메뉴 건너뛰기




Volumn 108, Issue 3, 2015, Pages 765-781

A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia

Author keywords

Character compatibility; Chlamydiae; Chlamydiales; Conserved signature indel; Conserved signature protein; Parachlamydiales; Phylogeny; Taxonomy

Indexed keywords

RIBOSOME RNA; BACTERIAL DNA; BACTERIAL PROTEIN; RIBOSOME DNA; RNA 16S;

EID: 84938745848     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-015-0532-1     Document Type: Article
Times cited : (21)

References (84)
  • 1
    • 26244439284 scopus 로고    scopus 로고
    • The chlamydial developmental cycle
    • COI: 1:CAS:528:DC%2BD2MXhtFSisLnK, PID: 16043254
    • Abdelrahman YM, Belland RJ (2005) The chlamydial developmental cycle. FEMS Microbiol Rev 29(5):949–959
    • (2005) FEMS Microbiol Rev , vol.29 , Issue.5 , pp. 949-959
    • Abdelrahman, Y.M.1    Belland, R.J.2
  • 2
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • COI: 1:CAS:528:DyaK2sXlvFyhu7w%3D, PID: 9254694
    • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schäffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 3
    • 74549118866 scopus 로고    scopus 로고
    • Large-scale parsimony analysis of metazoan indels in protein-coding genes
    • COI: 1:CAS:528:DC%2BC3cXntlGnuw%3D%3D, PID: 19864469
    • Belinky F, Cohen O, Huchon D (2010) Large-scale parsimony analysis of metazoan indels in protein-coding genes. Mol Biol Evol 27(2):441–451
    • (2010) Mol Biol Evol , vol.27 , Issue.2 , pp. 441-451
    • Belinky, F.1    Cohen, O.2    Huchon, D.3
  • 4
    • 84892815195 scopus 로고    scopus 로고
    • Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations
    • Bhandari V, Gupta RS (2014) Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations. Anton Leeuw Int J G 105(1):143–168
    • (2014) Anton Leeuw Int J G , vol.105 , Issue.1 , pp. 143-168
    • Bhandari, V.1    Gupta, R.S.2
  • 5
    • 0035153836 scopus 로고    scopus 로고
    • Molecular evolution of the Chlamydiaceae
    • COI: 1:CAS:528:DC%2BD3MXhtlaks7k%3D, PID: 11211261
    • Bush RM, Everett KD (2001) Molecular evolution of the Chlamydiaceae. Int J Syst Evol Microbiol 51(Pt 1):203–220
    • (2001) Int J Syst Evol Microbiol , vol.51 , pp. 203-220
    • Bush, R.M.1    Everett, K.D.2
  • 6
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • COI: 1:CAS:528:DC%2BD3cXisVSgt7g%3D, PID: 10742046
    • Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17(4):540–552
    • (2000) Mol Biol Evol , vol.17 , Issue.4 , pp. 540-552
    • Castresana, J.1
  • 9
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • COI: 1:CAS:528:DC%2BC3cXht1WhtbzM, PID: 20709691
    • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461
    • (2010) Bioinformatics , vol.26 , Issue.19 , pp. 2460-2461
    • Edgar, R.C.1
  • 10
    • 0032953638 scopus 로고    scopus 로고
    • Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms
    • COI: 1:CAS:528:DyaK1MXjt1CrurY%3D, PID: 10319462
    • Everett KD, Bush RM, Andersen AA (1999) Emended description of the order Chlamydiales, proposal of Parachlamydiaceae fam. nov. and Simkaniaceae fam. nov., each containing one monotypic genus, revised taxonomy of the family Chlamydiaceae, including a new genus and five new species, and standards for the identification of organisms. Int J Syst Bacteriol 49(Pt 2):415–440
    • (1999) Int J Syst Bacteriol , vol.49 , pp. 415-440
    • Everett, K.D.1    Bush, R.M.2    Andersen, A.A.3
  • 11
    • 22544445895 scopus 로고    scopus 로고
    • Novel chlamydiae in whiteflies and scale insects: endosymbionts ‘Candidatus Fritschea bemisiae’ strain Falk and ‘Candidatus Fritschea eriococci’ strain Elm
    • COI: 1:CAS:528:DC%2BD2MXovV2ntro%3D, PID: 16014485
