메뉴 건너뛰기




Volumn 5, Issue , 2015, Pages

An integrated phylogenomic approach toward pinpointing the origin of mitochondria

Author keywords

[No Author keywords available]

Indexed keywords

ALPHAPROTEOBACTERIA; GENETICS; GENOMICS; MITOCHONDRION; MOLECULAR EVOLUTION; PHYLOGENY; RICKETTSIACEAE; SYMBIOSIS;

EID: 84939803790     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep07949     Document Type: Article
Times cited : (117)

References (76)
  • 1
    • 0033166097 scopus 로고    scopus 로고
    • A comparative genomics approach to the evolution of eukaryotes and their mitochondria
    • Lang, B. F., Seif, E., Gray, M. W., O'Kelly, C. J., Burger, G. A comparative genomics approach to the evolution of eukaryotes and their mitochondria. J. Eukaryot. Microbiol. 46, 320-326 (1999).
    • (1999) J. Eukaryot. Microbiol. , vol.46 , pp. 320-326
    • Lang, B.F.1    Seif, E.2    Gray, M.W.3    O'Kelly, C.J.4    Burger, G.5
  • 2
    • 0034443285 scopus 로고    scopus 로고
    • Origin and evolution of the mitochondrial proteome
    • Kurland, C. G., Andersson, S. G. Origin and evolution of the mitochondrial proteome. Microbiol. Mol. Biol. Rev. 64, 786-820 (2000).
    • (2000) Microbiol. Mol. Biol. Rev. , vol.64 , pp. 786-820
    • Kurland, C.G.1    Andersson, S.G.2
  • 3
    • 0042266921 scopus 로고    scopus 로고
    • Reconstruction of the proto-mitochondrial metabolism
    • Gabaldon, T., Huynen, M. A. Reconstruction of the proto-mitochondrial metabolism. Science 301, 609 (2003).
    • (2003) Science , vol.301 , pp. 609
    • Gabaldon, T.1    Huynen, M.A.2
  • 4
    • 0033525788 scopus 로고    scopus 로고
    • Mitochondrial evolution
    • Gray, M. W., Burger, G., Lang, B. F. Mitochondrial evolution. Science 283, 1476-1481 (1999).
    • (1999) Science , vol.283 , pp. 1476-1481
    • Gray, M.W.1    Burger, G.2    Lang, B.F.3
  • 5
    • 0034913239 scopus 로고    scopus 로고
    • The origin and early evolution of mitochondria
    • REVIEWS1018
    • Gray, M. W., Burger, G., Lang, B. F. The origin and early evolution of mitochondria. Genome Biol. 2, REVIEWS1018 (2001).
    • (2001) Genome Biol , vol.2
    • Gray, M.W.1    Burger, G.2    Lang, B.F.3
  • 6
    • 2642689666 scopus 로고    scopus 로고
    • The hydrogen hypothesis for the first eukaryote
    • Martin, W.,Muller, M. The hydrogen hypothesis for the first eukaryote. Nature 392, 37-41 (1998).
    • (1998) Nature , vol.392 , pp. 37-41
    • Martin, W.1    Muller, M.2
  • 7
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410 (1978).
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 9
    • 0033004743 scopus 로고    scopus 로고
    • Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions
    • Foster, P. G., Hickey, D. A. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J. Mol. Evol. 48, 284-290 (1999).
    • (1999) J. Mol. Evol. , vol.48 , pp. 284-290
    • Foster, P.G.1    Hickey, D.A.2
  • 10
    • 0025952777 scopus 로고
    • Archaeal phylogeny: Reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts
    • Woese, C. R., Achenbach, L., Rouviere, P., Mandelco, L. Archaeal phylogeny: reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst. Appl. Microbiol. 14, 364-371 (1991).
    • (1991) Syst. Appl. Microbiol. , vol.14 , pp. 364-371
    • Woese, C.R.1    Achenbach, L.2    Rouviere, P.3    Mandelco, L.4
  • 11
    • 0027463557 scopus 로고
    • Ribosomal RNA trees misleading
    • Hasegawa, M.,Hashimoto, T. Ribosomal RNA trees misleading Nature 361, 23 (1993).
