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Volumn 4, Issue 6, 2009, Pages

Gene order phylogeny and the evolution of methanogens

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEAL GENOME; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; EURYARCHAEOTA; GENE ORDER; GENE SEQUENCE; GENETIC LINKAGE; METHANOBACTERIALES; METHANOBACTERIUM THERMOAUTOTROPHICUM; METHANOCOCCALES; METHANOCOCCUS JANNASCHII; METHANOCOCCUS MARIPALUDIS; METHANOGEN; METHANOSARCINA; METHANOTHERMUS; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHYLOGENY; TAXONOMY; THERMOCOCCALES; ARCHAEAL GENE; BIODIVERSITY; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION;

EID: 67650699549     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0006069     Document Type: Article
Times cited : (32)

References (31)
  • 1
    • 41349083576 scopus 로고    scopus 로고
    • Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea
    • Liu Y, Whitman WB (2008) Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea. Ann N Y Acad Sci 1125: 171-189.
    • (2008) Ann N Y Acad Sci , vol.1125 , pp. 171-189
    • Liu, Y.1    Whitman, W.B.2
  • 3
    • 20144364162 scopus 로고    scopus 로고
    • Higher-level classification of the Archaea: Evolution of methanogenesis and methanogens
    • Bapteste E, Brochier C, Boucher Y (2005) Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1: 353-363.
    • (2005) Archaea , vol.1 , pp. 353-363
    • Bapteste, E.1    Brochier, C.2    Boucher, Y.3
  • 4
    • 34247236709 scopus 로고    scopus 로고
    • Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis
    • Gao B, Gupta R (2007) Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 8: 86.
    • (2007) BMC Genomics , vol.8 , pp. 86
    • Gao, B.1    Gupta, R.2
  • 5
    • 0026598577 scopus 로고
    • Chloroplast DNA Evidence on the Ancient Evolutionary Split in Vascular Land Plants
    • Raubeson LA, Jansen RK (1992) Chloroplast DNA Evidence on the Ancient Evolutionary Split in Vascular Land Plants. Science 255: 1697-1699.
    • (1992) Science , vol.255 , pp. 1697-1699
    • Raubeson, L.A.1    Jansen, R.K.2
  • 6
    • 0028005619 scopus 로고
    • Chloroplast DNA Systematics: A Review of Methods and Data Analysis
    • Olmstead RG, Palmer JD (1994) Chloroplast DNA Systematics: A Review of Methods and Data Analysis. Am J Bot 81: 1205-1224.
    • (1994) Am J Bot , vol.81 , pp. 1205-1224
    • Olmstead, R.G.1    Palmer, J.D.2
  • 7
    • 0032770572 scopus 로고    scopus 로고
    • Gene Order Breakpoint Evidence in Animal Mitochondrial Phylogeny
    • Blanchette M, Kunisawa T, Sankoff D (1999) Gene Order Breakpoint Evidence in Animal Mitochondrial Phylogeny. J Mol Evol 49: 193-203.
    • (1999) J Mol Evol , vol.49 , pp. 193-203
    • Blanchette, M.1    Kunisawa, T.2    Sankoff, D.3
  • 8
    • 19544374490 scopus 로고    scopus 로고
    • Genome Rearrangement Distances and Gene Order Phylogeny in {gamma}-Proteobacteria
    • Belda E, Moya A, Silva FJ (2005) Genome Rearrangement Distances and Gene Order Phylogeny in {gamma}-Proteobacteria. Mol Biol Evol 22: 1456-1467.
    • (2005) Mol Biol Evol , vol.22 , pp. 1456-1467
    • Belda, E.1    Moya, A.2    Silva, F.J.3
  • 10
    • 0002880994 scopus 로고
    • Chloroplast and mitochondrial genome evolution in land plants
    • Herrmann R, ed, New York: Springer Verlag. pp
    • Palmer JD (1992) Chloroplast and mitochondrial genome evolution in land plants. In: Herrmann R, ed. Cell Organelles. New York: Springer Verlag. pp 99-133.
    • (1992) Cell Organelles , pp. 99-133
    • Palmer, J.D.1
  • 11
    • 23844520968 scopus 로고    scopus 로고
    • Steps toward accurate reconstruction of phylogenies from gene-order data
    • Moret BME, Tang J, Wang LS, Warnow T (2002) Steps toward accurate reconstruction of phylogenies from gene-order data. J Comput Syst Sci 65: 508-525.
    • (2002) J Comput Syst Sci , vol.65 , pp. 508-525
    • Moret, B.M.E.1    Tang, J.2    Wang, L.S.3    Warnow, T.4
  • 13
    • 33847737366 scopus 로고    scopus 로고
    • Comparative genomics and the evolution of prokaryotes
    • Abby S, Daubin V (2007) Comparative genomics and the evolution of prokaryotes. Trends Microbiol 15: 135-141.
    • (2007) Trends Microbiol , vol.15 , pp. 135-141
    • Abby, S.1    Daubin, V.2
  • 14
    • 1342271382 scopus 로고    scopus 로고
