메뉴 건너뛰기




Volumn 21, Issue 7, 2004, Pages 1445-1454

The chloroplast genome of Nymphaea alba: Whole-genome analyses and the problem of identifying the most basal angiosperm

Author keywords

Angiosperms; Chloroplast genomes; Gymnosperms; Molecular evolution; Nymphaea; Substitution rates

Indexed keywords

CHLOROPLAST DNA; NUCLEOTIDE;

EID: 3042683994     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh147     Document Type: Article
Times cited : (111)

References (49)
  • 1
    • 0037162534 scopus 로고    scopus 로고
    • Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution
    • Adams, K. L., Y. L. Qiu, M. Stoutemyer, and J. D. Palmer. 2002. Punctuated evolution of mitochondrial gene content: High and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc. Natl. Acad. Sci. USA 99:9905-9912.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 9905-9912
    • Adams, K.L.1    Qiu, Y.L.2    Stoutemyer, M.3    Palmer, J.D.4
  • 4
    • 0037819441 scopus 로고    scopus 로고
    • Widespread horizontal transfer of mitochondrial genes in flowering plants
    • Bergthorsson, U., K. L. Adams, B. Thomason, and J. D. Palmer. 2003. Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197-201.
    • (2003) Nature , vol.424 , pp. 197-201
    • Bergthorsson, U.1    Adams, K.L.2    Thomason, B.3    Palmer, J.D.4
  • 5
    • 1542347067 scopus 로고    scopus 로고
    • Neighbor-net: An agglomerative method for the construction of phylogenetic networks
    • Bryant, D., and Moulton, V. 2004. Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol. 21:255-265.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 255-265
    • Bryant, D.1    Moulton, V.2
  • 8
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
    • (1998) Genome Res. , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 9
    • 0000122573 scopus 로고
    • PHYLIP (phylogeny inference package). Version 3.2
    • Felsenstein, J. 1989. PHYLIP (phylogeny inference package). Version 3.2. Cladistics 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 10
    • 0035868707 scopus 로고    scopus 로고
    • Fossil evidence of water lilies (Nymphaeales) in the early Cretaceous
    • Friis, E. M., K. R. Pedersen, and P. R. Crane. 2001. Fossil evidence of water lilies (Nymphaeales) in the early Cretaceous. Nature 410:357-360.
    • (2001) Nature , vol.410 , pp. 357-360
    • Friis, E.M.1    Pedersen, K.R.2    Crane, P.R.3
  • 11
    • 0030970362 scopus 로고    scopus 로고
    • Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: Revised molecular estimates of two seed plant divergence times
    • Goremykin, V., S. Hansmann, and W. Martin. 1997. Evolutionary analysis of 58 proteins encoded in six completely sequenced chloroplast genomes: revised molecular estimates of two seed plant divergence times. Plant Syst. Evol. 206:337-351.
    • (1997) Plant Syst. Evol. , vol.206 , pp. 337-351
    • Goremykin, V.1    Hansmann, S.2    Martin, W.3
  • 12
    • 0041834716 scopus 로고    scopus 로고
    • Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm
    • Goremykin, V. V., K. I. Hirsch-Ernst, S. Wölfl, and F. H. Hellwig. 2003a. Analysis of the Amborella trichopoda chloroplast genome sequence suggests that Amborella is not a basal angiosperm. Mol. Biol. Evol. 20:14499-14505.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 14499-14505
    • Goremykin, V.V.1    Hirsch-Ernst, K.I.2    Wölfl, S.3    Hellwig, F.H.4
  • 13
    • 0042150196 scopus 로고    scopus 로고
    • The chloroplast genome of the "basal" angiosperm Calycanthus fertilis-structural and phylogenetic analyses
    • -. 2003b. The chloroplast genome of the "basal" angiosperm Calycanthus fertilis-structural and phylogenetic analyses. Plant Syst. Evol. 242:119-135.
    • (2003) Plant Syst. Evol. , vol.242 , pp. 119-135
  • 14
    • 0033666273 scopus 로고    scopus 로고
    • Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms
    • Graham, S. W., and R. G. Olmstead. 2000. Utility of 17 chloroplast genes for inferring the phylogeny of the basal angiosperms. Am. J. Bot. 87:1712-1730.
    • (2000) Am. J. Bot. , vol.87 , pp. 1712-1730
    • Graham, S.W.1    Olmstead, R.G.2
  • 15
    • 0039896642 scopus 로고
    • Untersuchungen über die entwicklung des embryos und der keimpflanze von nuphar luteum
    • Guttenberg, H. V., and R. Müller-Schröder. 1958. Untersuchungen über die Entwicklung des Embryos und der Keimpflanze von Nuphar luteum. Planta 51:481-510.