    • (1993) Nature , vol.361 , pp. 23
    • Hasegawa, M.1    Hashimoto, T.2
  • 12
    • 0028323420 scopus 로고
    • The chaperone connection to the origins of the eukaryotic organelles
    • Viale, A. M., Arakaki, A. K. The chaperone connection to the origins of the eukaryotic organelles. FEBS Lett. 341, 146-151 (1994).
    • (1994) FEBS Lett , vol.341 , pp. 146-151
    • Viale, A.M.1    Arakaki, A.K.2
  • 13
    • 0028960169 scopus 로고
    • Evolution of the chaperonin families (Hsp60, Hsp10 and TCP-1) of proteins and the origin of eukaryotic cells
    • Gupta, R. S. Evolution of the chaperonin families (Hsp60, Hsp10 and Tcp-1) of proteins and the origin of eukaryotic cells. Mol. Microbiol. 15, 1-11 (1995).
    • (1995) Mol. Microbiol. , vol.15 , pp. 1-11
    • Gupta, R.S.1
  • 14
    • 0034633691 scopus 로고    scopus 로고
    • Heat shock protein 60 sequence comparisons: Duplications, lateral transfer, and mitochondrial evolution
    • Karlin, S., Brocchieri, L. Heat shock protein 60 sequence comparisons: duplications, lateral transfer, and mitochondrial evolution. Proc. Natl. Acad. Sci. U. S. A. 97, 11348-11353 (2000).
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 11348-11353
    • Karlin, S.1    Brocchieri, L.2
  • 15
    • 0037733985 scopus 로고    scopus 로고
    • Mitochondrial connection to the origin of the eukaryotic cell
    • Emelyanov, V. V. Mitochondrial connection to the origin of the eukaryotic cell. Eur. J. Biochem. 270, 1599-1618 (2003).
    • (2003) Eur. J. Biochem. , vol.270 , pp. 1599-1618
    • Emelyanov, V.V.1
  • 16
    • 19344378727 scopus 로고    scopus 로고
    • Phylogenomics of the reproductive parasite wolbachia pipientis wmel: Astreamlined genomeoverrun by mobile genetic elements
    • Wu, M. et al. Phylogenomics of the Reproductive Parasite Wolbachia pipientis wMel: AStreamlined GenomeOverrun by Mobile Genetic Elements. PLoS Biol. 2, E69 (2004).
    • (2004) PLoS Biol , vol.2 , pp. E69
    • Wu, M.1
  • 17
    • 4143093598 scopus 로고    scopus 로고
    • A genome phylogeny for mitochondria among alphaproteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes
    • Esser, C. et al. A genome phylogeny for mitochondria among alphaproteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol. Biol. Evol. 21, 1643-1660 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1643-1660
    • Esser, C.1
  • 18
    • 28944434614 scopus 로고    scopus 로고
    • Genome phylogenies indicate a meaningful alphaproteobacterial phylogeny and support a grouping of the mitochondria with the rickettsiales
    • Fitzpatrick, D. A., Creevey, C. J.,McInerney, J. O. Genome Phylogenies Indicate a Meaningful Alphaproteobacterial Phylogeny and Support a Grouping of the Mitochondria with the Rickettsiales. Mol. Biol. Evol. 23, 74-85 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 74-85
    • Fitzpatrick, D.A.1    Creevey, C.J.2    McInerney, J.O.3
  • 19
    • 34347390665 scopus 로고    scopus 로고
    • A robust species tree for the alphaproteobacteria
    • Williams, K. P., Sobral, B. W., Dickerman, A. W. A robust species tree for the alphaproteobacteria. J. Bacteriol. 189, 4578-4586, doi:10.1128/JB.00269-07 (2007).
