메뉴 건너뛰기




Volumn 15, Issue 1, 2015, Pages

Ancient horizontal gene transfer and the last common ancestors Phylogenetics and phylogeography

Author keywords

Aminoacyl tRNA synthetase; Cenancestor; Horizontal gene transfer; Hypnolog; Last Universal Common Ancestor; LUCA

Indexed keywords

COMMON ANCESTRY; EXTINCTION; GENE TRANSFER; LIFE HISTORY; PHYLOGENETICS; PHYLOGEOGRAPHY; SPATIOTEMPORAL ANALYSIS; TAXONOMY;

EID: 84929145859     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-015-0350-0     Document Type: Article
Times cited : (45)

References (81)
  • 2
    • 38649114368 scopus 로고    scopus 로고
    • Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia
    • 2223567 1:CAS:528:DC%2BD1cXhsFSgsLk%3D 18055595
    • Fournier GP, Gogarten JP. Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J Bacteriol. 2008;190:1124-7.
    • (2008) J Bacteriol , vol.190 , pp. 1124-7
    • Fournier, G.P.1    Gogarten, J.P.2
  • 5
    • 78751596904 scopus 로고    scopus 로고
    • Horizontal gene transfer and the formation of groups of microorganisms
    • Caister Academic Press Hethersett, Norwich, UK
    • Williams D, Andam C, Gogarten J. Horizontal gene transfer and the formation of groups of microorganisms. In: Molecular phylogeny of microorganisms. Hethersett, Norwich, UK: Caister Academic Press; 2010. p. 167-84.
    • (2010) Molecular Phylogeny of Microorganisms , pp. 167-84
    • Williams, D.1    Andam, C.2    Gogarten, J.3
  • 6
    • 79851505378 scopus 로고    scopus 로고
    • Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes
    • 3029252 1:CAS:528:DC%2BC3MXhvVKmurs%3D 21298028
    • Treangen TJ, Rocha EPC. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet. 2011;7:e1001284.
    • (2011) PLoS Genet , vol.7 , pp. 1001284
    • Treangen, T.J.1    Rocha, E.P.C.2
  • 7
    • 23944506044 scopus 로고    scopus 로고
    • Mobile genetic elements: The agents of open source evolution
    • 1:CAS:528:DC%2BD2MXps1KjtbY%3D 16138100
    • Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol. 2005;3:722-32.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 722-32
    • Frost, L.S.1    Leplae, R.2    Summers, A.O.3    Toussaint, A.4
  • 8
    • 65549147639 scopus 로고    scopus 로고
    • Defining the mobilome
    • 1:CAS:528:DC%2BD1MXksFyhsbo%3D
    • Siefert JL. Defining the mobilome. Methods Mol Biol Clifton NJ. 2009;532:13-27.
    • (2009) Methods Mol Biol Clifton NJ , vol.532 , pp. 13-27
    • Siefert, J.L.1
  • 9
    • 33947593126 scopus 로고    scopus 로고
    • The ancient Virus World and evolution of cells
    • 1594570 16984643
    • Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol Direct. 2006;1:29.
    • (2006) Biol Direct , vol.1 , pp. 29
    • Koonin, E.V.1    Senkevich, T.G.2    Dolja, V.V.3
  • 10
    • 0035902449 scopus 로고    scopus 로고
    • Rolling-circle transposons in eukaryotes
    • 37501 1:CAS:528:DC%2BD3MXls1WitLo%3D 11447285
    • Kapitonov VV, Jurka J. Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci U S A. 2001;98:8714-9.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 8714-9
    • Kapitonov, V.V.1    Jurka, J.2
  • 11
    • 77958487981 scopus 로고    scopus 로고
    • Pervasive horizontal transfer of rolling-circle transposons among animals
    • 2997563 20693155
    • Thomas J, Schaack S, Pritham EJ. Pervasive horizontal transfer of rolling-circle transposons among animals. Genome Biol Evol. 2010;2:656-64.
