产生抗菌肽的海洋细菌（Bacillus subtilis）基因组分析
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摘要
Bacillus subtilis gt 1是一株来自海洋的革兰氏阳性菌,它含有抗菌肽基因可产生抗菌肽，和革兰氏阳性菌的模式菌Bacillus subtilis str.168关系很近。Bacillus subtilis的多个种已经完成了测序,但据我们所知,还没有海洋细菌的全基因组测序的相关报道。我们利用40bp的短读序数据对来自印度洋的Bacillus subtilis gt1的全基因组进行拼接。用从头拼接和基于参考基因组拼接的方法,结合PCR实验测序的方法,最终获得了一条拼接的基因组序列。基因组大小为4,247,908bp,GC含量品均44.8%,基于这条序列,我们预测了4331个蛋白质编码基因,平均长度844bp,77个tRNA,30个rRNA(10个rRNA操纵子)。蛋白质编码基因中81.7%的基因与Bacillus subtilis str.168的同源,有444个基因在Bacillus属未找到同源基因,其中392个在现有公共数据库中仍未找到同源基因。在这些基因中,我们找到了产生抗菌肽的基因位点及基因簇,包括核糖体及非核糖体相关的抗菌肽的基因。Bacillus subtilis gt 1可作为海洋细菌研究的模式菌,为海洋细菌的基础研究及应用提供了基础。
Bacillus subtilis gt 1 is a strain of Gram-positive, marine bacterium that can produce antimicrobial peptide (AMP). This strain is closely related to the well studied model organism Bacillus subtilis str.168. Many genomes of the Bacillus subtilis strains have been sequenced, but no record of whole genome sequencing from marine bacteria is reported to our knowledge. We determined the draft genome sequence of the B. subtilis gt 1. isolated from the Indian Ocean using short reads around 40 base-pairs (bp) in length. By de novo assembly and reference-guided assembly combined with PCR sequencing methods, the draft was constructed. The genome sequence of B. subtilis gt 1 comprises 4,247,908 bp with an average G+C content of 44.8%, containing 4331 predicted protein-coding genes that have an average length of 844 bp,30 rRNAs(10 rRNA operons), and 77 tRNA genes.81.7% of the predicted B. subtilis gt 1 coding sequences have B. subtilis str.168 orthologs, but 444 protein-coding genes were not found in genomes of Bacillus genus. Of these protein-coding genes, some candidate genes and gene clusters that involved in novel ribosomal or non-ribosomal antimicrobial peptide production were identified. B. subtilis gt 1 provides a model Gram-positive bacterium for marine bacteria, it is of great importance for basic and applied researches.
Bacillus subtilis gt 1 is a strain of Gram-positive, marine bacterium that can produce antimicrobial peptide (AMP). This strain is closely related to the well studied model organism Bacillus subtilis str.168. Many genomes of the Bacillus subtilis strains have been sequenced, but no record of whole genome sequencing from marine bacteria is reported to our knowledge. We determined the draft genome sequence of the B. subtilis gt 1. isolated from the Indian Ocean using short reads around 40 base-pairs (bp) in length. By de novo assembly and reference-guided assembly combined with PCR sequencing methods, the draft was constructed. The genome sequence of B. subtilis gt 1 comprises 4,247,908 bp with an average G+C content of 44.8%, containing 4331 predicted protein-coding genes that have an average length of 844 bp,30 rRNAs(10 rRNA operons), and 77 tRNA genes.81.7% of the predicted B. subtilis gt 1 coding sequences have B. subtilis str.168 orthologs, but 444 protein-coding genes were not found in genomes of Bacillus genus. Of these protein-coding genes, some candidate genes and gene clusters that involved in novel ribosomal or non-ribosomal antimicrobial peptide production were identified. B. subtilis gt 1 provides a model Gram-positive bacterium for marine bacteria, it is of great importance for basic and applied researches.
引文
Babasaki, K., T. Takao, Y. Shimonishi, and K. Kurahashi.1985. Subtilosin-a, a new antibiotic peptide produced by bacillus-subtilis-168-isolation, structural-analysis, and biogenesis. Journal of Biochemistry 98:585-603.