    • Everett KD, Thao M, Horn M, Dyszynski GE, Baumann P (2005) Novel chlamydiae in whiteflies and scale insects: endosymbionts ‘Candidatus Fritschea bemisiae’ strain Falk and ‘Candidatus Fritschea eriococci’ strain Elm. Int J Syst Evol Microbiol 55(Pt 4):1581–1587
    • (2005) Int J Syst Evol Microbiol , vol.55 , pp. 1581-1587
    • Everett, K.D.1    Thao, M.2    Horn, M.3    Dyszynski, G.E.4    Baumann, P.5
  • 13
    • 84856228043 scopus 로고    scopus 로고
    • Microbial systematics in the post-genomics era
    • Gao B, Gupta RS (2012) Microbial systematics in the post-genomics era. Anton Leeuw Int J G 101(1):45–54
    • (2012) Anton Leeuw Int J G , vol.101 , Issue.1 , pp. 45-54
    • Gao, B.1    Gupta, R.S.2
  • 14
    • 0036898759 scopus 로고    scopus 로고
    • Prokaryotic evolution in light of gene transfer
    • COI: 1:CAS:528:DC%2BD38Xps12hsL4%3D, PID: 12446813
    • Gogarten JP, Doolittle WF, Lawrence JG (2002) Prokaryotic evolution in light of gene transfer. Mol Biol Evol 19(12):2226–2238
    • (2002) Mol Biol Evol , vol.19 , Issue.12 , pp. 2226-2238
    • Gogarten, J.P.1    Doolittle, W.F.2    Lawrence, J.G.3
  • 15
    • 78649269681 scopus 로고    scopus 로고
    • International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of the Chlamydiae: minutes of the closed meeting, 21 June 2010, Hof bei Salzburg, Austria
    • PID: 21048222
    • Greub G (2010a) International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of the Chlamydiae: minutes of the closed meeting, 21 June 2010, Hof bei Salzburg, Austria. Int J Syst Evol Microbiol 60(Pt 11):2694
    • (2010) Int J Syst Evol Microbiol , vol.60 , pp. 2694
    • Greub, G.1
  • 16
    • 78649256511 scopus 로고    scopus 로고
    • International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of the Chlamydiae: minutes of the inaugural closed meeting, 21 March 2009, Little Rock, AR, USA
    • PID: 21048221
    • Greub G (2010b) International Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of the Chlamydiae: minutes of the inaugural closed meeting, 21 March 2009, Little Rock, AR, USA. Int J Syst Evol Microbiol 60(Pt 11):2691–2693
    • (2010) Int J Syst Evol Microbiol , vol.60 , pp. 2691-2693
    • Greub, G.1
  • 17
    • 84975073196 scopus 로고    scopus 로고
    • International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Chlamydiae minutes of the closed meeting, 23 February 2011, Ascona, Switzerland
    • Greub G (2013) International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Chlamydiae minutes of the closed meeting, 23 February 2011, Ascona, Switzerland. Int J Syst Evol Microbiol 63(Pt 5):1934–1935
    • (2013) Int J Syst Evol Microbiol , vol.63 , pp. 1934-1935
    • Greub, G.1
  • 18
    • 34547910719 scopus 로고    scopus 로고
    • Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae
    • COI: 1:CAS:528:DC%2BD2sXpslOjtrk%3D, PID: 17660429
    • Griffiths E, Gupta RS (2007) Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae. Microbiology 153(8):2648–2654
    • (2007) Microbiology , vol.153 , Issue.8 , pp. 2648-2654
    • Griffiths, E.1    Gupta, R.S.2
  • 19
    • 23844479263 scopus 로고    scopus 로고
    • Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification
    • COI: 1:CAS:528:DC%2BD2MXpsFGns74%3D, PID: 16079343
    • Griffiths E, Petrich AK, Gupta RS (2005) Conserved indels in essential proteins that are distinctive characteristics of Chlamydiales and provide novel means for their identification. Microbiology 151(8):2647–2657
    • (2005) Microbiology , vol.151 , Issue.8 , pp. 2647-2657
    • Griffiths, E.1    Petrich, A.K.2    Gupta, R.S.3
  • 20
    • 33645017409 scopus 로고    scopus 로고
    • BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species
    • PID: 16436211
    • Griffiths E, Ventresca MS, Gupta RS (2006) BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species. BMC Genomics 7:14
