Complete genome sequence of Cellulophaga lytica type strain (LIM-21T)

Johansen JE, Nielsen P, Sjøholm C. Description of Cellulophaga báltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov. Int J Syst Bacteriol 1999; 49:1231–1240. PubMed doi:10.1099/00207713-49-3-1231 Euzéby JP. List of bacterial names with standing in nomenclature: A folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed doi:10.1099/00207713-47-2-590 Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868. PubMed Nedashkovskaya OI, Suzuki M, Lysenko AM, Snauwaert C, Vancanneyt M, Swings J, Vysotskii MV, Mikhailov VV. Cellulophaga pacifica sp. nov. Int J Syst Evol Microbiol 2004; 54:609–613. PubMed doi:10.1099/ijs.0.02737-0 Kahng HY, Chung BS, Lee DH, Jung JS, Park JH, Joen CO. Cellulophaga tyrosinoxydans sp. nov., a tyrosinase producing bacterium isolated from seawater. Int J Syst Evol Microbiol 2009; 59:654–657. PubMed doi:10.1099/ijs.0.003210-0 Skerman VBD, McGowan V, Sneath PHA, eds. Approved Lists of Bacterial Names. [Approved Lists of Bacterial Names in IJSEM Online — Approved Lists of Bacterial Names Amended edition]. Int J Syst Bacteriol 1980; 30:225–420. doi:10.1099/00207713-30-1-225 DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl Environ Microbiol 2006; 72:5069–5072. PubMed doi:10.1128/AEM.03006-05 Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137. doi:10.1108/eb046814 Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452 Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMed Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642 Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184–200. doi:10.1007/978-3-642-02008-7_13 Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848 Abt B, Lu M, Misra M, Han C, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, et al. Complete genome sequence of Cellulophaga algicola type strain (IC166T). Stand Genomic Sci 2011; 4:72–80. PubMed doi:10.4056/sigs.1543845 Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360 Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576 Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119–169. Ludwig W, Euzeby J, Whitman WG. Draft taxonomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes. http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf. Taxonomic Outline 2008 Garrity GM, Holt J. Taxonomic outline of the Archaea and Bacteria. In: Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 1. The Archaea, deeply branching and phototrophic bacteria. Garrity GM, Boone DR, Castenholz RW (eds). 2001; 155–166. Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family F!avobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070. PubMed doi:10.1099/ijs.0.02136-0 List Editor. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List no. 41. Int J Syst Bacteriol 1992; 42:327–328. doi:10.1099/00207713-42-2-327 Reichenbach H. Order 1. Cytophagales Leadbetter 1974, 99AL. In: Holt JG (ed), Bergey’s Manual of Systematic Bacteriology, First Edition, Volume 3, The Williams and Wilkins Co., Baltimore, 1989, p. 2011–2013. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P. Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148. doi:10.1099/00207713-46-1-128 Lewin RA. A classification of flexibacteria. J Gen Microbiol 1969; 58:189–206. PubMed Reichenbach H. Genus I. Cytophaga Winogradsky 1929, 577, (AL) emend. In: Staley JT, Bryant MP, Pfenning N, Holt JG (eds). Bergey’s manual of systematic bacteriology. Vol. 3. Baltimore, Md. Williams & Wilkins, 1989, pp. 2015–2050. BAuA. Classification of bacteria and archaea in risk groups. TRBA 2005; 466:84. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556 Lewin RA, Lounsbery DM. Isolation, Cultivation and Characterization of Flexibacteria. J Gen Microbiol 1969; 58:145–170. PubMed Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:10.1016/j.syapm.2010.03.003 Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656 List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51–55. doi:10.1089/bio.2010.0029 The DOE Joint Genome Institute. http://www.jgi.doe.gov Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:10.1101/gr.074492.107 Han C, Chain P. 2006. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabina HR, Valafar H (eds), CSREA Press. June 26–29, 2006: 141–146. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119 Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457 Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393 Sandmann G. Carotenoid biosynthesis and biotechnological application. Arch Biochem Biophys 2001; 385:4–12. PubMed doi:10.1006/abbi.2000.2170 Sakai T, Ishizuka K, Kato I. Isolation and characterization of fucoidan-degrading marine bacterium. Mar Biotechnol 2003; 5:409–416. PubMed doi:10.1007/s10126-002-0118-6 Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Desphande S, Nolan M, Lucas S, Tice H, Cheng JF. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24T). Stand Genomic Sci 2010; 2:290–299. PubMed doi:10.4056/sigs.952166 Liu Y, Harrison PM, Kunin V, Gerstein M. Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes. Genome Biol 2004; 5:R64. PubMed doi:10.1186/gb-2004-5-9-r64 Auch AF, Von Jan M, Klenk HP, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134. PubMed doi:10.4056/sigs.531120 Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148. PubMed doi:10.4056/sigs.541628 McBride MJ, Xie G, Martens EC, Lapidus A, Henrissat B, Rhodes RG, Goltsman E, Wang W, Xu J, Hunnicutt DW. Novel features of the polysaccharide-digesting gliding bacterium Flavobacterium johnsoniae as revealed by genome sequence analysis. Appl Environ Microbiol 2009; 75:6864–6875. PubMed doi:10.1128/AEM.01495-09