    • (2007) J. Bacteriol. , vol.189 , pp. 4578-4586
    • Williams, K.P.1    Sobral, B.W.2    Dickerman, A.W.3
  • 20
    • 80053022270 scopus 로고    scopus 로고
    • Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales Pelagibacter ubique and Reclimonas americana mitochondrion
    • Georgiades, K., Madoui, M. A., Le, P., Robert, C., Raoult, D. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion. PLoS ONE 6, e24857, doi:10.1371/journal.pone.0024857 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e24857
    • Georgiades, K.1    Madoui Le A M, P.2    Robert, C.3    Raoult, D.4
  • 21
    • 84856080520 scopus 로고    scopus 로고
    • The SAR11 group of alphaproteobacteria is not related to the origin of mitochondria
    • Rodriguez-Ezpeleta, N., Embley, T. M. The SAR11 group of alphaproteobacteria is not related to the origin of mitochondria. PLoS ONE 7, e30520, doi:10.1371/journal.pone.0030520 (2012).
    • (2012) PLoS ONE , vol.7 , pp. e30520
    • Rodriguez-Ezpeleta, N.1    Embley, T.M.2
  • 22
    • 80051986176 scopus 로고    scopus 로고
    • Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade
    • Thrash, J. C. et al. Phylogenomic evidence for a common ancestor of mitochondria and the SAR11 clade. Sci Rep 1, 13, doi:10.1038/srep00013 (2011).
    • (2011) Sci Rep , vol.1 , pp. 13
    • Thrash, J.C.1
  • 23
    • 80052846879 scopus 로고    scopus 로고
    • A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade
    • Brindefalk, B., Ettema, T. J., Viklund, J., Thollesson, M., Andersson, S. G. A phylometagenomic exploration of oceanic alphaproteobacteria reveals mitochondrial relatives unrelated to the SAR11 clade. PLoS ONE 6, e24457, doi:10.1371/journal.pone.0024457 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e24457
    • Brindefalk, B.1    Ettema, T.J.2    Viklund, J.3    Thollesson, M.4    Andersson, S.G.5
  • 24
    • 84855864414 scopus 로고    scopus 로고
    • Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade
    • Viklund, J., Ettema, T. J., Andersson, S. G. Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol. Biol. Evol. 29, 599-615, doi:10.1093/molbev/msr203 (2012).
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 599-615
    • Viklund, J.1    Ettema, T.J.2    Andersson, S.G.3
  • 26
    • 10644253746 scopus 로고    scopus 로고
    • Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots
    • Stefanovic, S., Rice, D. W., Palmer, J. D. Long branch attraction, taxon sampling, and the earliest angiosperms: Amborella or monocots BMC Evol. Biol. 4, 35 (2004).
    • (2004) BMC Evol Biol , vol.4 , pp. 35
    • Stefanovic, S.1    Rice, D.W.2    Palmer, J.D.3
  • 27
    • 3042550872 scopus 로고    scopus 로고
    • Genome-scale phylogeny and the detection of systematic biases
    • Phillips, M. J., Delsuc, F., Penny, D. Genome-scale phylogeny and the detection of systematic biases. Mol. Biol. Evol. 21, 1455-1458 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1455-1458
    • Phillips, M.J.1    Delsuc, F.2    Penny, D.3
  • 28
    • 17744394753 scopus 로고    scopus 로고
    • Phylogenomics and the reconstruction of the tree of life
    • Delsuc, F., Brinkmann, H., Philippe, H. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6, 361-375 (2005).
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 361-375
    • Delsuc, F.1    Brinkmann, H.2    Philippe, H.3
  • 29
    • 4644350604 scopus 로고    scopus 로고
    • Genome-scale data angiosperm relationships and "ending incongruence": A cautionary tale in phylogenetics
    • Soltis, D. E. et al. Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. Trends Plant Sci. 9, 477-483 (2004).
    • (2004) Trends Plant Sci , vol.9 , pp. 477-483
    • Soltis, D.E.1
  • 30
    • 18144425198 scopus 로고    scopus 로고
    • The place of Amborella within the radiation of angiosperms
    • Lockhart, P. J., Penny, D. The place of Amborella within the radiation of angiosperms. Trends Plant Sci. 10, 201-202 (2005).