    • (2010) Genome Biol Evol , vol.2 , pp. 656-64
    • Thomas, J.1    Schaack, S.2    Pritham, E.J.3
  • 12
    • 84858194655 scopus 로고    scopus 로고
    • Gene capture by Helitron transposons reshuffles the transcriptome of maize
    • 3296258 1:CAS:528:DC%2BC38XmslKgu7k%3D 22174072
    • Barbaglia AM, Klusman KM, Higgins J, Shaw JR, Hannah LC, Lal SK. Gene capture by Helitron transposons reshuffles the transcriptome of maize. Genetics. 2012;190:965-75.
    • (2012) Genetics , vol.190 , pp. 965-75
    • Barbaglia, A.M.1    Klusman, K.M.2    Higgins, J.3    Shaw, J.R.4    Hannah, L.C.5    Lal, S.K.6
  • 15
    • 62349089758 scopus 로고    scopus 로고
    • Molecular domestication of transposable elements: From detrimental parasites to useful host genes
    • 1:CAS:528:DC%2BD1MXjtFKqsbc%3D
    • Sinzelle L, Izsvák Z, Ivics Z. Molecular domestication of transposable elements: from detrimental parasites to useful host genes. Cell Mol Life Sci CMLS. 2009;66:1073-93.
    • (2009) Cell Mol Life Sci CMLS , vol.66 , pp. 1073-93
    • Sinzelle, L.1    Izsvák, Z.2    Ivics, Z.3
  • 18
    • 0004149207 scopus 로고
    • 2 Oxford University Press, USA Oxford; New York
    • Dawkins R. The Selfish Gene. 2nd ed. Oxford; New York: Oxford University Press, USA; 1990.
    • (1990) The Selfish Gene
    • Dawkins, R.1
  • 19
  • 20
    • 0032770725 scopus 로고    scopus 로고
    • On the possibility of constructive neutral evolution
    • 1:CAS:528:DyaK1MXltFSksbY%3D 10441669
    • Stoltzfus A. On the possibility of constructive neutral evolution. J Mol Evol. 1999;49:169-81.
    • (1999) J Mol Evol , vol.49 , pp. 169-81
    • Stoltzfus, A.1
  • 21
    • 70350433462 scopus 로고    scopus 로고
    • Evolution of genes and organisms: The tree/web of life in light of horizontal gene transfer
    • 1:CAS:528:DC%2BD1MXhsFWksrzL 19845634
    • Olendzenski L, Gogarten JP. Evolution of genes and organisms: the tree/web of life in light of horizontal gene transfer. Ann N Y Acad Sci. 2009;1178:137-45.
    • (2009) Ann N y Acad Sci , vol.1178 , pp. 137-45
    • Olendzenski, L.1    Gogarten, J.P.2
  • 22
    • 0037173066 scopus 로고    scopus 로고
    • On the evolution of cells
    • 124369 1:CAS:528:DC%2BD38XltF2hsbc%3D 12077305
    • Woese CR. On the evolution of cells. Proc Natl Acad Sci U S A. 2002;99:8742-7.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 8742-7
    • Woese, C.R.1
  • 23
    • 67651064681 scopus 로고    scopus 로고
    • Horizontal gene transfer from extinct and extant lineages: Biological innovation and the coral of life
    • 2873001 1:CAS:528:DC%2BD1MXhtVSmsrzO 19571243
    • Fournier GP, Huang J, Gogarten JP. Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life. Philos Trans R Soc Lond B Biol Sci. 2009;364:2229-39.
    • (2009) Philos Trans R Soc Lond B Biol Sci , vol.364 , pp. 2229-39
    • Fournier, G.P.1    Huang, J.2    Gogarten, J.P.3
  • 25
    • 0026574207 scopus 로고
    • Recent evidence for evolution of the genetic code
    • 1:CAS:528:DyaK38Xit12jtrw%3D 1579111
    • Osawa S, Jukes TH, Watanabe K, Muto A. Recent evidence for evolution of the genetic code. Microbiol Rev. 1992;56:229-64.