    • (2006) BMC Genomics , vol.7 , pp. 14
    • Griffiths, E.1    Ventresca, M.S.2    Gupta, R.S.3
  • 21
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
    • COI: 1:CAS:528:DC%2BC3cXks1Kms7s%3D, PID: 20525638
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59(3):307–321
    • (2010) Syst Biol , vol.59 , Issue.3 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 22
    • 0031794743 scopus 로고    scopus 로고
    • Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes
    • COI: 1:CAS:528:DyaK1MXhs1OntQ%3D%3D, PID: 9841678
    • Gupta RS (1998) Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62(4):1435
    • (1998) Microbiol Mol Biol Rev , vol.62 , Issue.4 , pp. 1435
    • Gupta, R.S.1
  • 24
    • 0036597701 scopus 로고    scopus 로고
    • Critical issues in bacterial phylogeny
    • PID: 12167362
    • Gupta RS, Griffiths E (2002) Critical issues in bacterial phylogeny. Theor Popul Biol 61(4):423–434
    • (2002) Theor Popul Biol , vol.61 , Issue.4 , pp. 423-434
    • Gupta, R.S.1    Griffiths, E.2
  • 25
    • 33750982681 scopus 로고    scopus 로고
    • Chlamydiae-specific proteins and indels: novel tools for studies
    • COI: 1:CAS:528:DC%2BD28Xht1CmtrjK, PID: 17049238
    • Gupta RS, Griffiths E (2006) Chlamydiae-specific proteins and indels: novel tools for studies. Trends Microbiol 14(12):527–535
    • (2006) Trends Microbiol , vol.14 , Issue.12 , pp. 527-535
    • Gupta, R.S.1    Griffiths, E.2
  • 26
    • 39049145171 scopus 로고    scopus 로고
    • Phylogenomics and signature proteins for the Alphaproteobacteria and its main groups
    • PID: 18045498
    • Gupta RS, Mok A (2007) Phylogenomics and signature proteins for the Alphaproteobacteria and its main groups. BMC Microbiol 7(1):106
    • (2007) BMC Microbiol , vol.7 , Issue.1 , pp. 106
    • Gupta, R.S.1    Mok, A.2
  • 27
    • 33845871454 scopus 로고    scopus 로고
    • Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions
    • COI: 1:CAS:528:DC%2BD28XhtlCksbbF, PID: 17160641
    • Gupta RS, Sneath PH (2007) Application of the character compatibility approach to generalized molecular sequence data: branching order of the proteobacterial subdivisions. J Mol Evol 64(1):90–100
    • (2007) J Mol Evol , vol.64 , Issue.1 , pp. 90-100
    • Gupta, R.S.1    Sneath, P.H.2
  • 28
    • 84875834208 scopus 로고    scopus 로고
    • Molecular signatures for the PVC clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of bacteria provide insights into their evolutionary relationships
    • PID: 23060863
    • Gupta RS, Bhandari V, Naushad HS (2012) Molecular signatures for the PVC clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of bacteria provide insights into their evolutionary relationships. Front Microbiol 3:327
    • (2012) Front Microbiol , vol.3 , pp. 327
    • Gupta, R.S.1    Bhandari, V.2    Naushad, H.S.3
  • 29
    • 84925321451 scopus 로고    scopus 로고
    • Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov
    • PID: 25428416
    • Gupta RS, Naushad S, Baker S (2014) Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov. Int J Syst Evol Microbiol 65:1050–1069
    • (2014) Int J Syst Evol Microbiol , vol.65 , pp. 1050-1069
    • Gupta, R.S.1    Naushad, S.2    Baker, S.3
  • 30
    • 0038875361 scopus 로고    scopus 로고
    • Finding a maximum compatible tree is NP-hard for sequences and trees
    • Hamel AM, Steel M (1996) Finding a maximum compatible tree is NP-hard for sequences and trees. Appl Math Lett 9(2):55–59
    • (1996) Appl Math Lett , vol.9 , Issue.2 , pp. 55-59
    • Hamel, A.M.1    Steel, M.2
  • 31
    • 77953756375 scopus 로고    scopus 로고
    • Identifying cliques of convergent characters: concerted evolution in the cormorants and shags