Barbe, V., S. Cruveiller, F. Kunst, P. Lenoble, G. Meurice, A. Sekowska, D. Vallenet, T. Z. Wang,1. Moszer, C. Medigue, and A. Danchin.2009. From a consortium sequence to a unified sequence:the Bacillus subtilis 168 reference genome a decade later. Microbiology-Sgm 155:1758-1775.
Blunt, J. W., B. R. Copp, M. H. G. Munro, P. T. Northcote, and M. R. Prinsep.2010. Marine natural products. Natural Product Reports 27:165-237.
Canchaya, C., G. Fournous, and H. Brussow.2004. The impact of prophages on bacterial chromosomes. Molecular Microbiology 53:9-18.
Casjens, S.2003. Prophages and bacterial genomics:what have we learned so far? Molecular Microbiology 49:277-300.
Chen, X. H., A. Koumoutsi, R. Scholz, A. Eisenreich, K. Schneider, I. Heinemeyer, B. Morgenstern, B. Voss, W. R. Hess, O. Reva, H. Junge, B. Voigt, P. R. Jungblut, J. Vater, R. Sussmuth, H. Liesegang, A. Strittmatter, G. Gottschalk, and R. Borriss.2007. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nature Biotechnology 25:1007-1014.
Delcher, A. L., K. A. Bratke, E. C. Powers, and S. L. Salzberg.2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679.
Delong, E. F., G. S. Wickham, and N. R. Pace.1989. Phylogenetic stains-ribosomal ma-based probes for the identification of single cells. Science 243:1360-1363.
Ghai, R., T. Hain, and T. Chakraborty.2004. GenomeViz:visualizing microbial genomes. Bmc Bioinformatics 5:6.
Gioia, J., S. Yerrapragada, X. Qin, H. Y. Jiang, O. C. Igboeli, D. Muzny, S. Dugan-Rocha, Y. Ding, A. Hawes, W. Liu, L. Perez, C. Kovar, H. Dinh, S. Lee, L. Nazareth, P. Blyth, M. Holder, C. Buhay, M. R. TirumaIai,Y. M. Liu, I. Dasgupta, L. Bokhetache, M. Fujita, F. Karouia, P. E. Moorthy, J. Siefert, A. Uzman, P. Buzumbo, A. Verma, H. Zwiya, B. D. McWilliams, A. Olowu, K. D. Clinkenbeard, D. Newcombe, L. Golebiewski, J. F. Petrosino, W. L. Nicholson, G. E. Fox, K. Venkateswaran, S. K. Highlander, and G. M. Weinstock.2007. Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032. Plos One 2:10.
Grigoriev, A.1998. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Research 26:2286-2290.
Gueguen, Y, J. Gamier, L. Robert, M. P. Lefranc, I. Mougenot, J. de Lorgeril, M. Janech, P. S. Gross, G. W. Warr, B. Cuthbertson, M. A. Barracco, P. Bulet, A. Aumelas, Y. S. Yang, D. Bo, J. H. Xiang, A. Tassanakajon, D. Piquemal, and E. Bachere.2006. PenBase, the shrimp antimicrobial peptide penaeidin database:Sequence-based classification and recommended nomenclature. Developmental and Comparative Immunology 30:283-288.
Isnansetyo, A. and Y. Kamei.2003. MC21-A, a bactericidal antibiotic produced by a new marine bacterium, Pseudoalteromonas phenolica sp nov O-BC30(T) against methicillin-resistant Staphylococcus aureus. Antimicrobial Agents and Chemotherapy 47:480-488.
Iwai, H. and A. Pluckthun.1999. Circular beta-lactamase:stability enhancement by cyclizing the backbone. Febs Letters 459:166-172.
Kock,I., R. P. Maskey, M. A. F. Biabani, E. Helmke, and H. Laatsch.2005. 1-hydroxy-l-norresistomycin and resistoflavin methyl ether:New antibiotics from marine-derived streptomycetes. Journal of Antibiotics 58:530-534.
