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Volumn 14, Issue 6, 2013, Pages 11376-11391

The uneven rate of the molecular evolution of gene sequences of DNA-dependent RNA polymerase I of the genus Lamium L

Author keywords

Bayesian inference; BI; Maximum likelihood; Maximum Parsimony; ML; MP; NEP; Nucleus encoded plastid RNA polymerase; Parsimony informative; PEP; Phylogenetic informativeness; PI; Pi; Plastid encoded plastid RNA polymerase

Indexed keywords

DNA DEPENDENT RNA POLYMERASE I; DNA DIRECTED RNA POLYMERASE; UNCLASSIFIED DRUG; AMINO ACID;

EID: 84878443837     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms140611376     Document Type: Article
Times cited : (18)

References (46)
  • 1
    • 0024279293 scopus 로고
    • Chloroplast rpoA, rpoB, and rpoC genes specify at least three components of a chloroplast DNA-dependent RNA polymerase active in tRNA and mRNA transcription
    • Little, M.C.; Hallick, R.B. Chloroplast rpoA, rpoB, and rpoC genes specify at least three components of a chloroplast DNA-dependent RNA polymerase active in tRNA and mRNA transcription. J. Biol. Chem. 1988, 263, 14302-14307
    • (1988) J. Biol. Chem , vol.263 , pp. 14302-14307
    • Little, M.C.1    Hallick, R.B.2
  • 2
    • 0025289439 scopus 로고
    • Nucleotide sequence of the maize chloroplast rpoB/CI/C2 operon: Comparison between the derived protein primary structures from various organisms with respect to functional domains
    • Gabor, L.I.; Meinke, A.; Döry, I.; Kössel, H. Nucleotide sequence of the maize chloroplast rpoB/CI/C2 operon: Comparison between the derived protein primary structures from various organisms with respect to functional domains. Mol. Gen. Genet. 1990, 221, 379-394
    • (1990) Mol. Gen. Genet , vol.221 , pp. 379-394
    • Gabor, L.I.1    Meinke, A.2    Döry, I.3    Kössel, H.4
  • 3
    • 0032134421 scopus 로고    scopus 로고
    • RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme
    • Serino, G.; Maliga, P. RNA polymerase subunits encoded by the plastid rpo genes are not shared with the nucleus-encoded plastid enzyme. Plant Physiol. 1998, 117, 1165-1170
    • (1998) Plant Physiol , vol.117 , pp. 1165-1170
    • Serino, G.1    Maliga, P.2
  • 4
    • 0029934521 scopus 로고    scopus 로고
    • Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants
    • Allison, L.A.; Simon, L.D.; Maliga, P. Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J. 1996, 15, 2802-2809
    • (1996) EMBO J , vol.15 , pp. 2802-2809
    • Allison, L.A.1    Simon, L.D.2    Maliga, P.3
  • 5
    • 0031011722 scopus 로고    scopus 로고
    • The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids
    • Hajdukiewicz, P.T.J.; Allison, L.A.; Maliga, P. The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J. 1997, 16, 4041-4048
    • (1997) EMBO J , vol.16 , pp. 4041-4048
    • Hajdukiewicz, P.T.J.1    Allison, L.A.2    Maliga, P.3
  • 6
    • 0031735383 scopus 로고    scopus 로고
    • Responses of the transcriptional apparatus of barley chloroplasts to a prolonged dark period and to subsequent reillumination
    • Krause, K.; Falk, J.; Humbeck, K.; Krupinska, K. Responses of the transcriptional apparatus of barley chloroplasts to a prolonged dark period and to subsequent reillumination. Physiol. Plant. 1998, 104, 143-152
    • (1998) Physiol. Plant , vol.104 , pp. 143-152
    • Krause, K.1    Falk, J.2    Humbeck, K.3    Krupinska, K.4
  • 7
    • 37649009007 scopus 로고    scopus 로고
    • Phylogeny of flowering plants by the chloroplast genome sequences: In search of a Lucky Gene
    • Logacheva, M.D.; Penin, A.A.; Samigullin, T.H.; Vallejo-Roman, C.M.; Antonov, A.S. Phylogeny of flowering plants by the chloroplast genome sequences: In search of a "Lucky Gene". Biochemistry 2007, 72, 1324-1330
    • (2007) Biochemistry , vol.72 , pp. 1324-1330
    • Logacheva, M.D.1    Penin, A.A.2    Samigullin, T.H.3    Vallejo-Roman, C.M.4    Antonov, A.S.5
  • 9
    • 33847198333 scopus 로고    scopus 로고
    • Congruence of evolutionary relationships inside the Leuconostoc-Oenococcus-Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK
    • Chelo, I.M.; Zé-Zé, L.; Tenreiro, R. Congruence of evolutionary relationships inside the Leuconostoc-Oenococcus-Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK. Int. J. Syst. Evol. Microbiol. 2007, 57, 276-286