    • PID: 20547779
    • Holland BR, Spencer HG, Worthy TH, Kennedy M (2010) Identifying cliques of convergent characters: concerted evolution in the cormorants and shags. Syst Biol 59(4):433–445
    • (2010) Syst Biol , vol.59 , Issue.4 , pp. 433-445
    • Holland, B.R.1    Spencer, H.G.2    Worthy, T.H.3    Kennedy, M.4
  • 32
    • 53849114721 scopus 로고    scopus 로고
    • Chlamydiae as symbionts in eukaryotes
    • COI: 1:CAS:528:DC%2BD1cXht1Gls7zP, PID: 18473699
    • Horn M (2008) Chlamydiae as symbionts in eukaryotes. Annu Rev Microbiol 62:113–131
    • (2008) Annu Rev Microbiol , vol.62 , pp. 113-131
    • Horn, M.1
  • 33
    • 84930242763 scopus 로고    scopus 로고
    • Class I. Chlamydiia class. nov
    • Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W, (eds), 4, Springer, New York
    • Horn M (2011a) Class I. Chlamydiia class. nov. In: Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W (eds) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Springer, New York, p 844
    • (2011) Bergey’s manual of systematic bacteriology , pp. 844
    • Horn, M.1
  • 34
    • 84938744707 scopus 로고    scopus 로고
    • Family II. “Candidatus Clavichlamydiaceae
    • Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W, (eds), 4, Springer, New York
    • Horn M (2011b) Family II. “Candidatus Clavichlamydiaceae”. In: Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W (eds) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Springer, New York, p 865
    • (2011) Bergey’s manual of systematic bacteriology , pp. 865
    • Horn, M.1
  • 35
    • 84938762222 scopus 로고    scopus 로고
    • Family V. “Candidatus Piscichlamydiaceae
    • Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W, (eds), 4, Springer, New York
    • Horn M (2011c) Family V. “Candidatus Piscichlamydiaceae”. In: Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W (eds) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Springer, New York, p 872
    • (2011) Bergey’s manual of systematic bacteriology , pp. 872
    • Horn, M.1
  • 36
    • 84938751284 scopus 로고    scopus 로고
    • Family VI. Rhabdochlamydiaceae fam. nov
    • Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W, (eds), 4, Springer, New York
    • Horn M (2011d) Family VI. Rhabdochlamydiaceae fam. nov. In: Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W (eds) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Springer, New York, p 873
    • (2011) Bergey’s manual of systematic bacteriology , pp. 873
    • Horn, M.1
  • 37
    • 84859701867 scopus 로고    scopus 로고
    • Phylum XXIV. Chlamydiae Garrity and Holt 2001
    • Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W, (eds), 4, Springer, New York
    • Horn M (2011e) Phylum XXIV. Chlamydiae Garrity and Holt 2001. In: Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W (eds) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Springer, New York, pp 843–844
    • (2011) Bergey’s manual of systematic bacteriology , pp. 843-844
    • Horn, M.1
  • 38
    • 0035899885 scopus 로고    scopus 로고
    • Evidence for additional genus-level diversity of Chlamydiales in the environment
    • COI: 1:CAS:528:DC%2BD3MXnslCitrc%3D, PID: 11682181
    • Horn M, Wagner M (2001) Evidence for additional genus-level diversity of Chlamydiales in the environment. FEMS Microbiol Lett 204(1):71–74
    • (2001) FEMS Microbiol Lett , vol.204 , Issue.1 , pp. 71-74
    • Horn, M.1    Wagner, M.2
  • 40
    • 84926099013 scopus 로고    scopus 로고
    • Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives
    • COI: 1:CAS:528:DC%2BC2cXpvVSmurc%3D, PID: 24917519
    • Howard-Azzeh M, Shamseer L, Schellhorn HE, Gupta RS (2014) Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives. Photosynth Res 122(2):171–185