    • From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the gamma proteobacteria
    • Lerat E, Daubin V, Moran NA (2003) From Gene Trees to Organismal Phylogeny in Prokaryotes:The Case of the gamma proteobacteria. PLoS Biol 1: e19.
    • (2003) PLoS Biol , vol.1
    • Lerat, E.1    Daubin, V.2    Moran, N.A.3
  • 15
    • 33644700003 scopus 로고    scopus 로고
    • Toward Automatic Reconstruction of a Highly Resolved Tree of Life
    • Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, et al. (2006) Toward Automatic Reconstruction of a Highly Resolved Tree of Life. Science 311: 1283-1287.
    • (2006) Science , vol.311 , pp. 1283-1287
    • Ciccarelli, F.D.1    Doerks, T.2    von Mering, C.3    Creevey, C.J.4    Snel, B.5
  • 18
    • 38349128272 scopus 로고    scopus 로고
    • Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny
    • Bapteste E, Susko E, Leigh J, Ruiz-Trillo I, Bucknam J, et al. (2008) Alternative Methods for Concatenation of Core Genes Indicate a Lack of Resolution in Deep Nodes of the Prokaryotic Phylogeny. Mol Biol Evol 25: 83-91.
    • (2008) Mol Biol Evol , vol.25 , pp. 83-91
    • Bapteste, E.1    Susko, E.2    Leigh, J.3    Ruiz-Trillo, I.4    Bucknam, J.5
  • 19
    • 57149085868 scopus 로고    scopus 로고
    • Genomics of bacteria and archaea: The emerging dynamic view of the prokaryotic world
    • Koonin EV, Wolf YI (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36: 6688-6719.
    • (2008) Nucleic Acids Res , vol.36 , pp. 6688-6719
    • Koonin, E.V.1    Wolf, Y.I.2
  • 20
    • 0034565944 scopus 로고    scopus 로고
    • The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome
    • Brochier C, Philippe H, Moreira D (2000) The evolutionary history of ribosomal protein RpS14: horizontal gene transfer at the heart of the ribosome. Trends Genet 16: 529-533.
    • (2000) Trends Genet , vol.16 , pp. 529-533
    • Brochier, C.1    Philippe, H.2    Moreira, D.3
  • 23
    • 57049148533 scopus 로고    scopus 로고
    • The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods
    • McCann A, Cotton J, McInerney J (2008) The tree of genomes: An empirical comparison of genome-phylogeny reconstruction methods. BMC Evol Biol 8: 312.
    • (2008) BMC Evol Biol , vol.8 , pp. 312
    • McCann, A.1    Cotton, J.2    McInerney, J.3
  • 24
    • 40549120596 scopus 로고    scopus 로고
    • The RAST Server: Rapid Annotations using Subsystems Technology
    • Aziz R, Bartels D, Best A, DeJongh M, Disz T, et al. (2008) The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75.
    • (2008) BMC Genomics , vol.9 , pp. 75
    • Aziz, R.1    Bartels, D.2    Best, A.3    DeJongh, M.4    Disz, T.5
  • 25
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5
  • 26
    • 67650669451 scopus 로고    scopus 로고
    • A Combinatorial Approach to Genome-Wide Ortholog Assignment: Beyond Sequence Similarity Search
    • London, Canada: Springer-Verlag
    • Jiang T (2007) A Combinatorial Approach to Genome-Wide Ortholog Assignment: Beyond Sequence Similarity Search. Proceedings of the 18th annual symposium on Combinatorial Pattern Matching. London, Canada: Springer-Verlag.
    • (2007) Proceedings of the 18th annual symposium on Combinatorial Pattern Matching
    • Jiang, T.1
  • 28
    • 0035229986 scopus 로고    scopus 로고
    • New approaches for reconstructing phylogenies from gene order data
    • Moret BME, Wang L-S, Warnow T, Wyman SK (2001) New approaches for reconstructing phylogenies from gene order data. Bioinformatics 17: S165-173.
    • (2001) Bioinformatics , vol.17
    • Moret, B.M.E.1    Wang, L.-S.2    Warnow, T.3    Wyman, S.K.4
  • 29
    • 0036943052 scopus 로고    scopus 로고
    • Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle
    • Desper R, Gascuel O (2002) Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle. J Bioinform Comput Biol 9: 687-705.
    • (2002) J Bioinform Comput Biol , vol.9 , pp. 687-705
    • Desper, R.1    Gascuel, O.2
  • 30
    • 34547781750 scopus 로고    scopus 로고
    • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24: 1596-1599
    • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol Biol Evol 24: 1596-1599.
  • 31
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package
    • Felsenstein J (1989) PHYLIP - Phylogeny Inference Package Cladistics 5: 164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.