    • (2007) Int. J. Syst. Evol. Microbiol , vol.57 , pp. 276-286
    • Chelo, I.M.1    Zé-Zé, L.2    Tenreiro, R.3
  • 10
    • 0031112130 scopus 로고    scopus 로고
    • Phylogenetic analysis of the Triticaceae (Poaceae) based on rpoA sequence data
    • Petersen, G.; Seberg, O. Phylogenetic analysis of the Triticaceae (Poaceae) based on rpoA sequence data. Mol. Phyl. Evol. 1997, 7, 217-230
    • (1997) Mol. Phyl. Evol , vol.7 , pp. 217-230
    • Petersen, G.1    Seberg, O.2
  • 11
    • 75849132587 scopus 로고    scopus 로고
    • Evaluation of 10 plant barcodes in Bryophyta (Mosses)
    • Liu, Y.; Yan, H.F.; Cao, T.; Ge, X.J. Evaluation of 10 plant barcodes in Bryophyta (Mosses). J. Syst. Evol. 2010, 48, 36-46
    • (2010) J. Syst. Evol , vol.48 , pp. 36-46
    • Liu, Y.1    Yan, H.F.2    Cao, T.3    Ge, X.J.4
  • 15
    • 80052244690 scopus 로고    scopus 로고
    • Molecular phylogeny and taxonomy of the genus Lamium L. (Lamiaceae): Disentangling origins of presumed allotetraploids
    • Bendiksby, M.; Brysting, A.K.; Thorbek, L.; Gussarova, G.; Ryding, O. Molecular phylogeny and taxonomy of the genus Lamium L. (Lamiaceae): Disentangling origins of presumed allotetraploids. Taxon 2011, 60, 986-1000
    • (2011) Taxon , vol.60 , pp. 986-1000
    • Bendiksby, M.1    Brysting, A.K.2    Thorbek, L.3    Gussarova, G.4    Ryding, O.5
  • 17
    • 0030451420 scopus 로고    scopus 로고
    • Among site rate variation and its impact on phylogenetic analyses
    • Yang, Z. Among site rate variation and its impact on phylogenetic analyses. Trends. Ecol. Evol. 1996, 11, 367-372
    • (1996) Trends. Ecol. Evol , vol.11 , pp. 367-372
    • Yang, Z.1
  • 18
    • 0032416149 scopus 로고    scopus 로고
    • Models of molecular evolution and phylogeny
    • Lió, P.; Goldman, N. Models of molecular evolution and phylogeny. Genome Res. 1998, 8, 1233-1244
    • (1998) Genome Res , vol.8 , pp. 1233-1244
    • Lió, P.1    Goldman, N.2
  • 19
  • 20
    • 34447279942 scopus 로고    scopus 로고
    • Profiling phylogenetic informativeness
    • Townsend, J.P. Profiling phylogenetic informativeness. Syst. Biol. 2007, 56, 222-231
    • (2007) Syst. Biol , vol.56 , pp. 222-231
    • Townsend, J.P.1
  • 21
    • 79955371078 scopus 로고    scopus 로고
    • Taxon sampling and the optimal rates of evolution for phylogenetic inference
    • Townsend, J.P.; Leuenberger, C. Taxon sampling and the optimal rates of evolution for phylogenetic inference. Syst. Biol. 2011, 60, 358-365
    • (2011) Syst. Biol , vol.60 , pp. 358-365
    • Townsend, J.P.1    Leuenberger, C.2
  • 22
    • 56149119671 scopus 로고    scopus 로고
    • The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree
    • Townsend, J.P.; López-Giráldez F.; Friedman, R. The phylogenetic informativeness of nucleotide and amino acid sequences for reconstructing the vertebrate tree. J. Mol. Syst. Evol. 2008, 67, 437-447
    • (2008) J. Mol. Syst. Evol , vol.67 , pp. 437-447
    • Townsend, J.P.1    López-Giráldez, F.2    Friedman, R.3
  • 23
    • 0023822631 scopus 로고
    • Relationships between gene trees and species trees
    • Pamilo, P.; Nei, M. Relationships between gene trees and species trees. Mol. Biol. Evol. 1988, 5, 568-583
    • (1988) Mol. Biol. Evol , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 24
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • Maddison, W.P.; Knowles, L.L. Inferring phylogeny despite incomplete lineage sorting. Syst. Biol. 2006, 55, 21-30
    • (2006) Syst. Biol , vol.55 , pp. 21-30
    • Maddison, W.P.1    Knowles, L.L.2
  • 25
    • 84982335352 scopus 로고
    • Cytological and experimental studies on the genus Lamium
    • Jörgensen, C.A. Cytological and experimental studies on the genus Lamium. Hereditas 1927, 9, 126-136
    • (1927) Hereditas , vol.9 , pp. 126-136
    • Jörgensen, C.A.1
  • 26
    • 44649129685 scopus 로고
    • Status of Lamium hybridum Vill. (Labiatae)
    • Jones, S.B., Jr.; Jones, C.A. Status of Lamium hybridum Vill. (Labiatae). Am. Midl. Nat. 1965, 74, 503-505
    • (1965) Am. Midl. Nat , vol.74 , pp. 503-505
    • Jones Jr., S.B.1    Jones, C.A.2
  • 27
    • 84981837475 scopus 로고
    • Cytogenetic studies on relationships between annual species of Lamium
    • Bernström, P. Cytogenetic studies on relationships between annual species of Lamium. Hereditas 1955, 41, 1-122
    • (1955) Hereditas , vol.41 , pp. 1-122
    • Bernström, P.1