    • (1992) Microbiol Rev , vol.56 , pp. 229-64
    • Osawa, S.1    Jukes, T.H.2    Watanabe, K.3    Muto, A.4
  • 26
    • 79959482487 scopus 로고    scopus 로고
    • Association between translation efficiency and horizontal gene transfer within microbial communities
    • 3113575 1:CAS:528:DC%2BC3MXnvVKntrk%3D 21343180
    • Tuller T, Girshovich Y, Sella Y, Kreimer A, Freilich S, Kupiec M, et al. Association between translation efficiency and horizontal gene transfer within microbial communities. Nucleic Acids Res. 2011;39:4743-55.
    • (2011) Nucleic Acids Res , vol.39 , pp. 4743-55
    • Tuller, T.1    Girshovich, Y.2    Sella, Y.3    Kreimer, A.4    Freilich, S.5    Kupiec, M.6
  • 27
    • 77954993696 scopus 로고    scopus 로고
    • Rooting the ribosomal tree of life
    • 1:CAS:528:DC%2BC3cXptlegsbc%3D 20194428
    • Fournier GP, Gogarten JP. Rooting the ribosomal tree of life. Mol Biol Evol. 2010;27:1792-801.
    • (2010) Mol Biol Evol , vol.27 , pp. 1792-801
    • Fournier, G.P.1    Gogarten, J.P.2
  • 28
    • 0036575779 scopus 로고    scopus 로고
    • Recent emergence of the modern genetic code: A proposal
    • 1:CAS:528:DC%2BD38XjvFCgtrg%3D
    • Syvanen M. Recent emergence of the modern genetic code: a proposal. Trends Genet TIG. 2002;18:245-8.
    • (2002) Trends Genet TIG , vol.18 , pp. 245-8
    • Syvanen, M.1
  • 29
    • 71849108697 scopus 로고    scopus 로고
    • Deciphering synonymous codons in the three domains of life: Co-evolution with specific tRNA modification enzymes
    • 1:CAS:528:DC%2BD1MXhsFGgtrjE 19931533
    • Grosjean H, de Crécy-Lagard V, Marck C. Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett. 2010;584:252-64.
    • (2010) FEBS Lett , vol.584 , pp. 252-64
    • Grosjean, H.1    De Crécy-Lagard, V.2    Marck, C.3
  • 30
    • 33746092088 scopus 로고    scopus 로고
    • Collective evolution and the genetic code
    • 1502294 1:CAS:528:DC%2BD28XntFWmsLg%3D 16818880
    • Vetsigian K, Woese C, Goldenfeld N. Collective evolution and the genetic code. Proc Natl Acad Sci U S A. 2006;103:10696-701.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 10696-701
    • Vetsigian, K.1    Woese, C.2    Goldenfeld, N.3
  • 31
    • 0035478911 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthetases: Potential markers of genetic code development
    • 1:CAS:528:DC%2BD3MXnt1WjsbY%3D 11590011
    • Ribas de Pouplana L, Schimmel P. Aminoacyl-tRNA synthetases: potential markers of genetic code development. Trends Biochem Sci. 2001;26:591-6.
    • (2001) Trends Biochem Sci , vol.26 , pp. 591-6
    • Ribas De Pouplana, L.1    Schimmel, P.2
  • 32
    • 52949154680 scopus 로고    scopus 로고
    • Development of tRNA synthetases and connection to genetic code and disease
    • 1:CAS:528:DC%2BD1cXht1Cit7%2FM
    • Schimmel P. Development of tRNA synthetases and connection to genetic code and disease. Protein Sci Publ Protein Soc. 2008;17:1643-52.
    • (2008) Protein Sci Publ Protein Soc , vol.17 , pp. 1643-52
    • Schimmel, P.1
  • 33
    • 0025158208 scopus 로고
    • Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs
    • 1:CAS:528:DyaK3MXpslensg%3D%3D 2203971
    • Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990;347:203-6.