    • (2005) Trends Plant Sci , vol.10 , pp. 201-202
    • Lockhart, P.J.1    Penny, D.2
  • 31
    • 34047267637 scopus 로고
    • A canonical decomposition theory formetrics on a finite set
    • Bandelt, H. J., Dress, A. W. M. A canonical decomposition theory formetrics on a finite set. Adv. Math. 92, 47-105 (1992).
    • (1992) Adv. Math. , vol.92 , pp. 47-105
    • Bandelt, H.J.1    Dress, A.W.M.2
  • 33
    • 0033084970 scopus 로고    scopus 로고
    • Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant
    • Waddell, P. J., Cao, Y.,Hauf, J. Hasegawa, M. Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Syst. Biol. 48, 31-53 (1999).
    • (1999) Syst. Biol. , vol.48 , pp. 31-53
    • Waddell, P.J.1    Cao, Y.2    Hauf, J.3    Hasegawa, M.4
  • 34
    • 0037331918 scopus 로고    scopus 로고
    • Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei
    • Clements, K. D., Gray, R. D., Howard Choat, J. Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei). Mol. Phylogenet. Evol. 26, 190-201 (2003).
    • (2003) Mol. Phylogenet. Evol. , vol.26 , pp. 190-201
    • Clements, K.D.1    Gray, R.D.2    Howard Choat, J.3
  • 35
    • 21144475766 scopus 로고
    • Spectral analysis of phylogenetic data
    • Hendy, M. D.,Penny, D. Spectral analysis of phylogenetic data. J Classif 10, 5-24 (1993).
    • (1993) J Classif , vol.10 , pp. 5-24
    • Hendy, M.D.1    Penny, D.2
  • 36
    • 0028891511 scopus 로고
    • Use of spectral analysis to test hypotheses on the origin of pinnipeds
    • Lento, G. M.,Hickson, R. E., Chambers, G. K., Penny, D. Use of spectral analysis to test hypotheses on the origin of pinnipeds. Mol. Biol. Evol. 12, 28-52 (1995).
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 28-52
    • Lento, G.M.1    Ickson, R.E.2    Chambers, G.K.3    Penny, D.4
  • 37
    • 25144453704 scopus 로고    scopus 로고
    • Untangling long branches: Identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks
    • Kennedy, M., Holland, B. R., Gray, R. D., Spencer, H. G. Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Syst. Biol. 54, 620-633 (2005).
    • (2005) Syst. Biol. , vol.54 , pp. 620-633
    • Kennedy, M.1    Holland, B.R.2    Gray, R.D.3    Spencer, H.G.4
  • 38
    • 35448965597 scopus 로고    scopus 로고
    • Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
    • Wagele, J. W., Mayer, C. Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects. BMC Evol. Biol. 7, 147 (2007).
    • (2007) BMC Evol. Biol. , vol.7 , pp. 147
    • Wagele, J.W.1    Mayer, C.2
  • 39
    • 0033219008 scopus 로고    scopus 로고
    • The long and short of it: Branch lengths and the problem of placing the New Zealand short-tailed bat
    • Kennedy, M. et al. The long and short of it: branch lengths and the problem of placing the New Zealand short-tailed bat, Mystacina. Mol. Phylogenet. Evol. 13, 405-416 (1999).
    • (1999) Mystacina. Mol. Phylogenet. Evol. , vol.13 , pp. 405-416
    • Kennedy, M.1
  • 40
    • 0036184428 scopus 로고    scopus 로고
    • Testing the new animal phylogeny: First use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes
    • Mallatt, J., Winchell, C. J. Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. Mol. Biol. Evol. 19, 289-301 (2002).
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 289-301
    • Mallatt, J.1    Winchell, C.J.2
  • 41
    • 27744524191 scopus 로고    scopus 로고
    • An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics
    • Brinkmann, H., van der Giezen, M., Zhou, Y., Poncelin de Raucourt, G., Philippe, H. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst. Biol. 54, 743-757 (2005).