    • (2014) Photosynth Res , vol.122 , Issue.2 , pp. 171-185
    • Howard-Azzeh, M.1    Shamseer, L.2    Schellhorn, H.E.3    Gupta, R.S.4
  • 41
    • 84928215881 scopus 로고    scopus 로고
    • The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly
    • PID: 25670734
    • Jacquier N, Viollier PH, Greub G (2015) The role of peptidoglycan in chlamydial cell division: towards resolving the chlamydial anomaly. FEMS Microbiol Rev 39(2):262–275
    • (2015) FEMS Microbiol Rev , vol.39 , Issue.2 , pp. 262-275
    • Jacquier, N.1    Viollier, P.H.2    Greub, G.3
  • 43
    • 84863859939 scopus 로고    scopus 로고
    • The future of taxonomy
    • Gadd GM, Sariaslani S, (eds), 80, Academic Press Inc, San Diego
    • Jones AL (2012) The future of taxonomy. In: Gadd GM, Sariaslani S (eds) Adv Appl Microbiol, vol 80, 1st edn. Academic Press Inc, San Diego, pp 23–35
    • (2012) Adv Appl Microbiol , pp. 23-35
    • Jones, A.L.1
  • 44
    • 0038462736 scopus 로고    scopus 로고
    • Studies on lymphogranuloma venereum. III. The action of the sulfonamides on the agent of lymphogranuloma venereum
    • Jones H, Rake G, Stearns B (1945) Studies on lymphogranuloma venereum. III. The action of the sulfonamides on the agent of lymphogranuloma venereum. J Infect Dis 76:55–69
    • (1999) J Infect Dis , vol.76 , pp. 55-69
    • Jones, H.1    Rake, G.2    Stearns, B.3
  • 46
    • 84876518996 scopus 로고    scopus 로고
    • Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle
    • PID: 23221607
    • Kamneva OK, Knight SJ, Liberles DA, Ward NL (2012) Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol Evol 4(12):1375–1390
    • (2012) Genome Biol Evol , vol.4 , Issue.12 , pp. 1375-1390
    • Kamneva, O.K.1    Knight, S.J.2    Liberles, D.A.3    Ward, N.L.4
  • 47
    • 84893511241 scopus 로고    scopus 로고
    • Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes
    • COI: 1:CAS:528:DC%2BC2cXhtlClsr7I, PID: 24505072
    • Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64(Pt 2):346–351
    • (2014) Int J Syst Evol Microbiol , vol.64 , pp. 346-351
    • Kim, M.1    Oh, H.S.2    Park, S.C.3    Chun, J.4
  • 48
    • 24944587193 scopus 로고    scopus 로고
    • Towards a genome-based taxonomy for prokaryotes
    • COI: 1:CAS:528:DC%2BD2MXhtVWkt77I, PID: 16159757
    • Konstantinidis KT, Tiedje JM (2005) Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187(18):6258–6264
    • (2005) J Bacteriol , vol.187 , Issue.18 , pp. 6258-6264
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 49
    • 84938745776 scopus 로고    scopus 로고
    • AL
    • Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W, (eds), 4, Springer, New York
    • AL. In: Krieg N, Staley J, Brown D, Hedlund B, Paster B, Ward N, Ludwig W, Whitman W (eds) Bergey’s manual of systematic bacteriology, vol 4, 2nd edn. Springer, New York, pp 844–845
    • (2011) Bergey’s manual of systematic bacteriology , pp. 844-845
    • Kuo, C.-C.1    Horn, M.2    Stephens, R.S.3
  • 50
    • 84891160133 scopus 로고    scopus 로고
    • Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae
    • COI: 1:CAS:528:DC%2BC3sXhvFOmsLvN, PID: 23949660
    • Lagkouvardos I, Weinmaier T, Lauro FM, Cavicchioli R, Rattei T, Horn M (2014) Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae. ISME J 8(1):115–125
    • (2014) ISME J , vol.8 , Issue.1 , pp. 115-125
    • Lagkouvardos, I.1    Weinmaier, T.2    Lauro, F.M.3    Cavicchioli, R.4    Rattei, T.5    Horn, M.6
  • 51
    • 84891776336 scopus 로고    scopus 로고
    • POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes
    • COI: 1:CAS:528:DC%2BC2cXoslag, PID: 24198250
    • Lan Y, Morrison JC, Hershberg R, Rosen GL (2014) POGO-DB—a database of pairwise-comparisons of genomes and conserved orthologous genes. Nucleic Acids Res 42(Database issue):D625–D632