    • (1990) Nature , vol.347 , pp. 203-6
    • Eriani, G.1    Delarue, M.2    Poch, O.3    Gangloff, J.4    Moras, D.5
  • 34
    • 0034053846 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process
    • 1:CAS:528:DC%2BD3cXitFygsro%3D
    • Woese CR, Olsen GJ, Ibba M, Söll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev MMBR. 2000;64:202-36.
    • (2000) Microbiol Mol Biol Rev MMBR , vol.64 , pp. 202-36
    • Woese, C.R.1    Olsen, G.J.2    Ibba, M.3    Söll, D.4
  • 35
    • 0033912919 scopus 로고    scopus 로고
    • A view into the origin of life: Aminoacyl-tRNA synthetases
    • 1:STN:280:DC%2BD3cvhtVantg%3D%3D
    • Ribas de Pouplana L, Schimmel P. A view into the origin of life: aminoacyl-tRNA synthetases. Cell Mol Life Sci CMLS. 2000;57:865-70.
    • (2000) Cell Mol Life Sci CMLS , vol.57 , pp. 865-70
    • Ribas De Pouplana, L.1    Schimmel, P.2
  • 37
    • 0037166006 scopus 로고    scopus 로고
    • Pyrrolysine encoded by UAG in Archaea: Charging of a UAG-decoding specialized tRNA
    • 1:CAS:528:DC%2BD38XktFanur0%3D 12029131
    • Srinivasan G, James CM, Krzycki JA. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science. 2002;296:1459-62.
    • (2002) Science , vol.296 , pp. 1459-62
    • Srinivasan, G.1    James, C.M.2    Krzycki, J.A.3
  • 38
    • 27844438536 scopus 로고    scopus 로고
    • The direct genetic encoding of pyrrolysine
    • 1:CAS:528:DC%2BD2MXht1GnurzK 16256420
    • Krzycki JA. The direct genetic encoding of pyrrolysine. Curr Opin Microbiol. 2005;8:706-12.
    • (2005) Curr Opin Microbiol , vol.8 , pp. 706-12
    • Krzycki, J.A.1
  • 39
  • 40
    • 34047120199 scopus 로고    scopus 로고
    • Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase
    • 1851642 1:CAS:528:DC%2BD2sXjslOgsbk%3D 17267409
    • Herring S, Ambrogelly A, Polycarpo CR, Söll D. Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase. Nucleic Acids Res. 2007;35:1270-8.
    • (2007) Nucleic Acids Res , vol.35 , pp. 1270-8
    • Herring, S.1    Ambrogelly, A.2    Polycarpo, C.R.3    Söll, D.4
  • 41
    • 34548574926 scopus 로고    scopus 로고
    • High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis
    • 1976440 1:CAS:528:DC%2BD2sXpvFWgtro%3D 17626042
    • Zhang Y, Gladyshev VN. High content of proteins containing 21st and 22nd amino acids, selenocysteine and pyrrolysine, in a symbiotic deltaproteobacterium of gutless worm Olavius algarvensis. Nucleic Acids Res. 2007;35:4952-63.
    • (2007) Nucleic Acids Res , vol.35 , pp. 4952-63
    • Zhang, Y.1    Gladyshev, V.N.2
  • 42
    • 84890110026 scopus 로고    scopus 로고
    • Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis
    • 3814188 1:CAS:528:DC%2BC2cXltlChsb0%3D 23985970
    • Borrel G, O'Toole PW, Harris HMB, Peyret P, Brugère J-F, Gribaldo S. Phylogenomic data support a seventh order of Methylotrophic methanogens and provide insights into the evolution of Methanogenesis. Genome Biol Evol. 2013;5:1769-80.
    • (2013) Genome Biol Evol , vol.5 , pp. 1769-80
    • Borrel, G.1    O'Toole, P.W.2    Harris, H.M.B.3    Peyret, P.4    Brugère, J.-F.5    Gribaldo, S.6
  • 43
    • 34250793331 scopus 로고    scopus 로고
    • The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity
    • 2074874 1:CAS:528:DC%2BD2sXntFKnsL4%3D 17582401
    • Herring S, Ambrogelly A, Gundllapalli S, O'Donoghue P, Polycarpo CR, Söll D. The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity. FEBS Lett. 2007;581:3197-203.