Kunst, F. and N. Ogasawara and I. Moszer and A. M. Albertini and G. Alloni and V. Azevedo and M. G. Bertero and P. Bessieres and A. Bolotin and S. Borchert and R. Borriss and L. Boursier and A. Brans and M. Braun and S. C. Brignell and S. Bron and S. Brouillet and C. V. Bruschi and B. Caldwell and V. Capuano and N. M. Carter and S. K. Choi and J. J. Codani and I. F. Connerton and N. J. Cummings and R. A. Daniel and F. Denizot and K. M. Devine and A. Dusterhoft and S. D. Ehrlich and P. T. Emmerson and K. D. Entian and J. Errington and C. Fabret and E. Ferrari and D. Foulger and C. Fritz and M. Fujita and Y. Fujita and S. Fuma and A. Galizzi and N. Galleron and S. Y. Ghim and P. Glaser and A. Goffeau and E. J. Golightly and G. Grandi and G. Guiseppi and B. J. Guy and K. Haga and J. Haiech and C. R. Harwood and A. Henaut and H. Hilbert and S. Holsappel and S. Hosono and M. F. Hullo and M. Itaya and L. Jones and B. Joris and D. Karamata and Y. Kasahara and M. KlaerrBlanchard and C. Klein and Y. Kobayashi and P. Koetter and G. Koningstein and S. Krogh and M. Kumano and K. Kurita and A. Lapidus and S. Lardinois and J. Lauber and V. Lazarevic and S. M. Lee and A. Levine and H. Liu and S. Masuda and C. Mauel and C. Medigue and N. Medina and R. P. Mellado and M. Mizuno and D. Moestl and S. Nakai and M. Noback and D. Noone and M. Oreilly and K. Ogawa and A. Ogiwara and B. Oudega and S. H. Park and V. Parro and T. M. Pohl and D. Portetelle and S. Porwollik and A. M. Prescott and E. Presecan and P. Pujic and B. Purnelle and G. Rapoport and M. Rey and S. Reynolds and M. Rieger and C. Rivolta and E. Rocha and B. Roche and M. Rose and Y. Sadaie and T. Sato and E. Scanlan and S. Schleich and R. Schroeter and F. Scoffone and J. Sekiguchi and A. Sekowska and S. J. Seror and P. Serror and B. S. Shin and B. Soldo and A. Sorokin and E. Tacconi and T. Takagi and H. Takahashi and K. Takemaru and M. Takeuchi and A. Tamakoshi and T. Tanaka and P. Terpstra and A. Tognoni and V. Tosato and S. Uchiyama and M. Vandenbol and F. Vannier and A. Vassarotti and A. Viari and R. Wambutt and E. Wedler and H. Wedler and T. Weitzenegger and P. Winters and A. Wipat and H. Yamamoto and K. Yamane and K. Yasumoto and K. Yata and K. Yoshida and H. F. Yoshikawa and E. Zumstein and H. Yoshikawa and A. Danchin.1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256.
Kurtz, S., A. Phillippy, A..L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S. L. Salzberg.2004. Versatile and open software for comparing large genomes. Genome Biology 5:9.
Kwon, H. C., C. A. Kauffman, P. R. Jensen, and W. Fenical.2006. Marinomycins A-D, antitumor-antibiotics of a new structure class from a marine actinomycete of the recently discovered genus "Marinispora". Journal of the American Chemical Society 128:1622-1632.
Lagesen, K., P. Hallin, E. A. Rodland, H. H. Staerfeldt, T. Rognes, and D. W. Ussery.2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research 35:3100-3108.
Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins.2007. Clustal W and clustal X version 2.0. Bioinformatics 23:2947-2948.
Li, R. Q., Y. R. Li, K. Kristiansen, and J. Wang.2008. SOAP:short oligonucleotide alignment program. Bioinformatics 24:713-714.
Lowe, T. M. and S. R. Eddy.1997. tRNAscan-SE:A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:955-964.
MacLean, D., J. D. G. Jones, and D. J. Studholme.2009. Application of 'next-generation' sequencing technologies to microbial genetics. Nature Reviews Microbiology 7:287-296.
Manam, R. R., S. Teisan, D. J. White, B. Nicholson, J. Grodberg, S. T. C. Neuteboom, K. S. Lam, D. A. Mosca, G. K. Lloyd, and B. C. M. Potts.2005. Lajollamycin, a nitro-tetraene spiro-beta-lactone-gamma-iactam antibiotic from the marine actinomycete Streptomyces nodosus. Journal of Natural Products 68:240-243.