    • (1958) Planta , vol.51 , pp. 481-510
    • Guttenberg, H.V.1    Müller-Schröder, R.2
  • 16
    • 84990442741 scopus 로고
    • Seedlings of Nymphaeaceae
    • Haines, R. W., and K. A. Lye. 1975. Seedlings of Nymphaeaceae. J. Linn. Soc. Bot. 70:255-265.
    • (1975) J. Linn. Soc. Bot. , vol.70 , pp. 255-265
    • Haines, R.W.1    Lye, K.A.2
  • 17
    • 0023184824 scopus 로고
    • Edge lengths of trees from sequence data
    • Hendy, M. D., and D. Penny. 1987. Edge lengths of trees from sequence data. Math. Biosci. 83:157-165.
    • (1987) Math. Biosci. , vol.83 , pp. 157-165
    • Hendy, M.D.1    Penny, D.2
  • 18
    • 0024674380 scopus 로고
    • The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals
    • Hiratsuka, J., H. Shimada, R. Whittier et al. (16 co-authors). 1989. The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol. Gen. Genet. 217:185-194.
    • (1989) Mol. Gen. Genet. , vol.217 , pp. 185-194
    • Hiratsuka, J.1    Shimada, H.2    Whittier, R.3
  • 19
    • 3042637206 scopus 로고    scopus 로고
    • Using consensus networks to visualize contradictory evidence for species phylogeny
    • in press
    • Holland, B. R., K. T. Huber, V. Moulton, and P. J. Lockhart. (in press). Using consensus networks to visualize contradictory evidence for species phylogeny. Mol. Biol. Evol.
    • Mol. Biol. Evol.
    • Holland, B.R.1    Huber, K.T.2    Moulton, V.3    Lockhart, P.J.4
  • 20
    • 0033804270 scopus 로고    scopus 로고
    • Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable Euoenothera plastomes
    • Hupfer, H., M. Swiatek, S. Hornung, R. G. Hermann, R. M. Maier, W.-L. Chiu, and B. Sears. 2000. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable Euoenothera plastomes. Mol. Gen. Genet. 263:581-585.
    • (2000) Mol. Gen. Genet. , vol.263 , pp. 581-585
    • Hupfer, H.1    Swiatek, M.2    Hornung, S.3    Hermann, R.G.4    Maier, R.M.5    Chiu, W.-L.6    Sears, B.7
  • 21
    • 4644299089 scopus 로고    scopus 로고
    • The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated
    • in press
    • Jermiin, L. S., S. Y. W. Ho, F. Ababneh, J. Robinson, and A. W. D. Larkum. (in press). The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst. Biol.
    • Syst. Biol.
    • Jermiin, L.S.1    Ho, S.Y.W.2    Ababneh, F.3    Robinson, J.4    Larkum, A.W.D.5
  • 22
    • 0034739889 scopus 로고    scopus 로고
    • Complete structure of the chloroplast genome of a legume, Lotus japonicus
    • Kato, T., T. Kaneko, S. Sato, Y. Nakamura, and S. Tabata. 2000. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res. 7:323-330.
    • (2000) DNA Res. , vol.7 , pp. 323-330
    • Kato, T.1    Kaneko, T.2    Sato, S.3    Nakamura, Y.4    Tabata, S.5
  • 24
    • 3042549592 scopus 로고
    • Evolutionary relationships of monocots and dicots derived from studies of embryo and seedlings data
    • in Russian
    • Lodkina, M. M. 1988. Evolutionary relationships of monocots and dicots derived from studies of embryo and seedlings data. Botanichesky Zhurnal 73:617-629. (in Russian).
    • (1988) Botanichesky Zhurnal , vol.73 , pp. 617-629
    • Lodkina, M.M.1
  • 25
    • 0029160870 scopus 로고
    • Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing
    • Maier, R. M., K. Neckermann, G. L. Igloi, and H. Kossel. 1995. Complete sequence of the maize chloroplast genome: gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J. Mol. Biol. 251:614-628.
    • (1995) J. Mol. Biol. , vol.251 , pp. 614-628
    • Maier, R.M.1    Neckermann, K.2    Igloi, G.L.3    Kossel, H.4
  • 27
    • 0019321718 scopus 로고
    • Rapid isolation of high molecular weight DNA
    • Murray, M. G., and W. F. Thompson. 1980. Rapid isolation of high molecular weight DNA. Nucleic Acids Res. 8:4321-4325.
    • (1980) Nucleic Acids Res. , vol.8 , pp. 4321-4325
    • Murray, M.G.1    Thompson, W.F.2
  • 28
    • 0035674196 scopus 로고    scopus 로고
    • Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA
    • Ogihara, Y., K. Isono, T. Kojim et al. (19 co-authors). 2002. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol. Genet. Genomics 266:740-746.
    • (2002) Mol. Genet. Genomics , vol.266 , pp. 740-746
    • Ogihara, Y.1    Isono, K.2    Kojim, T.3
  • 29
    • 0022546644 scopus 로고
    • Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA
    • Ohyama, K., H. Fukuzawa, T. Kohchi et al. (13 co-authors). 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572-574.