    • (2007) FEBS Lett , vol.581 , pp. 3197-203
    • Herring, S.1    Ambrogelly, A.2    Gundllapalli, S.3    O'Donoghue, P.4    Polycarpo, C.R.5    Söll, D.6
  • 44
    • 84896859974 scopus 로고    scopus 로고
    • Unique characteristics of the pyrrolysine system in the 7th order of methanogens: Implications for the evolution of a genetic code expansion cassette
    • Borrel G, Gaci N, Peyret P, O'Toole PW, Gribaldo S, Brugère J-F. Unique characteristics of the pyrrolysine system in the 7th order of methanogens: implications for the evolution of a genetic code expansion cassette. Archaea Vanc BC. 2014;2014:374146.
    • (2014) Archaea Vanc BC , vol.2014 , pp. 374146
    • Borrel, G.1    Gaci, N.2    Peyret, P.3    O'Toole, P.W.4    Gribaldo, S.5    Brugère, J.-F.6
  • 45
    • 4644255236 scopus 로고    scopus 로고
    • Function of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases
    • 1:CAS:528:DC%2BD2cXnvFantro%3D 15450490
    • Krzycki JA. Function of genetically encoded pyrrolysine in corrinoid-dependent methylamine methyltransferases. Curr Opin Chem Biol. 2004;8:484-91.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 484-91
    • Krzycki, J.A.1
  • 46
    • 20144380970 scopus 로고    scopus 로고
    • RNA-dependent cysteine biosynthesis in archaea
    • 1:CAS:528:DC%2BD2MXisVyiuro%3D 15790858
    • Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, et al. RNA-dependent cysteine biosynthesis in archaea. Science. 2005;307:1969-72.
    • (2005) Science , vol.307 , pp. 1969-72
    • Sauerwald, A.1    Zhu, W.2    Major, T.A.3    Roy, H.4    Palioura, S.5    Jahn, D.6
  • 48
    • 1642339676 scopus 로고    scopus 로고
    • Cladogenesis, coalescence and the evolution of the three domains of life
    • 1:CAS:528:DC%2BD2cXisVGitb8%3D
    • Zhaxybayeva O, Gogarten JP. Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet TIG. 2004;20:182-7.
    • (2004) Trends Genet TIG , vol.20 , pp. 182-7
    • Zhaxybayeva, O.1    Gogarten, J.P.2
  • 49
    • 80053175926 scopus 로고    scopus 로고
    • Biased gene transfer and its implications for the concept of lineage
    • 3191353 21943000
    • Andam CP, Gogarten JP. Biased gene transfer and its implications for the concept of lineage. Biol Direct. 2011;6:47.
    • (2011) Biol Direct , vol.6 , pp. 47
    • Andam, C.P.1    Gogarten, J.P.2
  • 50
    • 33745763402 scopus 로고    scopus 로고
    • Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition
    • 1478180 1:CAS:528:DC%2BD28XltlGlu74%3D 16675947
    • Bilokapic S, Maier T, Ahel D, Gruic-Sovulj I, Söll D, Weygand-Durasevic I, et al. Structure of the unusual seryl-tRNA synthetase reveals a distinct zinc-dependent mode of substrate recognition. EMBO J. 2006;25:2498-509.
    • (2006) EMBO J , vol.25 , pp. 2498-509
    • Bilokapic, S.1    Maier, T.2    Ahel, D.3    Gruic-Sovulj, I.4    Söll, D.5    Weygand-Durasevic, I.6
  • 51
    • 84899815269 scopus 로고    scopus 로고
    • Coexistence of bacterial leucyl-tRNA synthetases with archaeal tRNA binding domains that distinguish tRNA(Leu) in the archaeal mode
    • 4005665 1:CAS:528:DC%2BC2cXntlyksr0%3D 24500203
    • Fang Z-P, Wang M, Ruan Z-R, Tan M, Liu R-J, Zhou M, et al. Coexistence of bacterial leucyl-tRNA synthetases with archaeal tRNA binding domains that distinguish tRNA(Leu) in the archaeal mode. Nucleic Acids Res. 2014;42:5109-24.