Mayer, A. M. S., A. D. Rodriguez, R. G. S. Berlinck, and M. T. Hamann.2007. Marine pharmacology in 2003-4:Marine compounds with anthelmintic antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiplatelet, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems, and other miscellaneous mechanisms of action. Comparative Biochemistry and Physiology C-Toxicology & Pharmacology 145:553-581.
Mayer, A. M. S., A. D. Rodriguez, R. G. S. Berlinck, and M. T. Hamann.2009. Marine pharmacology in 2005-6:Marine compounds with anthelmintic, antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems, and other miscellaneous mechanisms of action. Biochimica Et Biophysica Acta-General Subjects 1790:283-308.
Mrazek, J. and S. Karlin.1998. Strand compositional asymmetry in bacterial and large viral genomes. Proceedings of the National Academy of Sciences of the United States of America 95:3720-3725.
Nett, M., H. Ikeda, and B. S. Moore.2009. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Natural Product Reports 26:1362-1384.
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 Genomics 11:12.
Pop, M. and S. L. Salzberg.2008. Bioinformatics challenges of new sequencing technology. Trends in Genetics 24:142-149.
Rasko, D. A., J. Ravel, O. A. Okstad, E. Helgason, R. Z. Cer, L. X. Jiang, K. A. Shores, D. E. Fouts, N. J. Tourasse, S. V. Angiuoli, J. Kolonay, W. C. Nelson, A. B. Kolsto, C. M. Fraser, and T. D. Read.2004. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Research 32:977-988.
Read, T. D., S. N. Peterson, N. Tourasse, L. W. Baillie, I. T. Paulsen, K. E. Nelson, H. Tettelin, D. E. Fouts, J. A. Eisen, S. R. Gill, E. K. Holtzapple, O. A. Okstad, E. Helgason, J. Rilstone, M. Wu, J. F. Kolonay, M. J. Beanan, R. J. Dodson, L. M. Brinkac, M. Gwinn, R. T. DeBoy, R. Madpu, S. C. Daugherty, A. S. Durkin, D. H. Haft, W. C. Nelson, J. D. Peterson, M. Pop, H. M. Khouri, D. Radune, J. L. Benton, Y. Mahamoud,.L. X. Jiang, I. R. Hance, J. F. Weidman, K. J. Berry, R. D. Plaut, A. M. Wolf, K. L. Watkins, W. C. Nierman, A. Hazen, R. Cline, C. Redmond, J. E. Thwaite, O. White, S. L. Salzberg, B. Thomason, A. M. Friedlander, T. M. Koehler, P. C. Hanna, A. B. Kolsto, and C. M. Fraser.2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81-86.
Rey, M. W., P. Ramaiya, B. A. Nelson, S. D. Brody-Karpin, E. J. Zaretsky, M. Tang, A. L. de Leon, H. Xiang, V. Gusti, I. G. Clausen, P. B. Olsen, M. D. Rasmussen, J. T. Andersen, P. L. Jorgensen, T. S. Larsen, A. Sorokin, A. Bolotin, A. Lapidus, N. Galleron, S. D. Ehrlich, and R. M. Berka. 2004. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biology 5:12.
Rocha, E. P. C., A. Danchin, and A. Viari.1999. Universal replication biases in bacteria. Molecular Microbiology 32:11-16.
Simpson, J. T., K. Wong, S. D. Jackman, J. E. Schein, S. J. M. Jones, and I. Birol.2009. ABySS:A parallel assembler for short read sequence data. Genome Research 19:1117-1123.
Socha, A. M., D. Garcia, R. Sheffer, and D. C. Rowley.2006. Antibiotic bisanthraquinones produced by a streptomycete isolated from a cyanobacterium associated with Ecteinascidia turbinata. Journal of Natural Products 69:1070-1073.
Solanki, R., M. Khanna, and R. LaI.2008. Bioactive compounds from marine actinomycetes. Indian Journal of Microbiology 48:410-431.
