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Volumn 8, Issue 2, 2013, Pages 360-374

Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects

Author keywords

16s rRNA; Genomic Encyclopedia; Genomics; Phylogenetic diversity; Roseobacter clade; Taxon selection; Tree of life

Indexed keywords

ALGORITHM; ARTICLE; GENE SEQUENCE; HYPOTHESIS; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; ROSEOBACTER; SCORING SYSTEM; TAXONOMY; UNINDEXED SEQUENCE;

EID: 84879351437     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3446951     Document Type: Article
Times cited : (44)

References (53)
  • 1
    • 69949116874 scopus 로고    scopus 로고
    • IMG-ER: A system for microbial genome annotation expert review and curation
    • PubMed
    • Markowitz VM, Mavromatis K, Ivanova NN, Chen IA, Chu K, Kyrpides NC. IMG-ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. PubMed. http://dx.doi.org/10.1093/bioinformatics/btp393
    • (2009) Bioinformatics , vol.25 , pp. 2271-2278
    • Markowitz, V.M.1    Mavromatis, K.2    Ivanova, N.N.3    Chen, I.A.4    Chu, K.5    Kyrpides, N.C.6
  • 4
    • 77952889628 scopus 로고    scopus 로고
    • En route to a genome-based classification of Archaea and Bacteria?
    • 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) Syst Appl Microbiol , vol.33 , pp. 175-182
    • Klenk, H.P.1    Göker, M.2
  • 5
    • 0033059179 scopus 로고    scopus 로고
    • Misunderstanding the Bacteriological Code
    • .
    • Tindall BJ. Misunderstanding the Bacteriological Code. Int J Syst Bacteriol 1999; 49:1313-1316. PubMed. http://dx.doi.org/10.1099/00207713-49-3-1313
    • (1999) Int J Syst Bacteriol , vol.49 , pp. 1313-1316
    • Tindall, B.J.1
  • 6
    • 33751221612 scopus 로고    scopus 로고
    • Valid publication of names of prokaryotes according to the rules of nomenclature: Past history and current practice
    • .
    • Tindall BJ, Kämpfer P, Euzéby JP, Oren A. Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. Int J Syst Evol Microbiol 2006; 56:2715-2720.PubMed. http://dx.doi.org/10.1099/ijs.0.64780-0
    • (2006) Int J Syst Evol Microbiol , vol.56 , pp. 2715-2720
    • Tindall, B.J.1    Kämpfer, P.2    Euzéby, J.P.3    Oren, A.4
  • 11
    • 34548546830 scopus 로고    scopus 로고
    • Resource-aware taxon selection for maximizing phylogenetic diversity
    • PubMed
    • Pardi F, Goldman N. Resource-aware taxon selection for maximizing phylogenetic diversity. Syst Biol 2007; 56:431-444. PubMed. http://dx.doi.org/10.1080/10635150701411279
    • (2007) Syst Biol , vol.56 , pp. 431-444
    • Pardi, F.1    Goldman, N.2
  • 12
    • 72849134544 scopus 로고    scopus 로고
    • Taxon selection under split diversity
    • PubMed
    • Minh BQ, Klaere S, von Haeseler A. Taxon selection under split diversity. Syst Biol, 2009; 58:586-594. PubMed. http://dx.doi.org/10.1093/sysbio/syp058
    • (2009) Syst Biol , vol.58 , pp. 586-594
    • Minh, B.Q.1    Klaere, S.2    von Haeseler, A.3
  • 13
    • 80054855179 scopus 로고    scopus 로고
    • Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)
    • PubMed
    • Chang YJ, Land M, Hauser L, Chertkov O, Larimer F, Jeffries CD, Glavina del Rio T, Nolan M, Copeland A, Tice H, et al. Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T). Stand Genomic Sci 2011; 5:97-111. PubMed. http://dx.doi.org/10.4056/sigs.2114901
    • (2011) Stand Genomic Sci , vol.5 , pp. 97-111
    • Chang, Y.J.1    Land, M.2    Hauser, L.3    Chertkov, O.4    Larimer, F.5    Jeffries, C.D.6    Glavina del Rio, T.7    Nolan, M.8    Copeland, A.9    Tice, H.10
  • 15
    • 84861342725 scopus 로고    scopus 로고
    • Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010
    • PubMed,
