reducing the reliance on petroleum-based plastics.</p><p>In this study, we present the genome sequence and annotation of a new <italic>B. cereus</italic> strain tsu1. The strain, designated <italic>B. cereus</italic> strain tsu1, was isolated from a cellulose-agar plate. The bacterium is a Gram-positive, rod-shaped organism with a centrally located endospore, which is identical to the <italic>B. cereus</italic> species. Extracellular cellulase activity was observed when the bacteria were cultivated on 10% carboxymethyl cellulose (Acros Organics, NJ) agar plates followed by Congo-red staining (<xref rid="B1" ref-type="bibr">1</xref>). The extracellular cellulase proteins were identified using mass-spectrometry analysis of the proteins secreted into the growth broth containing cellulose substrate. Proteins were isolated by precipitation with 10% trichloroacetic acid in acetone followed by separation by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Coomassie blue stained protein bands were excised and digested with trypsin and analyzed by liquid chromatography (LC)/mass spectrometry (MS) (<xref rid="B2" ref-type="bibr">2</xref>). Mascot v2.3 was used to search the mass spectrometry data against NCBInr (firmicutes restriction). The PHB producing activity was confirmed using Sudan-black staining (<xref rid="B3" ref-type="bibr">3</xref>) and ion-exclusion high-pressure liquid chromatography analysis (<xref rid="B4" ref-type="bibr">4</xref>).</p><p>Genomic DNA was extracted from the abovementioned strain using the GenElute Bacterial genomic DNA kits for Gram-positive strains (Sigma, CA) according to the manufacturer’s instructions. The genome was sequenced on an Illumina HiSeq 2000 using TruSeq SBS kit v3 for paired-end 100 bp sequencing at the Genome Facility at Cornell University. For data quality control, the length of each read was trimmed with FASTX from the 3′ end of the read using a quality threshold of 20. The draft genome sequence was assembled into 67 contigs using velvet, Kmer = 79 (version 1.2.10), and then into 36 scaffolds using SSPACE (<xref rid="B5" ref-type="bibr">5</xref>) followed by CAP3 (<xref rid="B6" ref-type="bibr">6</xref>).</p><p>The draft genome sequence of <italic>Bacillus cereus</italic> strain tsu1 is 5.81 Mb in size with a G+C content of 34.8%. The genome contains a PhaA gene (beta keto-thiolase), PadR, PhaB, PhaC_N, and PHB_depo_C, and cellulase and hemicellulase genes. The 16s rRNA gene has a 99% identity to <italic>B. cereus</italic> and <italic>B. thuringiensis</italic>.</p><sec id="h1"><title>Nucleotide sequence accession number.</title><p>This whole-genome project has been deposited in NCBI/GenBank under the accession no. <ext-link ext-link-type="NCBI:nucleotide" xlink:href="JPYN00000000">JPYN00000000</ext-link>. The version described in this paper is the first version.</p></sec></sec></body><back><fn-group><fn fn-type="other"><p><bold>Citation</bold> Li H, Zhou S, Johnson T, Vercruysse K, Ropelewski AJ, Thannhauser TW. 2014. Draft genome sequence of a new <italic>Bacillus cereus</italic> strain tsu1. Genome Announc. 2(6):e01294-14. doi:10.1128/genomeA.01294-14.</p></fn></fn-group><ack><title>ACKNOWLEDGMENTS</title><p>This work was supported by National Institute of Food and Agriculture, 1890 Capacity Building Grants Program research grant No. <award-id id="G1">2010-02417</award-id>, and by the National Institutes of Health, National Institute of General Medical Sciences Minority Access to Research Careers grant <award-id id="G2">T36-GM-095335</award-id> to the Pittsburth Supercomputing Center. This work used Blacklight at the Pittsburgh Supercomputing Center, part of the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by <funding-source id="GS3">National Science Foundation</funding-source> grant number <award-id rid="GS3">ACI-1053575</award-id>.</p><p>Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.</p><p>We thank Charles Lee for technical advice on the isolation of the bacterial strain, Allison Pieja for PHB analysis, and Kevin Howe for protein identification.</p></ack><ref-list><title>REFERENCES</title><ref id="B1"><label>1.</label><mixed-citation publication-type="journal"><person-group person-group-type="author"><name><surname>Jakucs</surname><given-names>E</given-names></name><name><surname>Várallyay</surname><given-names>E</given-names></name></person-group><year>1995</year><article-title>A simple and rapid semiquantitative method for measuring cellulase activity in agar media</article-title>. <source>Acta Microbiol. 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