    • (2005) Syst. Biol. , vol.54 , pp. 743-757
    • Brinkmann, H.1    Van Der Giezen, M.2    Zhou, Y.3    Poncelin De Raucourt, G.4    Philippe, H.5
  • 42
    • 0031301965 scopus 로고    scopus 로고
    • Rodentmonophyly: Pitfalls of molecular phylogenies
    • Philippe,H. Rodentmonophyly: pitfalls of molecular phylogenies. J. Mol. Evol. 45, 712-715 (1997).
    • (1997) J. Mol. Evol. , vol.45 , pp. 712-715
    • Philippe, H.1
  • 43
    • 17744386162 scopus 로고    scopus 로고
    • Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa Lophotrochozoa, and Protostomia
    • Philippe, H., Lartillot, N., Brinkmann, H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol. Biol. Evol. 22, 1246-1253 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1246-1253
    • Philippe, H.1    Lartillot, N.2    Brinkmann, H.3
  • 44
    • 24744449757 scopus 로고    scopus 로고
    • Identifying the basal angiosperm node in chloroplast genome phylogenies: Sampling one's way out of the Felsenstein zone
    • Leebens-Mack, J. et al. Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone. Mol. Biol. Evol. 22, 1948-1963 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1948-1963
    • Leebens-Mack, J.1
  • 45
    • 39749201627 scopus 로고    scopus 로고
    • Broadly sampled multigene trees of eukaryotes
    • Yoon, H. S. et al. Broadly sampled multigene trees of eukaryotes. BMC Evol. Biol. 8, 14 (2008).
    • (2008) BMC Evol. Biol. , vol.8 , pp. 14
    • Yoon, H.S.1
  • 46
    • 84859165788 scopus 로고    scopus 로고
    • The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata
    • Pagani, I. et al. The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 40, D571-579, doi:10.1093/nar/gkr1100 (2012).
    • (2012) Nucleic Acids Res. , vol.40 , pp. D571-579
    • Pagani, I.1
  • 47
    • 72949101201 scopus 로고    scopus 로고
    • Aphylogeny-driven genomic encyclopaedia of Bacteria and Archaea
    • Wu, D. et al. Aphylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462, 1056-1060, doi:10.1038/nature08656 (2009).
    • (2009) Nature , vol.462 , pp. 1056-1060
    • Wu, D.1
  • 48
    • 58149200948 scopus 로고    scopus 로고
    • The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis
    • Cole, J. R. et al. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37, D141-145, doi:10.1093/nar/gkn879 (2009).
    • (2009) Nucleic Acids Res , vol.37 , pp. D141-145
    • Cole, J.R.1
  • 49
    • 25144472531 scopus 로고    scopus 로고
    • Phylogenetic diversity and the greedy algorithm
    • Steel, M. Phylogenetic diversity and the greedy algorithm. Syst. Biol. 54, 527-529 (2005).
    • (2005) Syst. Biol. , vol.54 , pp. 527-529
    • Steel, M.1
  • 50
    • 0344861878 scopus 로고    scopus 로고
    • Mitochondrial genomes: Anything goes
    • Burger, G., Gray, M. W., Lang, B. F. Mitochondrial genomes: anything goes. Trends Genet 19, 709-716 (2003).
    • (2003) Trends Genet , vol.19 , pp. 709-716
    • Burger, G.1    Gray, M.W.2    Lang, B.F.3
  • 51
    • 0019423856 scopus 로고
    • Sequence and organization of the human mitochondrial genome
    • Anderson, S. et al. Sequence and organization of the human mitochondrial genome. Nature 290, 457-465 (1981).
    • (1981) Nature , vol.290 , pp. 457-465
    • Anderson, S.1
  • 52
    • 0041401720 scopus 로고    scopus 로고
    • The dual origin of the yeast mitochondrial proteome
    • Karlberg, O., Canback, B., Kurland, C. G. Andersson, S.G. The dual origin of the yeast mitochondrial proteome. Yeast 17, 170-187 (2000).
