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Volumn 8, Issue 1, 2013, Pages 37-46

High-quality-draft genome sequence of the yellow-pigmented flavobacterium joostella marina type strain (En5T)

(31)  Stackebrandt, Erko a   Chertkov, Olga b,c   Lapidus, Alla b   Nolan, Matt b   Lucas, Susan b   Han, Cliff b,c   Cheng, Jan Fang b   Tapia, Roxanne b,c   Goodwin, Lynne A b,c   Bruce, David b,c   Pitluck, Sam b   Liolios, Konstantinos b   Mavromatis, Konstantinos b   Pagani, Ioanna b   Ivanova, Natalia b   Mikhailova, Natalia b   Huntemann, Marcel b   Pati, Amrita b   Chen, Amy d   Palaniappan, Krishna d   more..


Author keywords

Aerobic; Bacteroidetes; Flavobacteriaceae; Geba; Gram negative; Mesophile; Non motile

Indexed keywords

ACID PHOSPHATASE; ALKALINE PHOSPHATASE; ALPHA GLUCOSIDASE; ALPHA MANNOSIDASE; ARABINOSE; ARYL ACYLAMIDASE; BETA GALACTOSIDASE; BETA GLUCOSIDASE; CATALASE; CELLOBIOSE; COMPLEMENT COMPONENT C4; COMPLEMENT COMPONENT C8; ESCULIN; FATTY ACID; GLUCOSE; MALTOSE; MANNOSE; N ACETYL BETA GLUCOSAMINIDASE; NAPHTHOL AS BI PHOSPHOHYDROLASE; OXIDOREDUCTASE; PHOSPHATASE; POLYSORBATE 80; RNA 16S; STARCH; SUCROSE; TRYPSIN; UNCLASSIFIED DRUG;

EID: 84878400816     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3537045     Document Type: Article
Times cited : (5)

