메뉴 건너뛰기




Volumn 58, Issue 1, 2012, Pages 49-58

Reconstruction of structural evolution in the trnL intron P6b loop of symbiotic Nostoc (Cyanobacteria)

Author keywords

Homoplasy; Indels; Lichens; Nostoc; RNA secondary structure

Indexed keywords

ARTICLE; BACTERIAL GENE; CLADISTICS; CONTROLLED STUDY; GENOTYPE; HOMOPLASY; INDEL MUTATION; INTRON; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; NOSTOC; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; SPECIES IDENTIFICATION; STRUCTURAL EVOLUTION;

EID: 84857043121     PISSN: 01728083     EISSN: 14320983     Source Type: Journal    
DOI: 10.1007/s00294-011-0364-0     Document Type: Article
Times cited : (15)

References (45)
  • 2
    • 0034104829 scopus 로고    scopus 로고
    • The cyanobacterial origin and vertical transmission of the plastid tRNA(Leu) group-I intron
    • A Besendahl Y-L Qiu J Lee JD Palmer D Bhattacharya 2000 The cyanobacterial origin and vertical transmission of the plastid tRNALeu group-I-intron Curr Genet 37 12 23 10672439 10.1007/s002940050002 1:CAS:528:DC%2BD3cXitFartQ%3D%3D (Pubitemid 30160672)
    • (2000) Current Genetics , vol.37 , Issue.1 , pp. 12-23
    • Besendahl, A.1    Qiu, Y.-L.2    Lee, J.3    Palmer, J.D.4    Bhattacharya, D.5
  • 3
    • 0037594762 scopus 로고    scopus 로고
    • Noncoding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms
    • DOI 10.1046/j.1420-9101.2003.00577.x
    • T Borsch W Hilu D Quandt V Wilde C Neinhuis W Barthlott 2003 Non-coding plastid trnT-trnF sequences reveal a well resolved phylogeny of basal angiosperms J Evol Biol 16 558 576 14632220 10.1046/j.1420-9101.2003.00577.x 1:CAS:528:DC%2BD3sXmtVOisbY%3D (Pubitemid 36832255)
    • (2003) Journal of Evolutionary Biology , vol.16 , Issue.4 , pp. 558-576
    • Borsch, T.1    Hilu, K.W.2    Quandt, D.3    Wilde, V.4    Neinhuis, C.5    Barthlott, W.6
  • 4
    • 0036275713 scopus 로고    scopus 로고
    • Leu (UAA) intron: Evolutionary patterns in a genetic marker
    • Costa J-L, Paulsrud P, Lindblad P (2002) The cyanobacterial tRNALeu (UAA) intron: evolutionary patterns in a genetic marker. Mol Biol Evol 19(6):850-857 (Pubitemid 34602955)
    • (2002) Molecular Biology and Evolution , vol.19 , Issue.6 , pp. 850-857
    • Costa, J.-L.1    Paulsrud, P.2    Lindblad, P.3
  • 5
    • 0035458439 scopus 로고    scopus 로고
    • Genetic Diversity of Nostoc Symbionts Endophytically Associated with Two Bryophyte Species
    • DOI 10.1128/AEM.67.9.4393-4396.2001
    • J-L Costa P Paulsrud J Rikkinen P Lindblad 2001 Genetic diversity of Nostoc endophytically associated with two bryophyte species Appl Environ Microbiol 67 4393 4396 11526056 10.1128/AEM.67.9.4393-4396.2001 1:CAS:528:DC%2BD3MXmslWit7w%3D (Pubitemid 33641749)
    • (2001) Applied and Environmental Microbiology , vol.67 , Issue.9 , pp. 4393-4396
    • Costa, J.-L.1    Paulsrud, P.2    Rikkinen, J.3    Lindblad, P.4
  • 6
    • 0043285072 scopus 로고    scopus 로고
    • A partition function algorithm for nucleic acid secondary structure including pseudoknots
    • 12926009 10.1002/jcc.10296 1:CAS:528:DC%2BD3sXntFentL0%3D