    • (2000) Yeast , vol.17 , pp. 170-187
    • Karlberg, O.1    Canback, B.2    Kurland, C.G.3    Andersson, S.G.4
  • 53
    • 36949022294 scopus 로고    scopus 로고
    • From endosymbiont to host-controlled organelle: The hijacking of mitochondrial protein synthesis and metabolism
    • Gabaldon, T., Huynen, M. A. From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism. PLoS Comput. Biol. 3, e219 (2007).
    • (2007) PLoS Comput. Biol. , vol.3 , pp. e219
    • Gabaldon, T.1    Huynen, M.A.2
  • 54
    • 0026091126 scopus 로고
    • RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution
    • Nugent, J. M., Palmer, J. D. RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell 66, 473-481 (1991).
    • (1991) Cell , vol.66 , pp. 473-481
    • Nugent, J.M.1    Palmer, J.D.2
  • 55
    • 0033598682 scopus 로고    scopus 로고
    • Intracellular gene transfer in action: Dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes
    • Adams, K. L. et al. Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc. Natl. Acad. Sci. U. S. A. 96, 13863-13868 (1999).
    • (1999) Proc. Natl. Acad. Sci. U. S. A. , vol.96 , pp. 13863-13868
    • Adams, K.L.1
  • 56
    • 0026673926 scopus 로고
    • Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: Evidence for RNA-mediated gene transfer
    • Covello, P. S., Gray, M. W. Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: evidence for RNA-mediated gene transfer. EMBO J. 11, 3815-3820 (1992).
    • (1992) EMBO J , vol.11 , pp. 3815-3820
    • Covello, P.S.1    Gray, M.W.2
  • 57
    • 34548768028 scopus 로고    scopus 로고
    • Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes
    • Dunning Hotopp, J. C. et al. Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317, 1753-1756 (2007).
    • (2007) Science , vol.317 , pp. 1753-1756
    • Dunning Hotopp, J.C.1
  • 58
    • 84877788966 scopus 로고    scopus 로고
    • A phylum-level bacterial phylogenetic marker database
    • Wang, Z.,Wu, M. A phylum-level bacterial phylogenetic marker database. Mol Biol Evol 30, 1258-1262, doi:10.1093/molbev/mst059 (2013).
    • (2013) Mol Biol Evol , vol.30 , pp. 1258-1262
    • Wang, Z.1    Wu, M.2
  • 59
    • 84891442169 scopus 로고    scopus 로고
    • Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade
    • Viklund, J., Martijn, J., Ettema, T. J., Andersson, S. G. Comparative and Phylogenomic Evidence That the Alphaproteobacterium HIMB59 Is Not a Member of the Oceanic SAR11 Clade. PLoS ONE 8, e78858, doi:10.1371/journal.pone.0078858 (2013).
    • (2013) PLoS ONE , vol.8 , pp. e78858
    • Viklund, J.1    Martijn, J.2    Ettema, T.J.3    Andersson, S.G.4
  • 60
    • 84855824416 scopus 로고    scopus 로고
    • Accounting for alignment uncertainty in phylogenomics
    • Wu, M., Chatterji, S., Eisen, J. A. Accounting for alignment uncertainty in phylogenomics. PLoS One 7, e30288, doi:10.1371/journal.pone.0030288 (2012).
    • (2012) PLoS One , vol.7 , pp. e30288
    • Wu, M.1    Chatterji, S.2    Eisen, J.A.3
  • 61
    • 77955950911 scopus 로고    scopus 로고
    • Compositional heterogeneity and phylogenomic inference of metazoan relationships
    • Nesnidal, M. P., Helmkampf, M., Bruchhaus, I., Hausdorf, B. Compositional heterogeneity and phylogenomic inference of metazoan relationships. Mol. Biol. Evol. 27, 2095-2104, doi:10.1093/molbev/msq097 (2010).
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 2095-2104
    • Nesnidal, M.P.1    Helmkampf, M.2    Bruchhaus, I.3    Hausdorf, B.4
  • 63
    • 55649110049 scopus 로고    scopus 로고
    • A simple, fast, and accurate method of phylogenomic inference
    • Wu, M., Eisen, J. A. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 9, R151 (2008).