Soria-Mercado, I. E., A. Prieto-Davo, P. R. Jensen, and W. Fenical.2005. Antibiotic terpenoid chloro-dihydroquinones from a new marine actinomycete. Journal of Natural Products 68:904-910.
Steiner. H., D. Hultmark, A. Engstrom, H. Bennich, and H. G. Boman.1981. Sequence and specificity of 2 anti-bacterial proteins involved in insect immunity. Nature 292:246-248.
Stothard, P. and D. S. Wishart.2005. Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.
Tamura, K., J. Dudley, M. Nei. and S. Kumar.2007. MEGA4:Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599.
Tatusov, R. L., E. V. Koonin, and D. J. Lipman.1997. A genomic perspective on protein families. Science 278:631-637.
Thomas, S., S. Karnik, R. S. Barai, V. K. Jayaraman, and S. Idicula-Thomas.2010. CAMP:a useful resource for research on antimicrobial peptides. Nucleic Acids Research 38:D774-D780.
Wang, C. K. L., Q. Kaas, L. Chiche, and D. J. Craik.2008. CyBase:a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Research 36:D206-D210.
Wang, G. S., X. Li, and Z. Wang.2009. APD2:the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research 37:D933-D937.
Williams, N. K., P. Prosselkov, E. Liepinsh, I. Line, A. Sharipo, D. R. Littler, P. M. G. Curmi, G. Otting, and N. E. Dixon.2002. In vivo protein cyclization promoted by a circularly permuted Synechocystis sp PCC6803 DnaB mini-intein. Journal of Biological Chemistry 277:7790-7798.
Zerbino, D. R. and E. Birney.2008. Velvet:Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821-829.
Barbe, V., S. Cruveiller, F. Kunst, P. Lenoble, G. Meurice, A. Sekowska, D. Vallenet, T. Z. Wang,1. Moszer, C. Medigue, and A. Danchin.2009. From a consortium sequence to a unified sequence:the Bacillus subtilis 168 reference genome a decade later. Microbiology-Sgm 155:1758-1775.
Blunt, J. W., B. R. Copp, M. H. G. Munro, P. T. Northcote, and M. R. Prinsep.2010. Marine natural products. Natural Product Reports 27:165-237.
Canchaya, C., G. Fournous, and H. Brussow.2004. The impact of prophages on bacterial chromosomes. Molecular Microbiology 53:9-18.
Casjens, S.2003. Prophages and bacterial genomics:what have we learned so far? Molecular Microbiology 49:277-300.
Chen, X. H., A. Koumoutsi, R. Scholz, A. Eisenreich, K. Schneider, I. Heinemeyer, B. Morgenstern, B. Voss, W. R. Hess, O. Reva, H. Junge, B. Voigt, P. R. Jungblut, J. Vater, R. Sussmuth, H. Liesegang, A. Strittmatter, G. Gottschalk, and R. Borriss.2007. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nature Biotechnology 25:1007-1014.
Delcher, A. L., K. A. Bratke, E. C. Powers, and S. L. Salzberg.2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673-679.
Delong, E. F., G. S. Wickham, and N. R. Pace.1989. Phylogenetic stains-ribosomal ma-based probes for the identification of single cells. Science 243:1360-1363.
Ghai, R., T. Hain, and T. Chakraborty.2004. GenomeViz:visualizing microbial genomes. Bmc Bioinformatics 5:6.
Gioia, J., S. Yerrapragada, X. Qin, H. Y. Jiang, O. C. Igboeli, D. Muzny, S. Dugan-Rocha, Y. Ding, A. Hawes, W. Liu, L. Perez, C. Kovar, H. Dinh, S. Lee, L. Nazareth, P. Blyth, M. Holder, C. Buhay, M. R. TirumaIai,Y. M. Liu, I. Dasgupta, L. Bokhetache, M. Fujita, F. Karouia, P. E. Moorthy, J. Siefert, A. Uzman, P. Buzumbo, A. Verma, H. Zwiya, B. D. McWilliams, A. Olowu, K. D. Clinkenbeard, D. Newcombe, L. Golebiewski, J. F. Petrosino, W. L. Nicholson, G. E. Fox, K. Venkateswaran, S. K. Highlander, and G. M. Weinstock.2007. Paradoxical DNA Repair and Peroxide Resistance Gene Conservation in Bacillus pumilus SAFR-032. Plos One 2:10.