    • RM Dirks NA Pierce 2003 A partition function algorithm for nucleic acid secondary structure including pseudoknots J Comput Chem 24 1664 1677 12926009 10.1002/jcc.10296 1:CAS:528:DC%2BD3sXntFentL0%3D
    • (2003) J Comput Chem , vol.24 , pp. 1664-1677
    • Dirks, R.M.1    Pierce, N.A.2
  • 7
    • 3042554001 scopus 로고    scopus 로고
    • An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots
    • 15139042 10.1002/jcc.20057 1:CAS:528:DC%2BD2cXltFOju74%3D
    • RM Dirks NA Pierce 2004 An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots J Comput Chem 25 1295 1304 15139042 10.1002/jcc.20057 1:CAS:528:DC%2BD2cXltFOju74%3D
    • (2004) J Comput Chem , vol.25 , pp. 1295-1304
    • Dirks, R.M.1    Pierce, N.A.2
  • 8
    • 33847609597 scopus 로고    scopus 로고
    • Thermodynamic analysis of interacting nucleic acid strands
    • DOI 10.1137/060651100
    • RM Dirks JS Bois JM Schaeffer E Winfree NA Pierce 2007 Thermodynamic analysis of interacting nucleic acid strands SIAM Rev 49 65 88 10.1137/060651100 (Pubitemid 46351352)
    • (2007) SIAM Review , vol.49 , Issue.1 , pp. 65-88
    • Dirks, R.M.1    Bois, J.S.2    Schaeffer, J.M.3    Winfree, E.4    Pierce, N.A.5
  • 9
    • 50649084154 scopus 로고    scopus 로고
    • Very small mobile repeated elements in cyanobacterial genomes
    • 18599681 10.1101/gr.074336.107 1:CAS:528:DC%2BD1cXhtV2qsr3K
    • J Elhai M Kato S Cousins P Lindblad JL Costa 2008 Very small mobile repeated elements in cyanobacterial genomes Genome Res 18 1484 1499 18599681 10.1101/gr.074336.107 1:CAS:528:DC%2BD1cXhtV2qsr3K
    • (2008) Genome Res , vol.18 , pp. 1484-1499
    • Elhai, J.1    Kato, M.2    Cousins, S.3    Lindblad, P.4    Costa, J.L.5
  • 10
    • 48749114090 scopus 로고    scopus 로고
    • Phylogenetic patterns among Nostoc cyanobionts within bi- and tripartite lichens of the genus Pannaria
    • Elvebakk A, Papaefthimiou D, Robertsen EH, Liaimer A (2008) Phylogenetic patterns among Nostoc cyanobionts within bi- and tripartite lichens of the genus Pannaria. J Phycol 44:1049-1059
    • (2008) J Phycol , vol.44 , pp. 1049-1059
    • Elvebakk, A.1    Papaefthimiou, D.2    Robertsen, E.H.3    Liaimer, A.4
  • 11
    • 79955653031 scopus 로고    scopus 로고
    • Genotype variability of Nostoc symbionts associated with three epiphytic Nephroma species in a boreal forest landscape
    • 10.1639/0007-2745-114.1.220
    • K Fedrowitz U Kaasalainen J Rikkinen 2011 Genotype variability of Nostoc symbionts associated with three epiphytic Nephroma species in a boreal forest landscape The Bryologist 114 1 220 230 10.1639/0007-2745-114.1.220
    • (2011) The Bryologist , vol.114 , Issue.1 , pp. 220-230
    • Fedrowitz, K.1    Kaasalainen, U.2    Rikkinen, J.3
  • 12
    • 58249096079 scopus 로고    scopus 로고
    • An evaluation of four phylogenetic markers in Nostoc: Implications for cyanobacterial phylogenetic studies at the intragenic level
    • 18972163 10.1007/s00284-008-9302-x 1:CAS:528:DC%2BD1MXksVSgsQ%3D%3D
    • D Han Y Fan Z Hu 2009 An evaluation of four phylogenetic markers in Nostoc: implications for cyanobacterial phylogenetic studies at the intragenic level Curr Microbiol 58 170 176 18972163 10.1007/s00284-008-9302-x 1:CAS:528:DC%2BD1MXksVSgsQ%3D%3D