    • (2014) Nucleic Acids Res , vol.42 , pp. 5109-24
    • Fang, Z.-P.1    Wang, M.2    Ruan, Z.-R.3    Tan, M.4    Liu, R.-J.5    Zhou, M.6
  • 52
    • 77950448058 scopus 로고    scopus 로고
    • Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees
    • 2867768 20356385
    • Kück P, Meusemann K, Dambach J, Thormann B, von Reumont BM, Wägele JW, et al. Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees. Front Zool. 2010;7:10.
    • (2010) Front Zool , vol.7 , pp. 10
    • Kück, P.1    Meusemann, K.2    Dambach, J.3    Thormann, B.4    Von Reumont, B.M.5    Wägele, J.W.6
  • 53
    • 77954270711 scopus 로고    scopus 로고
    • GUIDANCE: A web server for assessing alignment confidence scores
    • 2896199 1:CAS:528:DC%2BC3cXotVSqtbs%3D 20497997
    • Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T. GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. 2010;38(Web Server issue):W23-8.
    • (2010) Nucleic Acids Res , vol.38 , Issue.WEB SERVER ISSUE , pp. 23-8
    • Penn, O.1    Privman, E.2    Ashkenazy, H.3    Landan, G.4    Graur, D.5    Pupko, T.6
  • 54
    • 84855824416 scopus 로고    scopus 로고
    • Accounting for alignment uncertainty in phylogenomics
    • 3260272 1:CAS:528:DC%2BC38XhslKmt74%3D 22272325
    • Wu M, Chatterji S, Eisen JA. Accounting for alignment uncertainty in phylogenomics. PLoS One. 2012;7:e30288.
    • (2012) PLoS One , vol.7 , pp. 30288
    • Wu, M.1    Chatterji, S.2    Eisen, J.A.3
  • 55
    • 84907288508 scopus 로고    scopus 로고
    • AliGROOVE-visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support
    • 4167143 25176556
    • Kück P, Meid SA, Groß C, Wägele JW, Misof B. AliGROOVE-visualization of heterogeneous sequence divergence within multiple sequence alignments and detection of inflated branch support. BMC Bioinformatics. 2014;15:294.
    • (2014) BMC Bioinformatics , vol.15 , pp. 294
    • Kück, P.1    Meid, S.A.2    Groß, C.3    Wägele, J.W.4    Misof, B.5
  • 56
    • 69949126557 scopus 로고    scopus 로고
    • PhyloBayes 3: A Bayesian software package for phylogenetic reconstruction and molecular dating
    • 1:CAS:528:DC%2BD1MXhtVelu7fP
    • Lartillot N, Lepage T, Blanquart S. PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinforma Oxf Engl. 2009;25:2286-8.
    • (2009) Bioinforma Oxf Engl , vol.25 , pp. 2286-8
    • Lartillot, N.1    Lepage, T.2    Blanquart, S.3
  • 57
    • 56349169406 scopus 로고    scopus 로고
    • Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria
    • 2584045 18834516
    • Boussau B, Guéguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol. 2008;8:272.
    • (2008) BMC Evol Biol , vol.8 , pp. 272
    • Boussau, B.1    Guéguen, L.2    Gouy, M.3
  • 58
    • 0030707877 scopus 로고    scopus 로고
    • A euryarchaeal lysyl-tRNA synthetase: Resemblance to class i synthetases
    • 1:CAS:528:DyaK2sXnt1ahtrk%3D 9353192
    • Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, et al. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science. 1997;278:1119-22.
    • (1997) Science , vol.278 , pp. 1119-22
    • Ibba, M.1    Morgan, S.2    Curnow, A.W.3    Pridmore, D.R.4    Vothknecht, U.C.5    Gardner, W.6
  • 60
    • 0032830481 scopus 로고    scopus 로고
    • Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
    • 10447505
    • Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999;9:689-710.