  • 28
    • 0001376969 scopus 로고
    • The origin of Lamium hybridum, a case study in the search for the parents of hybrid species
    • Taylor, R. The origin of Lamium hybridum, a case study in the search for the parents of hybrid species. Northwest Sci. 1991, 65, 116-124
    • (1991) Northwest Sci , vol.65 , pp. 116-124
    • Taylor, R.1
  • 29
    • 84878433972 scopus 로고    scopus 로고
    • Květena Českě Republiky; Slavík, B., Ed.; Academia: Praha, Czech Republic
    • Dvorakova, M. Lamium L.-hluchavka. In Květena Českě Republiky; Slavík, B., Ed.; Academia: Praha, Czech Republic, 2000; Volume 6, pp. 596-603
    • Lamium L.-hluchavka , vol.6 , pp. 596-603
    • Lamium, M.1
  • 32
    • 84878469073 scopus 로고    scopus 로고
    • Botanical Garden in Kew website. Available online, accessed on 24 March
    • Botanical Garden in Kew website. Available online: http://www.kew.org/barcoding/protocols/ (accessed on 24 March 2012).
    • (2012)
  • 34
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall, T.A. BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 1999, 41, 95-98
    • (1999) Nucl. Acids. Symp. Ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 35
    • 15844406550 scopus 로고    scopus 로고
    • HyPhy: Hypothesis testing using phylogenies
    • Pond, S.L.K.; Muse, S.V. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 2005, 21, 676-679
    • (2005) Bioinformatics , vol.21 , pp. 676-679
    • Pond, S.L.K.1    Muse, S.V.2
  • 36
    • 0034848170 scopus 로고    scopus 로고
    • DAMBE: Software package for data analysis in molecular biology and evolution
    • Xia, X.; Xie, Z. DAMBE: Software package for data analysis in molecular biology and evolution. J. Hered. 2001, 92, 371-373
    • (2001) J. Hered , vol.92 , pp. 371-373
    • Xia, X.1    Xie, Z.2
  • 37
    • 79957648061 scopus 로고    scopus 로고
    • PhyDesign: An online application for profiling phylogenetic informativeness
    • doi:10.1186/1471-2148-11-152
    • Lopez-Giraldez F.; Townsend, J.P. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Evol. Biol. 2011, doi:10.1186/1471-2148-11-152
    • (2011) BMC Evol. Biol
    • Lopez-Giraldez, F.1    Townsend, J.P.2
  • 39
    • 4143051195 scopus 로고    scopus 로고
    • Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior
    • Mayrose, I.; Graur, D.; Ben-Tal, N.; Pupko, T. Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior. Mol. Biol. Evol. 2004, 21, 1781-1791
    • (2004) Mol. Biol. Evol , vol.21 , pp. 1781-1791
    • Mayrose, I.1    Graur, D.2    Ben-Tal, N.3    Pupko, T.4
  • 40
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Hulsenbeck, J.P.; Ronquist, F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001, 17, 754-755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Hulsenbeck, J.P.1    Ronquist, F.2
  • 41
    • 45849154165 scopus 로고    scopus 로고
    • j ModelTest: Phylogenetic Model Averaging
    • Posada, D. j ModelTest: Phylogenetic Model Averaging. Mol. Biol. Evol. 2008, 25, 1253-1256
    • (2008) Mol. Biol. Evol , vol.25 , pp. 1253-1256
    • Posada, D.1
  • 42
    • 84878463628 scopus 로고    scopus 로고
    • Fig Tree, version 1.4.0. Software for molecular evolution, phylogenetics and epidemiology. Available online, accessed on 05 December
    • Fig Tree, version 1.4.0. Software for molecular evolution, phylogenetics and epidemiology. Available online: http://tree.bio.ed.ac.uk/software/figtree/ (accessed on 05 December 2012).
    • (2012)
  • 43
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
    • doi:10.1093/molbev/msr121
    • Tamura, K.; Peterson, D.; Peterson, N.; Stecher, G.; Nei, M.; Kumar, S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 2011, doi:10.1093/molbev/msr121
    • (2011) Mol. Biol. Evol
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 44
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein, J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985, 39, 783-791
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 46
    • 0034982702 scopus 로고    scopus 로고
    • Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains
    • McClellan, D.A.; McCracken, K.G. Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol. Biol. Evol. 2001, 18, 917-925.
    • (2001) Mol. Biol. Evol , vol.18 , pp. 917-925
    • McClellan, D.A.1    McCracken, K.G.2


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