    • (2009) Curr Microbiol , vol.58 , pp. 170-176
    • Han, D.1    Fan, Y.2    Hu, Z.3
  • 13
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • JP Huelsenbeck F Ronquist 2001 MrBayes: bayesian inference of phylogenetic trees Bioinformatics 17 754 755 11524383 10.1093/bioinformatics/17. 8.754 1:STN:280:DC%2BD3MvotV2isw%3D%3D (Pubitemid 32851390)
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 14
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • DOI 10.1126/science.1065889
    • JP Huelsenbeck F Ronquist R Nielsen JP Bollback 2001 Bayesian inference of phylogeny and its impact on evolutionary biology Science 294 2310 2314 11743192 10.1126/science.1065889 1:CAS:528:DC%2BD3MXptFGkt7k%3D (Pubitemid 33140548)
    • (2001) Science , vol.294 , Issue.5550 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 15
    • 0036806280 scopus 로고    scopus 로고
    • Potential applications and pitfalls of Bayesian inference of phylogeny
    • DOI 10.1080/10635150290102366
    • JP Huelsenbeck B Larget RE Miller F Ronquist 2002 Potential applications and pitfalls of bayesian inference of phylogeny Syst Biol 51 673 688 12396583 10.1080/10635150290102366 (Pubitemid 35294801)
    • (2002) Systematic Biology , vol.51 , Issue.5 , pp. 673-688
    • Huelsenbeck, J.P.1    Larget, B.2    Miller, R.E.3    Ronquist, F.4
  • 16
    • 0034491886 scopus 로고    scopus 로고
    • The evolution of non-coding chloroplast DNA and its application in plant systematics
    • SA Kelchner 2000 The evolution of non-coding chloroplast DNA and its application in plant systematics Ann Mo Bot Gard 87 482 498 10.2307/2666142 (Pubitemid 32116916)
    • (2000) Annals of the Missouri Botanical Garden , vol.87 , Issue.4 , pp. 482-498
    • Kelchner, S.A.1
  • 17
    • 0031306828 scopus 로고    scopus 로고
    • Molecular Evolution and Phylogenetic Utility of the Chloroplastrpl16Intron inChusqueaand the Bambusoideae (Poaceae)
    • DOI 10.1006/mpev.1997.0432, PII S1055790397904322
    • SA Kelchner LG Clark 1997 Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae) Mol Phyl Evol 8 385 397 10.1006/mpev.1997.0432 1:CAS:528:DyaK1cXjtVensw%3D%3D (Pubitemid 127347897)
    • (1997) Molecular Phylogenetics and Evolution , vol.8 , Issue.3 , pp. 385-397
    • Kelchner, S.A.1    Clark, L.G.2
  • 18
    • 0029811392 scopus 로고    scopus 로고
    • Hairpins create minute inversions in non coding regions of chloroplast DNA
    • DOI 10.1007/s002940050130
    • SA Kelchner JF Wendel 1996 Hairpins create minute inversions in non-coding regions of chloroplast DNA Curr Genet 30 259 262 8753656 10.1007/s002940050130 1:CAS:528:DyaK28XlvVCgtL8%3D (Pubitemid 26336192)
    • (1996) Current Genetics , vol.30 , Issue.3 , pp. 259-262
    • Kelchner, S.A.1    Wendel, J.F.2
  • 21
    • 33748594712 scopus 로고    scopus 로고
    • Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: Contrasting matK, trnT-F, and rbcL in basal angiosperms
    • DOI 10.1016/j.ympev.2006.06.017, PII S1055790306002624