References (50)
  • 2
    • 79151474058 scopus 로고    scopus 로고
    • Joostella atrarenae sp. nov., a novel member of the Flavobacteriaceae originating from the black sea sand of Jeju Island
    • PubMed
    • Kim BC, Lee HK, Kim MN, Jung MY, Chang YH, Lee J, Kee-Sun Shin KS. Joostella atrarenae sp. nov., a novel member of the Flavobacteriaceae originating from the black sea sand of Jeju Island. Curr Microbiol 2012; 62:606-611. PubMed http://dx.doi.org/10.1007/s00284-010-9750-y
    • (2012) Curr Microbiol , vol.62 , pp. 606-611
    • Kim, B.C.1    Lee, H.K.2    Kim, M.N.3    Jung, M.Y.4    Chang, Y.H.5    Lee, J.6    Kee-Sun, S.K.S.7
  • 3
    • 33845807865 scopus 로고    scopus 로고
    • Zhouia amylolytica gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from sed-iment of the South China Sea
    • PubMed
    • Liu ZP, Wang BJ, Dai X, Liu XY, Liu SJ. Zhouia amylolytica gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from sed-iment of the South China Sea. Int J Syst Evol Microbiol 2006; 56:2825-2829. PubMed http://dx.doi.org/10.1099/ijs.0.64587-0
    • (2006) Int J Syst Evol Microbiol , vol.56 , pp. 2825-2829
    • Liu, Z.P.1    Wang, B.J.2    Dai, X.3    Liu, X.Y.4    Liu, S.J.5
  • 4
    • 34249090962 scopus 로고    scopus 로고
    • Galbibacter mesophilus gen. nov., sp. nov., a novel member of the family
    • PubMed
    • Khan ST, Nakagawa Y, Harayama S. Galbibacter mesophilus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae. Int J Syst Evol Microbiol 2007; 57:969-973. PubMed http://dx.doi.org/10.1099/ijs.0.64729-0
    • (2007) Flavobacteriaceae. Int J Syst Evol Microbiol , vol.57 , pp. 969-973
    • Khan, S.T.1    Nakagawa, Y.2    Harayama, S.3
  • 5
    • 0001702209 scopus 로고
    • Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's Manual of Sys-tematic Bacteriology
    • Reichenbach H. 1989. Order 1. Cytophagales Leadbetter 1974, 99AL. In: Staley JT, Bryant MP, Pfennig N, Holt JG (eds) Bergey's Manual of Sys-tematic Bacteriology vol. 3. 1989; pp 2011-2013.
    • (1989) Order 1. Cytophagales Leadbetter 1974, 99AL , vol.3 , Issue.1989 , pp. 2011-2013
    • Reichenbach, H.1
  • 6
    • 0042032933 scopus 로고
    • Validation List No. 41
    • Validation List No. 41. Int J Syst Bacteriol 1992; 42:327-328. http://dx.doi.org/10.1099/00207713-42-2-327
    • (1992) Int J Syst Bacteriol , vol.42 , pp. 327-328
  • 11
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • PubMed
    • Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed http://dx.doi.org/10.1093/bioinformatics/18.3.452
    • (2002) Bioinformat-ics , vol.18 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 12
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Pub-Med
    • Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. Pub-Med http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
    • (2000) Mol Biol Evol , vol.17 , pp. 540-552
    • Castresana, J.1
  • 13
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web-servers
    • PubMed
    • Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758-771. PubMed http://dx.doi.org/10.1080/10635150802429642
    • (2008) Syst Biol , vol.57 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 14
    • 36849014457 scopus 로고    scopus 로고
    • An empirical test of the midpoint rooting method
    • Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669-674. http://dx.doi.org/10.1111/j.1095-8312.2007.00864.x
    • (2007) Biol J Linn Soc Lond , vol.92 , pp. 669-674
    • Hess, P.N.1    De Moraes, R.C.A.2
  • 16
    • 84878380064 scopus 로고    scopus 로고
    • PAUP*: Phylogenetic Analysis Us-ing Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland
    • Swofford DL. PAUP*: Phylogenetic Analysis Us-ing Parsimony (*and Other Methods), Version 4.0 b10. Sinauer Associates, Sunderland, 2002.
    • (2002)
    • Swofford, D.L.1
  • 17
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their as-sociated metadata
    • PubMed
    • Pagani I, Liolios K, Jansson J, Chen IM, Smirnova T, Nosrat B, Markowitz VM, Kyrpides NC. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their as-sociated metadata. Nucleic Acids Res 2012; 40:D571-D579. PubMed http://dx.doi.org/10.1093/nar/gkr1100
    • (2012) Nucleic Acids Res , vol.40
    • Pagani, I.1    Liolios, K.2    Jansson, J.3    Chen, I.M.4    Smirnova, T.5    Nosrat, B.6    Markowitz, V.M.7    Kyrpides, N.C.8
  • 22
    • 70350469953 scopus 로고    scopus 로고
    • Complete genome sequence of Robiginitalea biformata HTCC2501
    • PubMed
    • Oh HM, Giovannoni SJ, Lee K, Ferriera S, John-son J, Cho JC. Complete genome sequence of Robiginitalea biformata HTCC2501. J Bacteriol 2009; 191:7144-7145. PubMed http://dx.doi.org/10.1128/JB.01191-09
    • (2009) J Bacteriol , vol.191 , pp. 7144-7145
    • Oh, H.M.1    Giovannoni, S.J.2    Lee, K.3    Ferriera, S.4    John-Son, J.5    Cho, J.C.6
  • 25
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the do-mains Archaea, Bacteria, and Eucarya
    • PubMed
    • Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed http://dx.doi.org/10.1073/pnas.87.12.4576