Grigoriev, A.1998. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Research 26:2286-2290.
Gueguen, Y, J. Gamier, L. Robert, M. P. Lefranc, I. Mougenot, J. de Lorgeril, M. Janech, P. S. Gross, G. W. Warr, B. Cuthbertson, M. A. Barracco, P. Bulet, A. Aumelas, Y. S. Yang, D. Bo, J. H. Xiang, A. Tassanakajon, D. Piquemal, and E. Bachere.2006. PenBase, the shrimp antimicrobial peptide penaeidin database:Sequence-based classification and recommended nomenclature. Developmental and Comparative Immunology 30:283-288.
Isnansetyo, A. and Y. Kamei.2003. MC21-A, a bactericidal antibiotic produced by a new marine bacterium, Pseudoalteromonas phenolica sp nov O-BC30(T) against methicillin-resistant Staphylococcus aureus. Antimicrobial Agents and Chemotherapy 47:480-488.
Iwai, H. and A. Pluckthun.1999. Circular beta-lactamase:stability enhancement by cyclizing the backbone. Febs Letters 459:166-172.
Kock,I., R. P. Maskey, M. A. F. Biabani, E. Helmke, and H. Laatsch.2005. 1-hydroxy-l-norresistomycin and resistoflavin methyl ether:New antibiotics from marine-derived streptomycetes. Journal of Antibiotics 58:530-534.
Kunst, F. and N. Ogasawara and I. Moszer and A. M. Albertini and G. Alloni and V. Azevedo and M. G. Bertero and P. Bessieres and A. Bolotin and S. Borchert and R. Borriss and L. Boursier and A. Brans and M. Braun and S. C. Brignell and S. Bron and S. Brouillet and C. V. Bruschi and B. Caldwell and V. Capuano and N. M. Carter and S. K. Choi and J. J. Codani and I. F. Connerton and N. J. Cummings and R. A. Daniel and F. Denizot and K. M. Devine and A. Dusterhoft and S. D. Ehrlich and P. T. Emmerson and K. D. Entian and J. Errington and C. Fabret and E. Ferrari and D. Foulger and C. Fritz and M. Fujita and Y. Fujita and S. Fuma and A. Galizzi and N. Galleron and S. Y. Ghim and P. Glaser and A. Goffeau and E. J. Golightly and G. Grandi and G. Guiseppi and B. J. Guy and K. Haga and J. Haiech and C. R. Harwood and A. Henaut and H. Hilbert and S. Holsappel and S. Hosono and M. F. Hullo and M. Itaya and L. Jones and B. Joris and D. Karamata and Y. Kasahara and M. KlaerrBlanchard and C. Klein and Y. Kobayashi and P. Koetter and G. Koningstein and S. Krogh and M. Kumano and K. Kurita and A. Lapidus and S. Lardinois and J. Lauber and V. Lazarevic and S. M. Lee and A. Levine and H. Liu and S. Masuda and C. Mauel and C. Medigue and N. Medina and R. P. Mellado and M. Mizuno and D. Moestl and S. Nakai and M. Noback and D. Noone and M. Oreilly and K. Ogawa and A. Ogiwara and B. Oudega and S. H. Park and V. Parro and T. M. Pohl and D. Portetelle and S. Porwollik and A. M. Prescott and E. Presecan and P. Pujic and B. Purnelle and G. Rapoport and M. Rey and S. Reynolds and M. Rieger and C. Rivolta and E. Rocha and B. Roche and M. Rose and Y. Sadaie and T. Sato and E. Scanlan and S. Schleich and R. Schroeter and F. Scoffone and J. Sekiguchi and A. Sekowska and S. J. Seror and P. Serror and B. S. Shin and B. Soldo and A. Sorokin and E. Tacconi and T. Takagi and H. Takahashi and K. Takemaru and M. Takeuchi and A. Tamakoshi and T. Tanaka and P. Terpstra and A. Tognoni and V. Tosato and S. Uchiyama and M. Vandenbol and F. Vannier and A. Vassarotti and A. Viari and R. Wambutt and E. Wedler and H. Wedler and T. Weitzenegger and P. Winters and A. Wipat and H. Yamamoto and K. Yamane and K. Yasumoto and K. Yata and K. Yoshida and H. F. Yoshikawa and E. Zumstein and H. Yoshikawa and A. Danchin.1997. The complete genome sequence of the Gram-positive bacterium Bacillus subtilis. Nature 390:249-256.