    • (1999) Genome Res , vol.9 , pp. 689-710
    • Wolf, Y.I.1    Aravind, L.2    Grishin, N.V.3    Koonin, E.V.4
  • 61
    • 0031560769 scopus 로고    scopus 로고
    • Recognition of tRNA(Gly) by three widely diverged glycyl-tRNA synthetases
    • 1:CAS:528:DyaK2sXjsVCrurs%3D 9171287
    • Nameki N, Tamura K, Asahara H, Hasegawa T. Recognition of tRNA(Gly) by three widely diverged glycyl-tRNA synthetases. J Mol Biol. 1997;268:640-7.
    • (1997) J Mol Biol , vol.268 , pp. 640-7
    • Nameki, N.1    Tamura, K.2    Asahara, H.3    Hasegawa, T.4
  • 62
    • 0032005233 scopus 로고    scopus 로고
    • Glycyl-tRNA synthetase from Thermus thermophilus-wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems
    • 1:CAS:528:DyaK1cXhtVKku7o%3D
    • Mazauric MH, Keith G, Logan D, Kreutzer R, Giegé R, Kern D. Glycyl-tRNA synthetase from Thermus thermophilus-wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems. Eur J Biochem FEBS. 1998;251:744-57.
    • (1998) Eur J Biochem FEBS , vol.251 , pp. 744-57
    • Mazauric, M.H.1    Keith, G.2    Logan, D.3    Kreutzer, R.4    Giegé, R.5    Kern, D.6
  • 63
    • 0021770577 scopus 로고
    • The beta subunit of E. Coli glycyl-tRNA synthetase plays a major role in tRNA recognition
    • 318838 1:CAS:528:DyaL2cXksFSksLw%3D 6374618
    • Nagel GM, Cumberledge S, Johnson MS, Petrella E, Weber BH. The beta subunit of E. coli glycyl-tRNA synthetase plays a major role in tRNA recognition. Nucleic Acids Res. 1984;12:4377-84.
    • (1984) Nucleic Acids Res , vol.12 , pp. 4377-84
    • Nagel, G.M.1    Cumberledge, S.2    Johnson, M.S.3    Petrella, E.4    Weber, B.H.5
  • 64
  • 65
    • 1542272747 scopus 로고    scopus 로고
    • Comparative genomics, minimal gene-sets and the last universal common ancestor
    • 1:CAS:528:DC%2BD3sXosl2hsro%3D 15035042
    • Koonin EV. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol. 2003;1:127-36.
    • (2003) Nat Rev Microbiol , vol.1 , pp. 127-36
    • Koonin, E.V.1
  • 66
    • 77951557120 scopus 로고    scopus 로고
    • Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution
    • 2876114 20433725
    • Omelchenko MV, Galperin MY, Wolf YI, Koonin EV. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct. 2010;5:31.
    • (2010) Biol Direct , vol.5 , pp. 31
    • Omelchenko, M.V.1    Galperin, M.Y.2    Wolf, Y.I.3    Koonin, E.V.4
  • 67
    • 77953776263 scopus 로고    scopus 로고
    • Biased gene transfer mimics patterns created through shared ancestry
    • 2890805 1:CAS:528:DC%2BC3cXnvV2it7g%3D 20495090
    • Andam CP, Williams D, Gogarten JP. Biased gene transfer mimics patterns created through shared ancestry. Proc Natl Acad Sci U S A. 2010;107:10679-84.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 10679-84
    • Andam, C.P.1    Williams, D.2    Gogarten, J.P.3
  • 70
    • 84892153217 scopus 로고    scopus 로고
    • Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era
    • 1:CAS:528:DC%2BC3sXhvFegs7zJ 24364418
    • Reisinger B, Sperl J, Holinski A, Schmid V, Rajendran C, Carstensen L, et al. Evidence for the existence of elaborate enzyme complexes in the Paleoarchean era. J Am Chem Soc. 2014;136:122-9.