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 4576-4579
    • Woese, C.R.1    Kandler, O.2    Wheelis, M.L.3
  • 27
    • 84863628521 scopus 로고    scopus 로고
    • Validation List N. ° 143
    • Validation List N. ° 143. Int J Syst Evol Microbiol 2012; 62:1-4.
    • (2012) Int J Syst Evol Microbiol , vol.62 , pp. 1-4
  • 29
    • 84860771683 scopus 로고    scopus 로고
    • Validation List N. ° 145
    • Validation List N. ° 145. Int J Syst Evol Microbiol 2012; 62:1017-1019.
    • (2012) Int J Syst Evol Microbiol , vol.62 , pp. 1017-1019
  • 30
    • 13244252390 scopus 로고    scopus 로고
    • note
    • Judicial Commission of the International Commit-tee on Systematics of Prokaryotes. The nomencla-tural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005; 55:517-518. PubMed http://dx.doi.org/10.1099/ijs.0.63548-0
    • (2005) Int J Syst Evol Microbiol , vol.55 , pp. 517-518
  • 32
    • 0030052649 scopus 로고    scopus 로고
    • Cutting a Gordian knot: Emended classification and description of the ge-nus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (Basonym, Cytophaga aquatilis Strohl and Tait 1978)
    • Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K, Vandamme P. Cutting a Gordian knot: emended classification and description of the ge-nus 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. http://dx.doi.org/10.1099/00207713-46-1-128
    • (1996) Int J Syst Bacteriol , vol.46 , pp. 128-148
    • Bernardet, J.F.1    Segers, P.2    Vancanneyt, M.3    Berthe, F.4    Kersters, K.5    Vandamme, P.6
  • 33
    • 0035989637 scopus 로고    scopus 로고
    • Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended descrip-tion of the family
    • PubMed
    • Bernardet JF, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended descrip-tion of the family. Int J Syst Evol Microbiol 2002; 52:1049-1070. PubMed http://dx.doi.org/10.1099/ijs.0.02136-0
    • (2002) Int J Syst Evol Microbiol , vol.52 , pp. 1049-1070
    • Bernardet, J.F.1    Nakagawa, Y.2    Holmes, B.3
  • 36
    • 40449130547 scopus 로고    scopus 로고
    • Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants
    • PubMed
    • Herzog P, Winkler I, Wolking D, Kämpfer P, Lipski A. Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants. Int J Syst Evol Microbiol 2008; 58:26-33. PubMed http://dx.doi.org/10.1099/ijs.0.65362-0
    • (2008) Int J Syst Evol Microbiol , vol.58 , pp. 26-33
    • Herzog, P.1    Winkler, I.2    Wolking, D.3    Kämpfer, P.4    Lipski, A.5
  • 37
    • 77952889628 scopus 로고    scopus 로고
    • En route to a genome-based classification of Archaea and
    • PubMed
    • Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed http://dx.doi.org/10.1016/j.syapm.2010.03.003
    • (2010) Bacteria? Syst Appl Microbiol , vol.33 , pp. 175-182
    • Klenk, H.P.1    Göker, M.2
  • 39
    • 84871205244 scopus 로고    scopus 로고
    • The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and an-notation
    • PubMed
    • Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, et al. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and an-notation. PLoS ONE 2012; 7:e48837. PubMed http://dx.doi.org/10.1371/journal.pone.0048837
    • (2012) PLoS ONE , vol.7
    • Mavromatis, K.1    Land, M.L.2    Brettin, T.S.3    Quest, D.J.4    Copeland, A.5    Clum, A.6    Goodwin, L.7    Woyke, T.8    Lapidus, A.9    Klenk, H.P.10
  • 40
    • 84878412288 scopus 로고    scopus 로고
    • List of growth media used at DSMZ
    • List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technolog y/list-of-media-for-microorganisms.html.
  • 42
    • 84878397807 scopus 로고    scopus 로고
    • JGI website
    • JGI website. http://www.jgi.doe.gov
  • 43
    • 84878397066 scopus 로고    scopus 로고
    • The Phred/Phrap/Consed software package
    • The Phred/Phrap/Consed software package. http://www.phrap.com
  • 44
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
    • PubMed
    • Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed http://dx.doi.org/10.1101/gr.074492.107
    • (2008) Genome Res , vol.18 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2
  • 47
    • 77952299957 scopus 로고    scopus 로고
    • Prodigal: Prokaryotic gene recognition and translation initiation site identifi-cation
    • Pub-Med
    • Hyatt D, Chen GL, LoCascio PF, Land ML, Lar-imer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. Pub-Med http://dx.doi.org/10.1186/1471-2105-11-119
    • (2010) BMC Bioinformatics , vol.11 , pp. 119
    • Hyatt, D.1    Chen, G.L.2    Locascio, P.F.3    Land, M.L.4    Lar-Imer, F.W.5    Hauser, L.J.6
  • 50
    • 69949116874 scopus 로고    scopus 로고
    • IMG ER: A system for microbial ge-nome annotation expert review and curation
    • PubMed
    • Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed http://dx.doi.org/10.1093/bioinformatics/btp393
    • (2009) Bio-informatics , vol.25 , pp. 2271-2278
    • Markowitz, V.M.1    Ivanova, N.N.2    Chen, I.M.A.3    Chu, K.4    Kyrpides, N.C.5


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