    • (2008) Genome Biol , vol.9 , pp. R151
    • Wu, M.1    Eisen, J.A.2
  • 64
    • 84892566691 scopus 로고    scopus 로고
    • New rRNA genebased phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability
    • Ferla, M. P., Thrash, J. C., Giovannoni, S. J., Patrick, W. M. New rRNA genebased phylogenies of the Alphaproteobacteria provide perspective on major groups, mitochondrial ancestry and phylogenetic instability. PLoS ONE 8, e83383, doi:10.1371/journal.pone.0083383 (2013).
    • (2013) PLoS ONE , vol.8 , pp. e83383
    • Ferla, M.P.1    Thrash, J.C.2    Giovannoni, S.J.3    Patrick, W.M.4
  • 66
    • 81855199722 scopus 로고    scopus 로고
    • Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor
    • Sassera, D. et al. Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor. Mol. Biol. Evol. 28, 3285-3296, doi:10.1093/molbev/msr159 (2011).
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 3285-3296
    • Sassera, D.1
  • 67
    • 84859242353 scopus 로고    scopus 로고
    • Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2
    • Wu, M., Scott, A. J. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28, 1033-1034, doi:10.1093/bioinformatics/bts079 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 1033-1034
    • Wu, M.1    Scott, A.J.2
  • 68
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson, D. H., Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23, 254-267 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 254-267
    • Huson, D.H.1    Bryant, D.2
  • 69
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2-approximately maximumlikelihood trees for large alignments
    • Price, M. N., Dehal, P. S., Arkin, A. P. FastTree 2-approximately maximumlikelihood trees for large alignments. PLoS ONE 5, e9490, doi:10.1371/journal.pone.0009490 (2010).
    • (2010) PLoS ONE , vol.5 , pp. e9490
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 70
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa andmixed models
    • Stamatakis, A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa andmixed models. Bioinformatics 22, 2688-2690 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 2688-2690
    • Stamatakis, A.1
  • 71
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiontDNAwith Glimmer
    • Delcher, A. L., Bratke, K. A., Powers, E. C., Salzberg, S. L. Identifying bacterial genes and endosymbiontDNAwith Glimmer. Bioinformatics 23, 673-679 (2007).
    • (2007) Bioinformatics , vol.23 , pp. 673-679
    • Delcher, A.L.1    Bratke, K.A.2    Powers, E.C.3    Salzberg, S.L.4
  • 72
    • 80053174248 scopus 로고    scopus 로고
    • Genomic Insights into An Obligate Epibiotic Bacterial Predator: Micavibrio aeruginosavorus ARL-13
    • Wang, Z., Kadouri, D. E., Wu, M. Genomic Insights into An Obligate Epibiotic Bacterial Predator: Micavibrio aeruginosavorus ARL-13. BMC Genomics 12, 453, doi:10.1186/1471-2164-12-453 (2011).
    • (2011) BMC Genomics , vol.12 , pp. 453
    • Wang, Z.1    Kadouri, D.E.2    Wu, M.3
  • 73
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for largescale detection of protein families
    • Enright, A. J., Van Dongen, S., Ouzounis, C. A. An efficient algorithm for largescale detection of protein families. Nucleic Acids Res. 30, 1575-1584 (2002).
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 74
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K., Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059-3066 (2002).
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 75
    • 2442691520 scopus 로고    scopus 로고
    • A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
    • Lartillot, N., Philippe, H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 21, 1095-1109, doi:10.1093/molbev/msh112 (2004).
    • (2004) Mol Biol Evol , vol.21 , pp. 1095-1109
    • Lartillot, N.1    Philippe, H.2
  • 76
    • 47249122561 scopus 로고    scopus 로고
    • A site-and time-heterogeneous model of amino acid replacement
    • Blanquart, S., Lartillot, N. A site-and time-heterogeneous model of amino acid replacement. Mol. Biol. Evol. 25, 842-858 (2008).
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 842-858
    • Blanquart, S.1    Lartillot, N.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.