    • KF Müller T Borsch WH Khidir 2006 Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnF, and rbcL in basal angiosperms Mol Phyl Evol 41 99 117 10.1016/j.ympev.2006.06.017 (Pubitemid 44376584)
    • (2006) Molecular Phylogenetics and Evolution , vol.41 , Issue.1 , pp. 99-117
    • Muller, K.F.1    Borsch, T.2    Hilu, K.W.3
  • 22
    • 0033504552 scopus 로고    scopus 로고
    • The parsimony ratchet, a new method for rapid parsimony analysis
    • DOI 10.1006/clad.1999.0121
    • KC Nixon 1999 The parsimony ratchet, a new method for rapid parsimony analysis Cladistics 15 407 414 10.1111/j.1096-0031.1999.tb00277.x (Pubitemid 30203167)
    • (1999) Cladistics , vol.15 , Issue.4 , pp. 407-414
    • Nixon, K.C.1
  • 23
    • 28744439007 scopus 로고    scopus 로고
    • Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen fungus Peltigera
    • DOI 10.1080/09670260500342647
    • O'Brien H, Miadlikowska J, Lutzoni F (2005) Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen fungus Peltigera. Eur J Phycol 40:363-378 (Pubitemid 41759249)
    • (2005) European Journal of Phycology , vol.40 , Issue.4 , pp. 363-378
    • O'Brien, H.E.1    Miadlikowska, J.2    Lutzoni, F.3
  • 24
    • 2942672571 scopus 로고    scopus 로고
    • Repeat-type distribution in trnL intron does not correspond with species phylogeny: Comparison of the genetic markers 16S rRNA and trnL intron in heterocystous cyanobacteria
    • DOI 10.1099/ijs.0.02928-0
    • I Oksanen K Lohtander K Sivonen J Rikkinen 2004 Repeat type distribution in trnL intron does not correspond with species phylogeny: comparison of the genetic markers 16S rRNA and trnL intron in heterocystous cyanobacteria Int J Syst Evol Microbiol 54 765 772 15143022 10.1099/ijs.0.02928-0 1:CAS:528:DC%2BD2cXlt1ems7o%3D (Pubitemid 38771778)
    • (2004) International Journal of Systematic and Evolutionary Microbiology , vol.54 , Issue.3 , pp. 765-772
    • Oksanen, I.1    Lohtander, K.2    Sivonen, K.3    Rikkinen, J.4
  • 25
    • 9744245452 scopus 로고    scopus 로고
    • Bayesian estimation of ancestral character states on phylogenies
    • DOI 10.1080/10635150490522232
    • M Pagel A Meade 2004 A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data Syst Biol 53 571 581 15371247 10.1080/10635150490522232 (Pubitemid 39579641)
    • (2004) Systematic Biology , vol.53 , Issue.5 , pp. 673-684
    • Pagel, M.1    Meade, A.2    Barker, D.3
  • 26
    • 0030690292 scopus 로고    scopus 로고
    • Origin and evolution of group I introns in cyanobacterial tRNA genes
    • B Paquin SD Kathe SA Nierzwicki-Bauer DA Shub 1997 Origin and evolution of group-I introns in cyanobacterial tRNA genes J Bacteriol 179 6798 6806 9352932 1:CAS:528:DyaK2sXnt1arsrc%3D (Pubitemid 27465317)
    • (1997) Journal of Bacteriology , vol.179 , Issue.21 , pp. 6798-6806
    • Paquin, B.1    Kathe, S.D.2    Nierzwicki-Bauer, S.A.3    Shub, D.A.4
  • 27
    • 0031985854 scopus 로고    scopus 로고
    • Sequence variation of the tRNA(Leu) intron as a marker for genetic diversity and specificity of symbiotic cyanobacteria in some lichens
