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Volumn 306, Issue 1, 2006, Pages 70-88

A hexapod nuclear SSU rRNA secondary-structure model and catalog of taxon-specific structural variation

Author keywords

[No Author keywords available]

Indexed keywords

RIBOSOME RNA;

EID: 33644656352     PISSN: 15525007     EISSN: 15525015     Source Type: Journal    
DOI: 10.1002/jez.b.21040     Document Type: Article
Times cited : (18)

References (48)
  • 1
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    • Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. 2000. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289:905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 2
    • 0033805074 scopus 로고    scopus 로고
    • Cirripede phylogeny using a novel approach: Molecular morphometrics
    • Billoud B, Guerucci M-A, Masselot M, Deutsch JS. 2000. Cirripede phylogeny using a novel approach: molecular morphometrics. Mol Biol Evol 17:1435-1445.
    • (2000) Mol Biol Evol , vol.17 , pp. 1435-1445
    • Billoud, B.1    Guerucci, M.-A.2    Masselot, M.3    Deutsch, J.S.4
  • 3
    • 0034509627 scopus 로고    scopus 로고
    • Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene
    • Buckley TR, Simon C, Flook PK, Misof B. 2000. Secondary structure and conserved motifs of the frequently sequenced domains IV and V of the insect mitochondrial large subunit rRNA gene. Insect Mol Biol 9:565-580.
    • (2000) Insect Mol Biol , vol.9 , pp. 565-580
    • Buckley, T.R.1    Simon, C.2    Flook, P.K.3    Misof, B.4
  • 4
    • 0036182064 scopus 로고    scopus 로고
    • Evolved RNA secondary structure and the rooting of the universal tree of life
    • Caetano-Anollés G. 2002a. Evolved RNA secondary structure and the rooting of the universal tree of life. J Mol Evol 54:333-345.
    • (2002) J Mol Evol , vol.54 , pp. 333-345
    • Caetano-Anollés, G.1
  • 5
    • 0036606550 scopus 로고    scopus 로고
    • Tracing the evolution of RNA structure in ribosomes
    • Caetano-Anollés G. 2002b. Tracing the evolution of RNA structure in ribosomes. Nucleic Acids Res 30:2575-2587.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2575-2587
    • Caetano-Anollés, G.1
  • 7
    • 33644660883 scopus 로고    scopus 로고
    • Correction
    • [Correction: BioMed Central Bioinformatics. 3:15.], http://www.rna.icmb. utexas.edu/.
    • BioMed Central Bioinformatics , vol.3 , pp. 15
  • 8
    • 1842343465 scopus 로고
    • Strongly expanded 18S rRNA genes correlated with a particular morphology in the insect order Strepsiptera
    • Chalwatzis N, Baur A, Stetzer E, Kinzelbach R, Zimmermann FK. 1995. Strongly expanded 18S rRNA genes correlated with a particular morphology in the insect order Strepsiptera. Zoology 98:115-126.
    • (1995) Zoology , vol.98 , pp. 115-126
    • Chalwatzis, N.1    Baur, A.2    Stetzer, E.3    Kinzelbach, R.4    Zimmermann, F.K.5
  • 9
    • 0033814944 scopus 로고    scopus 로고
    • Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP
    • Collins LJ, Moulton V, Penny D. 2000. Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP. J Mol Evol 51:194-204.
    • (2000) J Mol Evol , vol.51 , pp. 194-204
    • Collins, L.J.1    Moulton, V.2    Penny, D.3
  • 10
    • 1642336483 scopus 로고    scopus 로고
    • Sampling properties of the bootstrap support in molecular phylogeny: Influence of nonindependence among sites
    • Galtier N. 2004. Sampling properties of the bootstrap support in molecular phylogeny: influence of nonindependence among sites. Syst Biol 53:38-46.
    • (2004) Syst Biol , vol.53 , pp. 38-46
    • Galtier, N.1
  • 11
    • 0027236838 scopus 로고
    • Comparative studies of RNA: Inferring higher-order structure from patterns of sequence variation
    • Gutell RR. 1993. Comparative studies of RNA: inferring higher-order structure from patterns of sequence variation. Curr Opin Struct Biol 3:313-322.