Kurtz, S., A. Phillippy, A..L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S. L. Salzberg.2004. Versatile and open software for comparing large genomes. Genome Biology 5:9.
Kwon, H. C., C. A. Kauffman, P. R. Jensen, and W. Fenical.2006. Marinomycins A-D, antitumor-antibiotics of a new structure class from a marine actinomycete of the recently discovered genus "Marinispora". Journal of the American Chemical Society 128:1622-1632.
Lagesen, K., P. Hallin, E. A. Rodland, H. H. Staerfeldt, T. Rognes, and D. W. Ussery.2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Research 35:3100-3108.
Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson, and D. G. Higgins.2007. Clustal W and clustal X version 2.0. Bioinformatics 23:2947-2948.
Li, R. Q., Y. R. Li, K. Kristiansen, and J. Wang.2008. SOAP:short oligonucleotide alignment program. Bioinformatics 24:713-714.
Lowe, T. M. and S. R. Eddy.1997. tRNAscan-SE:A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Research 25:955-964.
MacLean, D., J. D. G. Jones, and D. J. Studholme.2009. Application of 'next-generation' sequencing technologies to microbial genetics. Nature Reviews Microbiology 7:287-296.
Manam, R. R., S. Teisan, D. J. White, B. Nicholson, J. Grodberg, S. T. C. Neuteboom, K. S. Lam, D. A. Mosca, G. K. Lloyd, and B. C. M. Potts.2005. Lajollamycin, a nitro-tetraene spiro-beta-lactone-gamma-iactam antibiotic from the marine actinomycete Streptomyces nodosus. Journal of Natural Products 68:240-243.
Mayer, A. M. S., A. D. Rodriguez, R. G. S. Berlinck, and M. T. Hamann.2007. Marine pharmacology in 2003-4:Marine compounds with anthelmintic antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiplatelet, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems, and other miscellaneous mechanisms of action. Comparative Biochemistry and Physiology C-Toxicology & Pharmacology 145:553-581.
Mayer, A. M. S., A. D. Rodriguez, R. G. S. Berlinck, and M. T. Hamann.2009. Marine pharmacology in 2005-6:Marine compounds with anthelmintic, antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems, and other miscellaneous mechanisms of action. Biochimica Et Biophysica Acta-General Subjects 1790:283-308.
Mrazek, J. and S. Karlin.1998. Strand compositional asymmetry in bacterial and large viral genomes. Proceedings of the National Academy of Sciences of the United States of America 95:3720-3725.
Nett, M., H. Ikeda, and B. S. Moore.2009. Genomic basis for natural product biosynthetic diversity in the actinomycetes. Natural Product Reports 26:1362-1384.
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 Genomics 11:12.
Pop, M. and S. L. Salzberg.2008. Bioinformatics challenges of new sequencing technology. Trends in Genetics 24:142-149.
Rasko, D. A., J. Ravel, O. A. Okstad, E. Helgason, R. Z. Cer, L. X. Jiang, K. A. Shores, D. E. Fouts, N. J. Tourasse, S. V. Angiuoli, J. Kolonay, W. C. Nelson, A. B. Kolsto, C. M. Fraser, and T. D. Read.2004. The genome sequence of Bacillus cereus ATCC 10987 reveals metabolic adaptations and a large plasmid related to Bacillus anthracis pXO1. Nucleic Acids Research 32:977-988.