    • P Paulsrud P Lindblad 1998 Sequence variation of the tRNALeu intron as a marker for genetic diversity and specificity of symbiotic cyanobacteria in some lichens Appl Environ Microbiol 64 310 315 9435083 1:CAS:528:DyaK1cXitVaqtA%3D%3D (Pubitemid 28040330)
    • (1998) Applied and Environmental Microbiology , vol.64 , Issue.1 , pp. 310-315
    • Paulsrud, P.1    Lindblad, P.2
  • 28
    • 0031926150 scopus 로고    scopus 로고
    • Cyanobiont specificity in some Nostoc-containing lichens and in a Peltigera aphthosa photosymbiodeme
    • DOI 10.1046/j.1469-8137.1998.00220.x
    • P Paulsrud J Rikkinen P Lindblad 1998 Cyanobiont specificity in some Nostoc-containing lichens and in a Peltigera aphthosa photosymbiodeme New Phytol 139 517 524 10.1046/j.1469-8137.1998.00220.x 1:CAS:528:DyaK1cXlsleqsbc%3D (Pubitemid 28362069)
    • (1998) New Phytologist , vol.139 , Issue.3 , pp. 517-524
    • Paulsrud, P.1    Rikkinen, J.2    Lindblad, P.3
  • 29
    • 0034072472 scopus 로고    scopus 로고
    • Spatial patterns of photobiont diversity in some Nostoc-containing lichens
    • DOI 10.1046/j.1469-8137.2000.00647.x
    • P Paulsrud J Rikkinen P Lindblad 2000 Spatial patterns of photobiont diversity in some Nostoc-containing lichens New Phytol 146 291 299 10.1046/j.1469-8137.2000.00647.x (Pubitemid 30334185)
    • (2000) New Phytologist , vol.146 , Issue.2 , pp. 291-299
    • Paulsrud, P.1    Rikkinen, J.2    Lindblad, P.3
  • 30
    • 0034784382 scopus 로고    scopus 로고
    • Field investigations on cyanobacterial specificity in Peltigera aphthosa
    • DOI 10.1046/j.0028-646x.2001.00234.x
    • P Paulsrud J Rikkinen P Lindblad 2001 Field investigations on cyanobacterial specificity in Peltigera aphthosa New Phytol 152 117 123 10.1046/j.0028-646x.2001.00234.x (Pubitemid 32943694)
    • (2001) New Phytologist , vol.152 , Issue.1 , pp. 117-123
    • Paulsrud, P.1    Rikkinen, J.2    Lindblad, P.3
  • 31
    • 34347334360 scopus 로고    scopus 로고
    • Ancient paralogy in the cpDNA trnL-F region in Annonaceae: Implications for plant molecular systematics
    • DOI 10.3732/ajb.94.6.1003
    • MD Pirie MP Balcázar Vargas M Botermans F Bakker LW Chatrou 2007 Ancient paralogy in the cpDNA trnL-F region in Annonaceae: implications for plant molecular systematic Am J Bot 94 1003 1016 21636470 10.3732/ajb.94.6.1003 (Pubitemid 47013708)
    • (2007) American Journal of Botany , vol.94 , Issue.6 , pp. 1003-1016
    • Pirie, M.D.1    Vargas, M.P.B.2    Botermans, M.3    Bakker, F.T.4    Chatrou, L.W.5
  • 32
    • 23744492971 scopus 로고    scopus 로고
    • UAA intron in bryophytes
    • DOI 10.1016/j.ympev.2005.03.014, PII S1055790305000898
    • D Quandt M Stech 2005 Molecular evolution of the trnL (UAA) intron in bryophytes Mol Phylogenet Evol 36 429 443 16005648 10.1016/j.ympev.2005.03.014 1:CAS:528:DC%2BD2MXnslyjtL0%3D (Pubitemid 41138882)
    • (2005) Molecular Phylogenetics and Evolution , vol.36 , Issue.3 , pp. 429-443
    • Quandt, D.1    Stech, M.2
  • 35
    • 0037135145 scopus 로고    scopus 로고
    • Lichen guilds share related cyanobacterial symbionts
    • DOI 10.1126/science.1072961