    • (1986) Nature , vol.322 , pp. 572-574
    • Ohyama, K.1    Fukuzawa, H.2    Kohchi, T.3
  • 30
    • 0031773680 scopus 로고
    • Modeltest: Testing the model of DNA substitution
    • Posada, D., and K. A. Crandall. 1988. Modeltest: testing the model of DNA substitution. Bioinformatics. 14:817-818.
    • (1988) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 33
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425:798-804.
    • (2003) Nature , vol.425 , pp. 798-804
    • Rokas, A.1    Williams, B.L.2    King, N.3    Carroll, S.B.4
  • 34
    • 0033615372 scopus 로고    scopus 로고
    • Complete structure of the chloroplast genome of Arabidopsis thaliana
    • Sato, S., Y. Nakamura, T. Kaneko, E. Asamizu, and S. Tabata. 1999. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res. 6:283-290.
    • (1999) DNA Res , vol.6 , pp. 283-290
    • Sato, S.1    Nakamura, Y.2    Kaneko, T.3    Asamizu, E.4    Tabata, S.5
  • 35
    • 0344861871 scopus 로고    scopus 로고
    • A decade of progress in plant molecular phylogenetics
    • Savolainen, V., and M. W. Chase. 2003. A decade of progress in plant molecular phylogenetics. Trends Genet. 19:717-724.
    • (2003) Trends Genet. , vol.19 , pp. 717-724
    • Savolainen, V.1    Chase, M.W.2
  • 36
    • 0347257588 scopus 로고
    • Some morphological peculiarities of the Nymphaeaceae and Helobiae
    • Schaffner, J. H. 1904. Some morphological peculiarities of the Nymphaeaceae and Helobiae. Ohio Nat. 4:83-92.
    • (1904) Ohio Nat. , vol.4 , pp. 83-92
    • Schaffner, J.H.1
  • 37
    • 0347257589 scopus 로고
    • Phylogenetic taxonomy of plants
    • -. 1934. Phylogenetic taxonomy of plants. Quart. Rev. Biol. 9:129-160.
    • (1934) Quart. Rev. Biol. , vol.9 , pp. 129-160
  • 38
    • 0035082732 scopus 로고    scopus 로고
    • The plastid chromosome of spinach (Spinacia oleracea): Complete nucleotide sequence and gene organization
    • Schmitz-Linneweber, C., R. M. Maier, J. P. Alcaraz, A. Cottet, R. G. Herrmann, and R. Mache. 2001. The plastid chromosome of spinach (Spinacia oleracea): complete nucleotide sequence and gene organization. Plant Mol. Biol. 45:307-315.
    • (2001) Plant Mol. Biol. , vol.45 , pp. 307-315
    • Schmitz-Linneweber, C.1    Maier, R.M.2    Alcaraz, J.P.3    Cottet, A.4    Herrmann, R.G.5    Mache, R.6
  • 39
    • 84968989005 scopus 로고
    • The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression
    • Shinozaki, K., M. Ohme, M. Tanaka et al. (23 co-authors). 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:2043-2049.
    • (1986) EMBO J , vol.5 , pp. 2043-2049
    • Shinozaki, K.1    Ohme, M.2    Tanaka, M.3
  • 40
    • 0033604619 scopus 로고    scopus 로고
    • Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology
    • Soltis, P. S., D. E. Soltis, and M. W. Chase. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402:402-403.
    • (1999) Nature , vol.402 , pp. 402-403
    • Soltis, P.S.1    Soltis, D.E.2    Chase, M.W.3
  • 42
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies
    • Strimmer, K., and A. von Haeseler. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13:964-969.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 46
    • 1342288009 scopus 로고    scopus 로고
    • LDDist: A Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences
    • Tholesson, M. 2004. LDDist: a Perl module for calculating LogDet pair-wise distances for protein and nucleotide sequences. Bioinformatics 20:416-418.
    • (2004) Bioinformatics , vol.20 , pp. 416-418
    • Tholesson, M.1
  • 47
    • 0028509254 scopus 로고
    • TREECON for Windows: A software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment
    • Van de Peer, Y., and R. De Wachter. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10:569-570.
    • (1994) Comput. Applic. Biosci. , vol.10 , pp. 569-570
    • Van De Peer, Y.1    De Wachter, R.2
  • 48
    • 0028043489 scopus 로고
    • Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii
    • Wakasugi, T., J. Tsudzuki, S. Ito, K. Nakashima, T. Tsudzuki, and M. Sugiura. 1994. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc. Natl. Acad. Sci. USA 91:9794-9798.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 9794-9798
    • Wakasugi, T.1    Tsudzuki, J.2    Ito, S.3    Nakashima, K.4    Tsudzuki, T.5    Sugiura, M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.