    • (2014) Nucleic Acids Res , vol.42 , Issue.Database issue , pp. 625-632
    • Lan, Y.1    Morrison, J.C.2    Hershberg, R.3    Rosen, G.L.4
  • 52
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • COI: 1:CAS:528:DC%2BD1cXotlKgsbg%3D, PID: 18367465
    • Le SQ, Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25(7):1307–1320
    • (2008) Mol Biol Evol , vol.25 , Issue.7 , pp. 1307-1320
    • Le, S.Q.1    Gascuel, O.2
  • 53
    • 84930257326 scopus 로고    scopus 로고
    • The phylum Chlamydiae
    • Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F, (eds), Springer, Berlin
    • Lory S (2014) The phylum Chlamydiae. In: Rosenberg E, DeLong E, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin, pp 497–499
    • (2014) The prokaryotes , pp. 497-499
    • Lory, S.1
  • 54
    • 84873193284 scopus 로고    scopus 로고
    • Incorporating indels as phylogenetic characters: impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)
    • PID: 23147269
    • Luan PT, Ryder OA, Davis H, Zhang YP, Yu L (2013) Incorporating indels as phylogenetic characters: impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora). Mol Phylogenet Evol 66(3):748–756
    • (2013) Mol Phylogenet Evol , vol.66 , Issue.3 , pp. 748-756
    • Luan, P.T.1    Ryder, O.A.2    Davis, H.3    Zhang, Y.P.4    Yu, L.5
  • 56
    • 84893518970 scopus 로고    scopus 로고
    • Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria
    • COI: 1:CAS:528:DC%2BC2cXhtlClsr7L, PID: 24505075
    • Naushad HS, Lee B, Gupta RS (2014) Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria. Int J Syst Evol Microbiol 64(2):366–383
    • (2014) Int J Syst Evol Microbiol , vol.64 , Issue.2 , pp. 366-383
    • Naushad, H.S.1    Lee, B.2    Gupta, R.S.3
  • 57
    • 84925461513 scopus 로고    scopus 로고
    • A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives
    • PID: 25481407
    • Naushad S, Adeolu M, Wong S, Sohail M, Schellhorn HE, Gupta RS (2015) A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives. Antonie Van Leeuwenhoek 107(2):467–485
    • (2015) Antonie Van Leeuwenhoek , vol.107 , Issue.2 , pp. 467-485
    • Naushad, S.1    Adeolu, M.2    Wong, S.3    Sohail, M.4    Schellhorn, H.E.5    Gupta, R.S.6
  • 58
    • 84938762223 scopus 로고    scopus 로고
    • NCBI (2015) NCBI genome database
    • NCBI (2015) NCBI genome database. http://www.ncbi.nlm.nih.gov/genome/
  • 59
    • 40949104851 scopus 로고    scopus 로고
    • Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis
    • PID: 18307777
    • Pannekoek Y, Morelli G, Kusecek B, Morre SA, Ossewaarde JM, Langerak AA, van der Ende A (2008) Multi locus sequence typing of Chlamydiales: clonal groupings within the obligate intracellular bacteria Chlamydia trachomatis. BMC Microbiol 8:42
    • (2008) BMC Microbiol , vol.8 , pp. 42
    • Pannekoek, Y.1    Morelli, G.2    Kusecek, B.3    Morre, S.A.4    Ossewaarde, J.M.5    Langerak, A.A.6    van der Ende, A.7
  • 60
    • 84891817929 scopus 로고    scopus 로고
    • LPSN—list of prokaryotic names with standing in nomenclature
    • PID: 24243842
    • Parte AC (2013) LPSN—list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 42:D613–D616
    • (2013) Nucleic Acids Res , vol.42 , pp. 613-616
    • Parte, A.C.1
  • 62
    • 12444313041 scopus 로고    scopus 로고
    • Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda
    • PID: 15764565
    • Pisani D (2004) Identifying and removing fast-evolving sites using compatibility analysis: an example from the Arthropoda. Syst Biol 53(6):978–989
    • (2004) Syst Biol , vol.53 , Issue.6 , pp. 978-989
    • Pisani, D.1
  • 63
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2—approximately maximum-likelihood trees for large alignments