    • (1993) Curr Opin Struct Biol , vol.3 , pp. 313-322
    • Gutell, R.R.1
  • 12
    • 0028071557 scopus 로고
    • Collection of small subunit (16S- and 16S-like) ribosomal RNA structures
    • Gutell RR. 1994. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures. Nucleic Acids Res 22:3502-3507.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 13
    • 0026466830 scopus 로고
    • Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
    • Gutell RR, Power A, Hertz GZ, Putz EJ, Stormo GD. 1992. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res 20:5785-5795.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5785-5795
    • Gutell, R.R.1    Power, A.2    Hertz, G.Z.3    Putz, E.J.4    Stormo, G.D.5
  • 14
    • 0036600570 scopus 로고    scopus 로고
    • The accuracy of ribosomal RNA comparative structure models
    • Gutell RR, Lee JC, Cannone JJ. 2002. The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12:301-310.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 301-310
    • Gutell, R.R.1    Lee, J.C.2    Cannone, J.J.3
  • 15
    • 0002051540 scopus 로고    scopus 로고
    • BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT
    • Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95-98.
    • (1999) Nucleic Acids Symp Ser , vol.41 , pp. 95-98
    • Hall, T.A.1
  • 16
    • 0034043777 scopus 로고    scopus 로고
    • The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence
    • Hickson RE, Simon C, Perrey SW. 2000. The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence. Mol Biol Evol 17:530-539.
    • (2000) Mol Biol Evol , vol.17 , pp. 530-539
    • Hickson, R.E.1    Simon, C.2    Perrey, S.W.3
  • 17
    • 0034522921 scopus 로고    scopus 로고
    • RNA secondary structure: Physical and computational aspects
    • Higgs PG. 2000. RNA secondary structure: physical and computational aspects. Quart Rev Biophys 33:199-253.
    • (2000) Quart Rev Biophys , vol.33 , pp. 199-253
    • Higgs, P.G.1
  • 20
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker IL, Fekete M, Stadler P. 2002. Secondary structure prediction for aligned RNA sequences. J Mol Biol 319:1059-1066.
    • (2002) J Mol Biol , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.3
  • 21
    • 0141721420 scopus 로고    scopus 로고
    • RNA-based phylogenetic methods: Application to mammalian mitochondrial RNA sequences
    • Hudelot C, Gowri-Shankar V, Jow H, Rattray M, Higgs PG. 2003. RNA-based phylogenetic methods: Application to mammalian mitochondrial RNA sequences. Mol Phylogenet Evol 28:241-252.
    • (2003) Mol Phylogenet Evol , vol.28 , pp. 241-252
    • Hudelot, C.1    Gowri-Shankar, V.2    Jow, H.3    Rattray, M.4    Higgs, P.G.5
  • 22
    • 0036728808 scopus 로고    scopus 로고
    • Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution
    • Jow H, Hudelot C, Rattray M, Higgs PG. 2002. Bayesian phylogenetics using an RNA substitution model applied to early mammalian evolution. Mol Biol Evol 19:1591-1601.
    • (2002) Mol Biol Evol , vol.19 , pp. 1591-1601
    • Jow, H.1    Hudelot, C.2    Rattray, M.3    Higgs, P.G.4
  • 23
    • 0029365329 scopus 로고
    • Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: An example of alignment and data presentation from frogs
    • Kjer KM. 1995. Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from frogs. Mol Phylogenet Evol 4:314-330.
    • (1995) Mol Phylogenet Evol , vol.4 , pp. 314-330
    • Kjer, K.M.1
  • 24
    • 3242721251 scopus 로고    scopus 로고
    • Aligned 18S and insect phylogeny
    • Kjer KM. 2004. Aligned 18S and insect phylogeny. Syst Biol 53:506-514.
    • (2004) Syst Biol , vol.53 , pp. 506-514
    • Kjer, K.M.1
  • 25
    • 0034025097 scopus 로고    scopus 로고
    • Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures
    • Lydeard C, Holznagel WE, Schnare MN, Gutell RR. 2000. Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures. Mol Phylogenet Evol 15:83-102.
    • (2000) Mol Phylogenet Evol , vol.15 , pp. 83-102
    • Lydeard, C.1    Holznagel, W.E.2    Schnare, M.N.3    Gutell, R.R.4
  • 26
    • 0001705679 scopus 로고    scopus 로고
    • Phylogeny of the carabid bettles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae)
    • Maddison DR, Baker MD, Ober KA. 1999. Phylogeny of the carabid bettles as inferred from 18S ribosomal DNA (Coleoptera: Carabidae). Syst Entomol 24:103-138.
    • (1999) Syst Entomol , vol.24 , pp. 103-138
    • Maddison, D.R.1    Baker, M.D.2    Ober, K.A.3
  • 27
    • 0344664006 scopus 로고    scopus 로고
    • Comparative analysis of mt 16S rRNA secondary structures of Odonates and its relevance to phylogenetic problems in insect systematics
    • Misof B, Fleck G. 2003. Comparative analysis of mt 16S rRNA secondary structures of Odonates and its relevance to phylogenetic problems in insect systematics. Insect Mol Biol 12:535-547.
    • (2003) Insect Mol Biol , vol.12 , pp. 535-547
    • Misof, B.1    Fleck, G.2
  • 28
    • 0036789261 scopus 로고    scopus 로고
    • An empirical analysis of mt 16S rRNA covarion-like evolution in insects: Site-specific rate variation is clustered and frequently detected
    • Misof B, Anderson CL, Buckley TR, Erpenbeck D, Rickert A, Misof K. 2002. An empirical analysis of mt 16S rRNA covarion-like evolution in insects: site-specific rate variation is clustered and frequently detected. J Mol Evol 55:460-469.
    • (2002) J Mol Evol , vol.55 , pp. 460-469
    • Misof, B.1    Anderson, C.L.2    Buckley, T.R.3    Erpenbeck, D.4    Rickert, A.5    Misof, K.6
  • 30
    • 0033775948 scopus 로고    scopus 로고
    • 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, Hemiptera)
    • Ouvrard D, Campbell BC, Bourgoin T, Chan KL. 2000. 18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, Hemiptera). Mol Phylogenet Evol 16:403-417.
    • (2000) Mol Phylogenet Evol , vol.16 , pp. 403-417
    • Ouvrard, D.1    Campbell, B.C.2    Bourgoin, T.3    Chan, K.L.4
  • 31
    • 0034667925 scopus 로고    scopus 로고
    • Comparative analysis of secondary structure of insect mitochomdrial small subunit ribosomal RNA using maximum weighted matching
    • Page RDM. 2000. Comparative analysis of secondary structure of insect mitochomdrial small subunit ribosomal RNA using maximum weighted matching. Nucleic Acids Res 28:3839-3845.
    • (2000) Nucleic Acids Res , vol.28 , pp. 3839-3845
    • Page, R.D.M.1
  • 32
    • 0035984509 scopus 로고    scopus 로고
    • Louse (Insecta: Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable
    • Page RDM, Cruickshank R, Johnson KP. 2002. Louse (Insecta: Phthiraptera) mitochondrial 12S rRNA secondary structure is highly variable. Insect Mol Biol 11:361-369.
    • (2002) Insect Mol Biol , vol.11 , pp. 361-369
    • Page, R.D.M.1    Cruickshank, R.2    Johnson, K.P.3
  • 33
    • 0033980890 scopus 로고    scopus 로고
    • Comparative sequence analysis and patterns of covariation in RNA secondary structures
    • Parsch J, Braverman JM, Stephan W. 2000. Comparative sequence analysis and patterns of covariation in RNA secondary structures. Genetics 154:909-921.
    • (2000) Genetics , vol.154 , pp. 909-921
    • Parsch, J.1    Braverman, J.M.2    Stephan, W.3
  • 36
    • 0030829855 scopus 로고    scopus 로고
    • RnaViz, a program for the visualisation of RNA secondary structure
    • de Rijk P, de Wachter R. 1997. RnaViz, a program for the visualisation of RNA secondary structure. Nucleic Acids Res 25:4679-4684.
    • (1997) Nucleic Acids Res , vol.25 , pp. 4679-4684
    • De Rijk, P.1    De Wachter, R.2
  • 37
    • 0029091043 scopus 로고
    • Estimating substitution rates in ribosomal RNA