    • Klenk HP, Lapidus A, Chertkov O, Copeland A, Del Rio TG, Nolan M, Lucas S, Chen F, Tice H, Cheng JF, et al. Complete genome sequence of the thermophilic, hydrogen-oxidizing Bacillus tusciae type strain (T2T) and reclassification in the new genus, Kyrpidia gen. nov. as Kyrpidia tusciae comb. nov. and emendation of the family Alicyclobacillaceae da Costa and Rainey, 2010. Stand Genomic Sci 2011; 5:121-134. PubMed. http://dx.doi.org/10.4056/sigs.2144922
    • (2011) Stand Genomic Sci , vol.5 , pp. 121-134
    • Klenk, H.P.1    Lapidus, A.2    Chertkov, O.3    Copeland, A.4    Del Rio, T.G.5    Nolan, M.6    Lucas, S.7    Chen, F.8    Tice, H.9    Cheng, J.F.10
  • 16
    • 84863601275 scopus 로고    scopus 로고
    • Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta
    • PubMed
    • Abt B, Han C, Scheuner C, Lu M, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, et al. Complete genome sequence of the termite hindgut bacterium Spirochaeta coccoides type strain (SPN1T), reclassification in the genus Sphaerochaeta as Sphaerochaeta coccoides comb. nov. and emendations of the family Spirochaetaceae and the genus Sphaerochaeta. Stand Genomic Sci 2012; 6:194-209. PubMed. http://dx.doi.org/10.4056/sigs.2796069
    • (2012) Stand Genomic Sci , vol.6 , pp. 194-209
    • Abt, B.1    Han, C.2    Scheuner, C.3    Lu, M.4    Lapidus, A.5    Nolan, M.6    Lucas, S.7    Hammon, N.8    Deshpande, S.9    Cheng, J.F.10
  • 17
    • 43949120140 scopus 로고    scopus 로고
    • Diversity, ecology, and genomics of the Roseobacter clade: A short overview
    • PubMed
    • Brinkhoff T, Giebel HA, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch Microbiol 2008; 189:531-539. PubMed. http://dx.doi.org/10.1007/s00203-008-0353-y
    • (2008) Arch Microbiol , vol.189 , pp. 531-539
    • Brinkhoff, T.1    Giebel, H.A.2    Simon, M.3
  • 18
    • 26844510681 scopus 로고    scopus 로고
    • Overview of the marine Roseobacter lineage
    • PubMed
    • Buchan A, González JM, Moran MA. Overview of the marine Roseobacter lineage. Appl Environ Microbiol 2005; 71:5665-5677. PubMed. http://dx.doi.org/10.1128/AEM.71.10.5665-5677.2005
    • (2005) Appl Environ Microbiol , vol.71 , pp. 5665-5677
    • Buchan, A.1    González, J.M.2    Moran, M.A.3
  • 19
    • 33646193540 scopus 로고    scopus 로고
    • In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, Bergey's Manual of Systematic Bacteriology, Second Edition, Part C, Springer, New York
    • Garrity GM, Bell JA, Lilburn T. Order III. Rhodobacterales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 161.
    • (2005) Rhodobacterales Ord. Nov , vol.2 , pp. 161
    • Garrity, G.M.1    Bell, J.A.2    Lilburn, T.3    Order, I.I.I.4
  • 20
    • 84255195560 scopus 로고    scopus 로고
    • The history of the tetracyclines
    • PubMed
    • Nelson ML, Levy SB. The history of the tetracyclines. Ann N Y Acad Sci 2011; 1241:1732. PubMed. http://dx.doi.org/10.1111/j.1749-6632.2011.06354.x
    • (2011) Ann N Y Acad Sci , vol.1241 , pp. 1732
    • Nelson, M.L.1    Levy, S.B.2
  • 21
    • 33644521754 scopus 로고    scopus 로고
    • Update on an old successful antibiotic class
    • PubMed
    • Pace JL, Yang G. Glycopeptides: Update on an old successful antibiotic class. Biochem Pharmacol 2006; 71:968-980. PubMed. http://dx.doi.org/10.1016/j.bcp.2005.12.005
    • (2006) Biochem Pharmacol , vol.71 , pp. 968-980
    • Pace, J.L.1    Glycopeptides, Y.G.2
  • 22
    • 82355169031 scopus 로고    scopus 로고
    • Penicillin: The medicine with the greatest impact on the therapeutic outcomes
    • PubMed
    • Kardos N, Demain AL. Penicillin: the medicine with the greatest impact on the therapeutic outcomes. Appl Microbiol Biotechnol 2011; 92:677-687. PubMed. http://dx.doi.org/10.1007/s00253-011-3587-6