    • PID: 20224823
    • Price MN, Dehal PS, Arkin AP (2010) FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS One 5(3):e9490
    • (2010) PLoS One , vol.5 , Issue.3 , pp. 9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 65
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • PID: 11050348
    • Rokas A, Holland PWH (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15(11):454–459
    • (2000) Trends Ecol Evol , vol.15 , Issue.11 , pp. 454-459
    • Rokas, A.1    Holland, P.W.H.2
  • 66
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • COI: 1:CAS:528:DC%2BD3sXotlWqsbc%3D, PID: 14574403
    • Rokas A, Williams BL, King N, Carroll SB (2003) Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425(6960):798–804
    • (2003) Nature , vol.425 , Issue.6960 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 67
    • 0032901106 scopus 로고    scopus 로고
    • Analysis of the 16S rRNA gene of micro-organism WSU 86-1044 from an aborted bovine foetus reveals that it is a member of the order Chlamydiales: proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov
    • COI: 1:CAS:528:DyaK1MXjt1Cru7s%3D, PID: 10319478
    • Rurangirwa FR, Dilbeck PM, Crawford TB, McGuire TC, McElwain TF (1999) Analysis of the 16S rRNA gene of micro-organism WSU 86-1044 from an aborted bovine foetus reveals that it is a member of the order Chlamydiales: proposal of Waddliaceae fam. nov., Waddlia chondrophila gen. nov., sp. nov. Int J Syst Bacteriol 49(Pt 2):577–581
    • (1999) Int J Syst Bacteriol , vol.49 , pp. 577-581
    • Rurangirwa, F.R.1    Dilbeck, P.M.2    Crawford, T.B.3    McGuire, T.C.4    McElwain, T.F.5
  • 68
    • 84977771284 scopus 로고    scopus 로고
    • Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species
    • PID: 25618261
    • Sachse K, Bavoil PM, Kaltenboeck B, Stephens RS, Kuo CC, Rossello-Mora R, Horn M (2015) Emendation of the family Chlamydiaceae: proposal of a single genus, Chlamydia, to include all currently recognized species. Syst Appl Microbiol 38(2):99–103
    • (2015) Syst Appl Microbiol , vol.38 , Issue.2 , pp. 99-103
    • Sachse, K.1    Bavoil, P.M.2    Kaltenboeck, B.3    Stephens, R.S.4    Kuo, C.C.5    Rossello-Mora, R.6    Horn, M.7
  • 69
    • 84917677922 scopus 로고    scopus 로고
    • Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species
    • PID: 25566316
    • Sawana A, Adeolu M, Gupta RS (2014) Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 5:429
    • (2014) Front Genet , vol.5 , pp. 429
    • Sawana, A.1    Adeolu, M.2    Gupta, R.S.3
  • 72
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
    • COI: 1:CAS:528:DC%2BC2cXmvFCjsbc%3D, PID: 24451623
    • Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313
    • (2014) Bioinformatics , vol.30 , Issue.9 , pp. 1312-1313
    • Stamatakis, A.1
  • 73
    • 60049087090 scopus 로고    scopus 로고
    • Divergence without difference: phylogenetics and taxonomy of Chlamydia resolved
    • COI: 1:CAS:528:DC%2BD1MXislartr4%3D, PID: 19281563
    • Stephens RS, Myers G, Eppinger M, Bavoil PM (2009) Divergence without difference: phylogenetics and taxonomy of Chlamydia resolved. FEMS Immunol Med Microbiol 55(2):115–119
    • (2009) FEMS Immunol Med Microbiol , vol.55 , Issue.2 , pp. 115-119
    • Stephens, R.S.1    Myers, G.2    Eppinger, M.3    Bavoil, P.M.4
  • 74
    • 0038462742 scopus 로고
    • Taxonomy of the Chlamydiae: reasons for Classifying Organisms of the Genus Chlamydia, Family Chlamydiaceae, in a Separate Order, Chlamydiales ord. nov
    • Storz J, Page LA (1971) Taxonomy of the Chlamydiae: reasons for Classifying Organisms of the Genus Chlamydia, Family Chlamydiaceae, in a Separate Order, Chlamydiales ord. nov. Int J Syst Bacteriol 21(4):332–334