    • Rzhetsky A. 1995. Estimating substitution rates in ribosomal RNA. Genetics 141:771-783.
    • (1995) Genetics , vol.141 , pp. 771-783
    • Rzhetsky, A.1
  • 38
    • 0035156561 scopus 로고    scopus 로고
    • RNA sequence evolution with secondary structure constraints: Comparison of substitution rate models using maximum likelihood methods
    • Savill NJ, Hoyle DC, Higgs PG. 2001. RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum likelihood methods. Genetics 157:399-411.
    • (2001) Genetics , vol.157 , pp. 399-411
    • Savill, N.J.1    Hoyle, D.C.2    Higgs, P.G.3
  • 39
    • 0028512129 scopus 로고
    • A stochastic model for the evolution of autocorrelated DNA sequences
    • Schoeniger M, von Haeseler A. 1994. A stochastic model for the evolution of autocorrelated DNA sequences. Mol Phylogenet Evol 3:240-247.
    • (1994) Mol Phylogenet Evol , vol.3 , pp. 240-247
    • Schoeniger, M.1    Von Haeseler, A.2
  • 40
    • 0029784930 scopus 로고    scopus 로고
    • The rate of compensatory evolution
    • Stephan W. 1996. The rate of compensatory evolution. Genetics 144:419-426.
    • (1996) Genetics , vol.144 , pp. 419-426
    • Stephan, W.1
  • 41
    • 0031730497 scopus 로고    scopus 로고
    • An RNA folding method capable of identifying pseudoknots and base triples
    • Tabaska JE, Cary RB, Gabow HN, Stormo GD. 1998. An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics 14:691-699.
    • (1998) Bioinformatics , vol.14 , pp. 691-699
    • Tabaska, J.E.1    Cary, R.B.2    Gabow, H.N.3    Stormo, G.D.4
  • 42
    • 0034700136 scopus 로고    scopus 로고
    • Molecular phylogenetic analysis of evolutionary trends in stonefly wing structure and locomotor behavior
    • USA
    • Thomas MA, Walsh KA, Wolf MR, McPheron BA, Marden JH. 2000. Molecular phylogenetic analysis of evolutionary trends in stonefly wing structure and locomotor behavior. Proc Natl Acad Sci USA 97:13178-13183.
    • (2000) Proc Natl Acad Sci , vol.97 , pp. 13178-13183
    • Thomas, M.A.1    Walsh, K.A.2    Wolf, M.R.3    McPheron, B.A.4    Marden, J.H.5
  • 43
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. 1997. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876-4882.
    • (1997) Nucleic Acids Res , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 44
    • 0028874337 scopus 로고
    • Neighbor joining and the maximum likelihood with RNA sequences: Addressing the interdependence of sites
    • Tillier ERM, Collins RA. 1995. Neighbor joining and the maximum likelihood with RNA sequences: addressing the interdependence of sites. Mol Biol Evol 12:7-15.
    • (1995) Mol Biol Evol , vol.12 , pp. 7-15
    • Tillier, E.R.M.1    Collins, R.A.2
  • 45
    • 0031894830 scopus 로고    scopus 로고
    • High apparent rate of simultaneous compensatory base pair substitutions in ribosomal RNA
    • Tillier ERM, Collins RA. 1998. High apparent rate of simultaneous compensatory base pair substitutions in ribosomal RNA. Genetics 148:1993-2002.
    • (1998) Genetics , vol.148 , pp. 1993-2002
    • Tillier, E.R.M.1    Collins, R.A.2
  • 46
    • 0030208308 scopus 로고    scopus 로고
    • Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania)
    • Titus TA, Frost DR. 1996. Molecular homology assessment and phylogeny in the lizard family Opluridae (Squamata: Iguania). Mol Phylogenet Evol 6:49-62.
    • (1996) Mol Phylogenet Evol , vol.6 , pp. 49-62
    • Titus, T.A.1    Frost, D.R.2
  • 47
    • 0035945246 scopus 로고    scopus 로고
    • Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA
    • Wuyts J, Van de Peer Y, de Wachter R. 2001. Distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal RNA. Nucleic Acids Res 29:5017-5028.
    • (2001) Nucleic Acids Res , vol.29 , pp. 5017-5028
    • Wuyts, J.1    Van De Peer, Y.2    De Wachter, R.3


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