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References (45)
-
M. Cabrera, Y. Nghiem, J. Miller (1988)
mutM, a second mutator locus in Escherichia coli that generates G.C----T.A transversionsJournal of Bacteriology, 170
-
MD Topal, SR DiGuiseppi, NK Sinha (1980)
Molecular basis for substitution mutationsJ Biol Chem, 255
-
Wen-Hsiung Li, Chung-I Wu, C. Luo (2005)
Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implicationsJournal of Molecular Evolution, 21
-
W. Brown, E. Prager, Alice Wang, A. Wilson (2005)
Mitochondrial DNA sequences of primates: Tempo and mode of evolutionJournal of Molecular Evolution, 18
-
D. Clary, D. Wolstenholme (2005)
Drosophila mitochondrial DNA: Conserved sequences in the A+T-rich region and supporting evidence for a secondary structure model of the small ribosomal RNAJournal of Molecular Evolution, 25
-
D. Maddison, W. Maddison (2003)
MacClade 4: analysis of phy-logeny and character evolution -
Rudolf Schmid, W. Clayton, S. Renvoize (1987)
Genera Graminum: Grasses of the World -
DL Swofford, GJ Olsen (1990)
Molecular systematics -
Loredana Nigro, M. Solignac, P. Sharp (1991)
Mitochondrial DNA sequence divergence in theMelanogaster and oriental species subgroups ofDrosophilaJournal of Molecular Evolution, 33
-
K. Tamura (1992)
The rate and pattern of nucleotide substitution in Drosophila mitochondrial DNA.Molecular biology and evolution, 9 5
-
WP Maddison, DR Maddison (1992)
MacClade: analysis of phylogeny and character evolution, version 3.0 -
E. Pahlich, Chr. Gerlitz (1980)
A rapid DNA isolation procedure for small quantities of fresh leaf tissuePhytochemistry, 19
-
Y. Nghiem, M. Cabrera, C. Cupples, Jeffrey Miller (1988)
The mutY gene: a mutator locus in Escherichia coli that generates G.C----T.A transversions.Proceedings of the National Academy of Sciences of the United States of America, 85 8
-
R. DeSalle, T. Freedman, E. Prager, A. Wilson (2005)
Tempo and mode of sequence evolution in mitochondrial DNA of HawaiianDrosophilaJournal of Molecular Evolution, 26
-
M. Michaels, C. Cruz, J. Miller (1990)
mutA and mutC: two mutator loci in Escherichia coli that stimulate transversions.Proceedings of the National Academy of Sciences of the United States of America, 87
-
M. Topal, S. DiGuiseppi, N. Sinha (1980)
Molecular basis for substitution mutations. Effect of primer terminal and template residues on nucleotide selection by phage T4 DNA polymerase in vitro.The Journal of biological chemistry, 255 24
-
M. Topal, J. Fresco (1976)
Complementary base pairing and the origin of substitution mutationsNature, 263
-
B. Gaut, S. Muse, W. Clark, M. Clegg (1992)
Relative rates of nucleotide substitution at the rbcl locus of monocotyledonous plantsJournal of Molecular Evolution, 35
-
G. Hudson, J. Mahon, P. Anderson, M. Gibbs, M. Badger, T. Andrews, P. Whitfeld (1990)
Comparisons of rbcL genes for the large subunit of ribulose-bisphosphate carboxylase from closely related C3 and C4 plant species.The Journal of biological chemistry, 265 2
-
J. Doebley, M. Durbin, E. Golenberg, M. Clegg, D. Ma (1990)
EVOLUTIONARY ANALYSIS OF THE LARGE SUBUNIT OF CARBOXYLASE (rbcL) NUCLEOTIDE SEQUENCE AMONG THE GRASSES (GRAMINEAE)Evolution, 44
-
BY Terachi, Y. Ogihara, K. Tsunewaki, K. Tsunewaki (1990)
The molecular basis of genetic diversity among cytoplasms of Triticum and AegilopsTheoretical and Applied Genetics, 80
-
L. Mendelman, M. Boosalis, J. Petruska, Myron Goodman (1989)
Nearest neighbor influences on DNA polymerase insertion fidelity.The Journal of biological chemistry, 264 24
-
G. Zurawski, M. Clegg, A. Brown (1984)
The Nature of Nucleotide Sequence Divergence between Barley and Maize Chloroplast DNA.Genetics, 106 4
-
T Gojobori, WH Li, D Grant (1982)
Patterns of nucleotide substitution in pseudogenesJ Mol Evol, 18
-
DL Swofford (1991)
PAUP: phylogenetic analysis using parsimony, version 3.0s -
D. Wolstenholme, D. Clary (1985)
Sequence evolution of Drosophila mitochondrial DNA.Genetics, 109 4
-
M. Nei (1987)
Molecular Evolutionary Genetics -
J. Hiratsuka, H. Shimada, R. Whittier, T. Ishibashi, M. Sakamoto, M. Mori, C. Kondo, Yasuko Honji, Chongrong Sun, B. Meng, Yu-Qing Li, A. Kanno, Y. Nishizawa, A. Hirai, K. Shinozaki, M. Sugiura (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 cerealsMolecular and General Genetics MGG, 217
-
R. Blake, S. Hess, J. Nicholson-Tuell (1992)
The influence of nearest neighbors on the rate and pattern of spontaneous point mutationsJournal of Molecular Evolution, 34
-
Madeleine Jones, R. Wagner, Miroslav Radman (1987)
Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence.Genetics, 115 4
-
B. Morton, M. Clegg (1993)
A chloroplast DNA mutational hotspot and gene conversion in a noncoding region near rbcL in the grass family (Poaceae)Current Genetics, 24
-
B. Kramer, W. Kramer, H. Fritz (1984)
Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coliCell, 38
-
J. Devereux, P. Haeberli, O. Smithies (1984)
A comprehensive set of sequence analysis programs for the VAXNucleic acids research, 12 1 Pt 1
-
F. Tajima, M. Nei (2005)
Biases of the estimates of DNA divergence obtained by the restriction enzyme techniqueJournal of Molecular Evolution, 18
-
M. Akiyama, H. Maki, M. Sekiguchi, T. Horiuchi (1989)
A specific role of MutT protein: to prevent dG.dA mispairing in DNA replication.Proceedings of the National Academy of Sciences of the United States of America, 86 11
-
Michael Clegg (1993)
Chloroplast gene sequences and the study of plant evolution.Proceedings of the National Academy of Sciences of the United States of America, 90
-
C. Stephenson, P. Karran (1989)
Selective binding to DNA base pair mismatches by proteins from human cells.The Journal of biological chemistry, 264 35
-
James Smith (1993)
Phylogenetic Hypotheses for the Monocotyledons Constructed from rbc L Sequence DataAnnals of the Missouri Botanical Garden, 80
-
JJ Doyle, JL Doyle (1987)
A rapid DNA isolation procedure for small quantities of fresh leaf materialPhytochem Bull, 19
-
T Terachi, Y Ogihara, K Tsunewaki (1987)
The molecular basis of genetic diversity among cytoplasms of Triticum and Aegilops. 8. Complete nucleotide sequences of the rbcL genes encoding H- and L-type rubisco large subunits in common wheat and Ae crassa 4XJpn J Genet, 62
-
Y. Satta, H. Ishiwa, S. Chigusa (1987)
Analysis of nucleotide substitutions of mitochondrial DNAs in Drosophila melanogaster and its sibling species.Molecular biology and evolution, 4 6
-
T. Gojobori, Wen-Hsiung Li, D. Graur (2005)
Patterns of nucleotide substitution in pseudogenes and functional genesJournal of Molecular Evolution, 18
-
Josef Jiricny, M. Hughes, N. Corman, Brian Rudkin (1988)
A human 200-kDa protein binds selectively to DNA fragments containing G.T mismatches.Proceedings of the National Academy of Sciences of the United States of America, 85 23
-
M. Radman, R. Wagner (1986)
Mismatch repair in Escherichia coli.Annual review of genetics, 20
-
MR Duvall, GH Learn, LE Eguiarte, MT Clegg (1993)
Phylogenetic analysis of rbcL sequence identifies Acorus calamus as the primal extant monocotyledonProc Natl Acad Sci USA, 90
- Publisher
- Springer Journals
- Copyright
- Copyright © 1995 by Springer-Verlag New York Inc
- Subject
- Life Sciences; Evolutionary Biology; Microbiology; Plant Sciences; Plant Genetics and Genomics; Animal Genetics and Genomics; Cell Biology
- ISSN
- 0022-2844
- eISSN
- 1432-1432
- DOI
- 10.1007/BF00175818
- Publisher site
- See Article on Publisher Site
Abstract
Nucleotide sequence from a region of the chloroplast genome is presented for 12 species spanning four subfamilies of the grass family. The region contains the coding sequence for the rbcL gene and the intergenic spacer between the gene coding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase rbcL and the photosystem I gene psal. This intergenic spacer contains a pseudogene for rpl23 as well as two noncoding segments with different A+T contents. Using the sequence of rbcL a chloroplast phylogeny of this family was constructed by parsimony. Variable sites of the two noncoding segments were traced onto the phylogeny to study the dynamics of base substitution. This was also performed for the fourfold-degenerate sites of the rbcL gene. A wide variation in transversion/transition is observed between the two noncoding segments and between the noncoding DNA and the fourfold-degenerate sites of rbcL This variation is correlated with regional A+T content. As regional A+T content decreases, the ratio of transversions to transitions also decreases. Substitutions were then scored in relation to neighboring base composition. The composition of the two bases immediately flanking each substitution is highly correlated with the transversion/transition bias. When both the 5′ and 3′ flanking bases are an A or a T, transversions are observed 2.2 times as frequently as transitions. When either or both neighbors are a C or a G, the opposite trend is found; transitions are observed 1.5 times more frequently than transversions.
Journal
Journal of Molecular Evolution – Springer Journals
Published: Jul 5, 2004