    • (2011) Appl Microbiol Biotechnol , vol.92 , pp. 677-687
    • Kardos, N.1    Demain, A.L.2
  • 23
    • 70349496578 scopus 로고    scopus 로고
    • The aminocoumarins: Biosynthesis and biology
    • PubMed
    • Heide L. The aminocoumarins: biosynthesis and biology. Nat Prod Rep 2009; 26:1241-1250. PubMed. http://dx.doi.org/10.1039/b808333a
    • (2009) Nat Prod Rep , vol.26 , pp. 1241-1250
    • Heide, L.1
  • 24
    • 9744275238 scopus 로고    scopus 로고
    • Lincosamides: Chemical structure, biosynthesis, mechanism of action, resistance, and applications
    • PubMed
    • Spízek J, Novotná J, Rezanka T. Lincosamides: chemical structure, biosynthesis, mechanism of action, resistance, and applications. Adv Appl Microbiol 2004; 56:121-154. PubMed. http://dx.doi.org/10.1016/S0065-2164(04)56004-5
    • (2004) Adv Appl Microbiol , vol.56 , pp. 121-154
    • Spízek, J.1    Novotná, J.2    Rezanka, T.3
  • 25
    • 84255195557 scopus 로고    scopus 로고
    • Macrolides antibiotics in the ribosome exit tunnel: Species-specific binding and action
    • PubMed
    • Kannan K, Mankin AS. Macrolides antibiotics in the ribosome exit tunnel: species-specific binding and action. Ann N Y Acad Sci 2011; 1241:33-47. PubMed. http://dx.doi.org/10.1111/M749-6632.2011.06315.x
    • (2011) Ann N Y Acad Sci , vol.1241 , pp. 33-47
    • Kannan, K.1    Mankin, A.S.2
  • 26
    • 0026092940 scopus 로고    scopus 로고
    • Microbial sources of carotenoid pigments used in foods and feeds
    • Nelis HJ, De Leenheer AP. Microbial sources of carotenoid pigments used in foods and feeds. J Appl Microbiol 1991; 70:181-191. http://dx.doi.org/10.1111/j.1365-2672.1991.tb02922.x
    • J Appl Microbiol 1991 , vol.70 , pp. 181-191
    • Nelis, H.J.1    de Leenheer, A.P.2
  • 27
    • 0028850367 scopus 로고
    • Siderophores: Structure and function of microbial iron transport compounds
    • PubMed
    • Neilands JB. Siderophores: structure and function of microbial iron transport compounds. J Biol Chem 1995; 270:26723-26726. PubMed
    • (1995) J Biol Chem , vol.270 , pp. 26723-26726
    • Neilands, J.B.1
  • 29
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • PubMed
    • Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368-376. PubMed. http://dx.doi.org/10.1007/BF01734359
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 30
    • 84959747425 scopus 로고    scopus 로고
    • Toward defining the course of evolution: Minimum change for a specific tree topology
    • Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406-416. http://dx.doi.org/10.2307/2412116
    • Syst Zool 1971 , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 31
    • 84894507883 scopus 로고    scopus 로고
    • http://bioruby.open-bio.org
  • 33
    • 37549027613 scopus 로고    scopus 로고
    • SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
    • PubMed
    • Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 2007; 35:7188-7196. PubMed. http://dx.doi.org/10.1093/nar/gkm864
    • (2007) Nucleic Acids Res , vol.35 , pp. 7188-7196
    • Pruesse, E.1    Quast, C.2    Knittel, K.3    Fuchs, B.M.4    Ludwig, W.5    Peplies, J.6    Glöckner, F.O.7
  • 34
    • 0025300402 scopus 로고
    • Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya
    • PubMed,
    • 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. 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
  • 35
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated 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 associated metadata. Nucleic Acids Res 2012; 40:D571-D579. PubMed. http://dx.doi.org/10.1093/nar/gkr1100http://www.bacterio.cict.fr
    • (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
  • 36