    • (1971) Int J Syst Bacteriol , vol.21 , Issue.4 , pp. 332-334
    • Storz, J.1    Page, L.A.2
  • 75
    • 84874704727 scopus 로고    scopus 로고
    • Molecular characterization of “Candidatus Parilichlamydia carangidicola”, a novel Chlamydia-like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, “Candidatus Parilichlamydiaceae” fam. nov. (order Chlamydiales)
    • COI: 1:CAS:528:DC%2BC3sXkvVGksL0%3D, PID: 23275507
    • Stride M, Polkinghorne A, Miller T, Groff J, LaPatra S, Nowak B (2013) Molecular characterization of “Candidatus Parilichlamydia carangidicola”, a novel Chlamydia-like epitheliocystis agent in yellowtail kingfish, Seriola lalandi (Valenciennes), and the proposal of a new family, “Candidatus Parilichlamydiaceae” fam. nov. (order Chlamydiales). Appl Environ Microbiol 79(5):1590–1597
    • (2013) Appl Environ Microbiol , vol.79 , Issue.5 , pp. 1590-1597
    • Stride, M.1    Polkinghorne, A.2    Miller, T.3    Groff, J.4    LaPatra, S.5    Nowak, B.6
  • 76
    • 34547489084 scopus 로고    scopus 로고
    • Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments
    • COI: 1:CAS:528:DC%2BD2sXhtFKrs7%2FP, PID: 17654362
    • Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56(4):564–577
    • (2007) Syst Biol , vol.56 , Issue.4 , pp. 564-577
    • Talavera, G.1    Castresana, J.2
  • 77
    • 84890330527 scopus 로고    scopus 로고
    • MEGA6: molecular evolutionary genetics analysis version 6.0
    • COI: 1:CAS:528:DC%2BC3sXhvVKhurzP, PID: 24132122
    • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729
    • (2013) Mol Biol Evol , vol.30 , Issue.12 , pp. 2725-2729
    • Tamura, K.1    Stecher, G.2    Peterson, D.3    Filipski, A.4    Kumar, S.5
  • 78
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • Miura RM, (ed), American Mathematical Society, Providence
    • Tavaré S (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura RM (ed) Lectures on mathematics in the life sciences, 17th edn. American Mathematical Society, Providence, pp 57–86
    • (1986) Lectures on mathematics in the life sciences , pp. 57-86
    • Tavaré, S.1
  • 79
    • 33750918484 scopus 로고    scopus 로고
    • Criblamydia sequanensis, a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture
    • COI: 1:CAS:528:DC%2BD2sXisl2htA%3D%3D, PID: 17107554
    • Thomas V, Casson N, Greub G (2006) Criblamydia sequanensis, a new intracellular Chlamydiales isolated from Seine river water using amoebal co-culture. Environ Microbiol 8(12):2125–2135
    • (2006) Environ Microbiol , vol.8 , Issue.12 , pp. 2125-2135
    • Thomas, V.1    Casson, N.2    Greub, G.3
  • 80
    • 33744927902 scopus 로고    scopus 로고
    • The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance
    • COI: 1:CAS:528:DC%2BD28Xls1aktrc%3D, PID: 16704931
    • Wagner M, Horn M (2006) The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. Curr Opin Biotechnol 17(3):241–249
    • (2006) Curr Opin Biotechnol , vol.17 , Issue.3 , pp. 241-249
    • Wagner, M.1    Horn, M.2
  • 81
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • COI: 1:CAS:528:DC%2BD3MXjtFyktr4%3D, PID: 11319253
    • Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18(5):691–699
    • (2001) Mol Biol Evol , vol.18 , Issue.5 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 84
    • 48549092314 scopus 로고    scopus 로고
    • Inference of phylogenetic relationships among key angiosperm lineages using a compatibility method on a molecular data set
    • Yin-Long Q, Estabrook GF (2008) Inference of phylogenetic relationships among key angiosperm lineages using a compatibility method on a molecular data set. J Syst Evol 46(2):130–141
    • (2008) J Syst Evol , vol.46 , Issue.2 , pp. 130-141
    • Yin-Long, Q.1    Estabrook, G.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.