    • Rikkinen J, Oksanen I, Lohtander K (2002) Lichen guild share related cyanobacterial symbionts. Science 297(5580):357 (Pubitemid 34790757)
    • (2002) Science , vol.297 , Issue.5580 , pp. 357
    • Rikkinen, J.1    Oksanen, I.2    Lohtander, K.3
  • 36
    • 0033056104 scopus 로고    scopus 로고
    • Complex evolutionary patterns of tRNA(UAA)/(Leu) group I introns in cyanobacterial radiation
    • K Rudi KS Jakobsen 1999 Complex evolutionary patterns of tRNALeu (UAA) group-I introns in cyanobacterial radiation J Bacteriol 181 3445 3451 10348857 1:CAS:528:DyaK1MXjs1yrurc%3D (Pubitemid 29259295)
    • (1999) Journal of Bacteriology , vol.181 , Issue.11 , pp. 3445-3451
    • Rudi, K.1    Jakobsen, K.S.2
  • 37
    • 0036174167 scopus 로고    scopus 로고
    • Leu(UAA) group I intron by both horizontal intron transfer and recombination of the entire tRNA locus
    • Leu (UAA) group I intron by both horizontal intron transfer and recombination of the entire tRNA locus J Bacteriol 184 666 671 11790735 10.1128/JB.184.3.666-671.2002 1:CAS:528:DC%2BD38XntVGhsQ%3D%3D (Pubitemid 34150212)
    • (2002) Journal of Bacteriology , vol.184 , Issue.3 , pp. 666-671
    • Rudi, K.1    Fossheim, T.2    Jakobsen, K.S.3
  • 38
    • 0346735286 scopus 로고    scopus 로고
    • Phylogeny and Self-Splicing Ability of the Plastid tRNA-Leu Group I Intron
    • DOI 10.1007/s00239-003-2533-3
    • D Simon D Fewer T Friedl D Bhattacharya 2003 Phylogeny and self-splicing ability of the plastid tRNA-Leu group I intron J Mol Evol 57 710 720 14745540 10.1007/s00239-003-2533-3 1:CAS:528:DC%2BD2cXjsVemtQ%3D%3D (Pubitemid 37543985)
    • (2003) Journal of Molecular Evolution , vol.57 , Issue.6 , pp. 710-720
    • Simon, D.1    Fewer, D.2    Friedl, T.3    Bhattacharya, D.4
  • 39
    • 70350340383 scopus 로고    scopus 로고
    • When morphology and molecules tell us different stories: A case-in-point with Leptodon corsicus, a new and unique endemic moss species from Corsica
    • 10.1179/174328209X455299
    • A Sotiaux J Enroth S Olsson D Quandt A Vanderpoorten 2009 When morphology and molecules tell us different stories: a case-in-point with Leptodon corsicus, a new and unique endemic moss species from Corsica J Bryol 31 186 196 10.1179/174328209X455299
    • (2009) J Bryol , vol.31 , pp. 186-196
    • Sotiaux, A.1    Enroth, J.2    Olsson, S.3    Quandt, D.4    Vanderpoorten, A.5
  • 40
    • 75149150388 scopus 로고    scopus 로고
    • TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses
    • 20051126 10.1186/1471-2105-11-7
    • BC Stöver KF Müller 2010 TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses BMC Bioinformatics 11 7 20051126 10.1186/1471-2105-11-7
    • (2010) BMC Bioinformatics , vol.11 , pp. 7
    • Stöver, B.C.1    Müller, K.F.2
  • 45
    • 0024477261 scopus 로고
    • On findings all suboptimal foldings of an RNA molecule
    • M Zuker 1989 On finding all suboptimal foldings of an RNA molecule Science 244 48 52 2468181 10.1126/science.2468181 1:CAS:528:DyaL1MXkt1SnsbY%3D (Pubitemid 19130742)
    • (1989) Science , vol.244 , Issue.4900 , pp. 48-52
    • Zuker, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.