    • 24344500901 scopus 로고    scopus 로고
    • Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources
    • Dawyndt P, Vancanneyt M, De Meyer H, Swings J. Knowledge accumulation and resolution of data inconsistencies during the integration of microbial information sources. IEEE Trans Knowl Data Eng 2005; 17:1111-1126. http://dx.doi.org/10.1109/TKDE.2005.131
    • (2005) IEEE Trans Knowl Data Eng , vol.17 , pp. 1111-1126
    • Dawyndt, P.1    Vancanneyt, M.2    de Meyer, H.3    Swings, J.4
  • 38
    • 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. Bioinformatics 2002; 18:452-464. PubMed. http://dx.doi.org/10.1093/bioinformatics/18.3.452
    • (2002) Bioinformatics , vol.18 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 39
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • PubMed
    • Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed.http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
    • (2000) Mol Biol Evol , vol.17 , pp. 540-552
    • Castresana, J.1
  • 40
    • 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
  • 43
    • 45849153461 scopus 로고    scopus 로고
    • Genomic sequencing of single microbial cells from environmental samples
    • PubMed,
    • Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS. Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 2008; 11:198-204. PubMed. http://dx.doi.org/10.1016/j.mib.2008.05.006
    • (2008) Curr Opin Microbiol , vol.11 , pp. 198-204
    • Ishoey, T.1    Woyke, T.2    Stepanauskas, R.3    Novotny, M.4    Lasken, R.S.5
  • 46
    • 77952891045 scopus 로고    scopus 로고
    • Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs
    • PubMed,
    • 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. http://dx.doi.org/10.4056/sigs.541628
    • (2010) Stand Genomic Sci , vol.2 , pp. 142-148
    • Auch, A.F.1    Klenk, H.P.2    Göker, M.3
  • 47
    • 84959773356 scopus 로고
    • The information content of the phylogenetic system
    • Farris JS. The information content of the phylogenetic system. Syst Zool 1979; 28:483-519. http://dx.doi.org/10.2307/2412562
    • (1979) Syst Zool , vol.28 , pp. 483-519
    • Farris, J.S.1
  • 49
    • 84868267319 scopus 로고    scopus 로고
    • Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha proteobacterium Starkeya novella type strain (ATCC 8093T)
    • PubMed
    • Kappler U, Davenport K, Beatson S, Lucas S, Lapidus A, Copeland A, Berry KW, Del Rio TG, Hammon N, Dalin E, et al. Complete genome sequence of the facultatively chemolithoautotrophic and methylotrophic alpha proteobacterium Starkeya novella type strain (ATCC 8093T). Stand Genomic Sci 2012; 7:44-58. PubMed.
    • (2012) Stand Genomic Sci , vol.7 , pp. 44-58
    • Kappler, U.1    Davenport, K.2    Beatson, S.3    Lucas, S.4    Lapidus, A.5    Copeland, A.6    Berry, K.W.7    Del Rio, T.G.8    Hammon, N.9    Dalin, E.10
  • 51
    • 84960589752 scopus 로고
    • Formal definitions of paraphyly and polyphyly
    • Farris JS. Formal definitions of paraphyly and polyphyly. Syst Zool 1974; 23:548-554. http://dx.doi.org/10.2307/2412474
    • (1974) Syst Zool , vol.23 , pp. 548-554
    • Farris, J.S.1
  • 52
    • 0001802596 scopus 로고
    • Phylogenetic systematics
    • Hennig W. Phylogenetic systematics. Annu Rev Entomol 1965; 10:97-116. http://dx.doi.org/10.1146/annurev.en.10.010165.000525
    • (1965) Annu Rev Entomol , vol.10 , pp. 97-116
    • Hennig, W.1
  • 53
    • 0001138328 scopus 로고
    • A K-means clustering algorithm
    • Hartigan JA, Wong MA. A K-means clustering algorithm. Appl Stat 1979; 28:100-108. http://dx.doi.org/10.2307/2346830
    • (1979) Appl Stat , vol.28 , pp. 100-108
    • Hartigan, J.A.1    Wong, M.A.2


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