    • (2014) J Am Chem Soc , vol.136 , pp. 122-9
    • Reisinger, B.1    Sperl, J.2    Holinski, A.3    Schmid, V.4    Rajendran, C.5    Carstensen, L.6
  • 71
    • 0002695225 scopus 로고
    • Evolution of proton pumping ATPases: Rooting the tree of life
    • 1:CAS:528:DyaK38XmtVOmtb4%3D 24408574
    • Gogarten JP, Taiz L. Evolution of proton pumping ATPases: rooting the tree of life. Photosynth Res. 1992;33:137-46.
    • (1992) Photosynth Res , vol.33 , pp. 137-46
    • Gogarten, J.P.1    Taiz, L.2
  • 72
    • 33750273036 scopus 로고    scopus 로고
    • Protein superfamily evolution and the last universal common ancestor (LUCA)
    • 1:CAS:528:DC%2BD28XhtFSnsLfO 17021929
    • Ranea JAG, Sillero A, Thornton JM, Orengo CA. Protein superfamily evolution and the last universal common ancestor (LUCA). J Mol Evol. 2006;63:513-25.
    • (2006) J Mol Evol , vol.63 , pp. 513-25
    • Ranea, J.A.G.1    Sillero, A.2    Thornton, J.M.3    Orengo, C.A.4
  • 73
    • 4344618574 scopus 로고    scopus 로고
    • Ancestral lipid biosynthesis and early membrane evolution
    • 15337120
    • Peretó J, López-García P, Moreira D. Ancestral lipid biosynthesis and early membrane evolution. Trends Biochem Sci. 2004;29:469-77.
    • (2004) Trends Biochem Sci , vol.29 , pp. 469-77
    • Peretó, J.1    López-García, P.2    Moreira, D.3
  • 74
    • 0242371471 scopus 로고    scopus 로고
    • Horizontal gene transfer accelerates genome innovation and evolution
    • 1:CAS:528:DC%2BD3sXotlWjsrk%3D 12777514
    • Jain R, Rivera MC, Moore JE, Lake JA. Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol. 2003;20:1598-602.
    • (2003) Mol Biol Evol , vol.20 , pp. 1598-602
    • Jain, R.1    Rivera, M.C.2    Moore, J.E.3    Lake, J.A.4
  • 75
    • 0023471213 scopus 로고
    • The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code
    • 1:CAS:528:DyaL1cXlt1Cmtrc%3D 3454288
    • Fitch WM, Upper K. The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harb Symp Quant Biol. 1987;52:759-67.
    • (1987) Cold Spring Harb Symp Quant Biol , vol.52 , pp. 759-67
    • Fitch, W.M.1    Upper, K.2
  • 77
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • 390337 1:CAS:528:DC%2BD2cXisF2ks7w%3D 15034147
    • Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792-7.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1792-7
    • Edgar, R.C.1
  • 78
    • 79954529507 scopus 로고    scopus 로고
    • ProtTest 3: Fast selection of best-fit models of protein evolution
    • 1:CAS:528:DC%2BC3MXksFKltbs%3D
    • Darriba D, Taboada GL, Doallo R, Posada D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinforma Oxf Engl. 2011;27:1164-5.
    • (2011) Bioinforma Oxf Engl , vol.27 , pp. 1164-5
    • Darriba, D.1    Taboada, G.L.2    Doallo, R.3    Posada, D.4
  • 79
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • 14530136
    • Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52:696-704.
    • (2003) Syst Biol , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 80
    • 45849154166 scopus 로고    scopus 로고
    • An improved general amino acid replacement matrix
    • 1:CAS:528:DC%2BD1cXotlKgsbg%3D 18367465
    • Le SQ, Gascuel O. An improved general amino acid replacement matrix. Mol Biol Evol. 2008;25:1307-20.
    • (2008) Mol Biol Evol , vol.25 , pp. 1307-20
    • Le, S.Q.1    Gascuel, O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.