Read, T. D., S. N. Peterson, N. Tourasse, L. W. Baillie, I. T. Paulsen, K. E. Nelson, H. Tettelin, D. E. Fouts, J. A. Eisen, S. R. Gill, E. K. Holtzapple, O. A. Okstad, E. Helgason, J. Rilstone, M. Wu, J. F. Kolonay, M. J. Beanan, R. J. Dodson, L. M. Brinkac, M. Gwinn, R. T. DeBoy, R. Madpu, S. C. Daugherty, A. S. Durkin, D. H. Haft, W. C. Nelson, J. D. Peterson, M. Pop, H. M. Khouri, D. Radune, J. L. Benton, Y. Mahamoud,.L. X. Jiang, I. R. Hance, J. F. Weidman, K. J. Berry, R. D. Plaut, A. M. Wolf, K. L. Watkins, W. C. Nierman, A. Hazen, R. Cline, C. Redmond, J. E. Thwaite, O. White, S. L. Salzberg, B. Thomason, A. M. Friedlander, T. M. Koehler, P. C. Hanna, A. B. Kolsto, and C. M. Fraser.2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:81-86.
Rey, M. W., P. Ramaiya, B. A. Nelson, S. D. Brody-Karpin, E. J. Zaretsky, M. Tang, A. L. de Leon, H. Xiang, V. Gusti, I. G. Clausen, P. B. Olsen, M. D. Rasmussen, J. T. Andersen, P. L. Jorgensen, T. S. Larsen, A. Sorokin, A. Bolotin, A. Lapidus, N. Galleron, S. D. Ehrlich, and R. M. Berka. 2004. Complete genome sequence of the industrial bacterium Bacillus licheniformis and comparisons with closely related Bacillus species. Genome Biology 5:12.
Rocha, E. P. C., A. Danchin, and A. Viari.1999. Universal replication biases in bacteria. Molecular Microbiology 32:11-16.
Simpson, J. T., K. Wong, S. D. Jackman, J. E. Schein, S. J. M. Jones, and I. Birol.2009. ABySS:A parallel assembler for short read sequence data. Genome Research 19:1117-1123.
Socha, A. M., D. Garcia, R. Sheffer, and D. C. Rowley.2006. Antibiotic bisanthraquinones produced by a streptomycete isolated from a cyanobacterium associated with Ecteinascidia turbinata. Journal of Natural Products 69:1070-1073.
Solanki, R., M. Khanna, and R. LaI.2008. Bioactive compounds from marine actinomycetes. Indian Journal of Microbiology 48:410-431.
Soria-Mercado, I. E., A. Prieto-Davo, P. R. Jensen, and W. Fenical.2005. Antibiotic terpenoid chloro-dihydroquinones from a new marine actinomycete. Journal of Natural Products 68:904-910.
Steiner. H., D. Hultmark, A. Engstrom, H. Bennich, and H. G. Boman.1981. Sequence and specificity of 2 anti-bacterial proteins involved in insect immunity. Nature 292:246-248.
Stothard, P. and D. S. Wishart.2005. Circular genome visualization and exploration using CGView. Bioinformatics 21:537-539.
Tamura, K., J. Dudley, M. Nei. and S. Kumar.2007. MEGA4:Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24:1596-1599.
Tatusov, R. L., E. V. Koonin, and D. J. Lipman.1997. A genomic perspective on protein families. Science 278:631-637.
Thomas, S., S. Karnik, R. S. Barai, V. K. Jayaraman, and S. Idicula-Thomas.2010. CAMP:a useful resource for research on antimicrobial peptides. Nucleic Acids Research 38:D774-D780.
Wang, C. K. L., Q. Kaas, L. Chiche, and D. J. Craik.2008. CyBase:a database of cyclic protein sequences and structures, with applications in protein discovery and engineering. Nucleic Acids Research 36:D206-D210.
Wang, G. S., X. Li, and Z. Wang.2009. APD2:the updated antimicrobial peptide database and its application in peptide design. Nucleic Acids Research 37:D933-D937.
Williams, N. K., P. Prosselkov, E. Liepinsh, I. Line, A. Sharipo, D. R. Littler, P. M. G. Curmi, G. Otting, and N. E. Dixon.2002. In vivo protein cyclization promoted by a circularly permuted Synechocystis sp PCC6803 DnaB mini-intein. Journal of Biological Chemistry 277:7790-7798.
Zerbino, D. R. and E. Birney.2008. Velvet:Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18:821-829.