Chloroplast-Expressed Glutamine Synthetase (ncpGS): Potential Utility for Phylogenetic Studies with an Example from Oxalis (Oxalidaceae)

Molecular Phylogenetics and Evolution

Volumn 12, Issue 3, 1999, Pages 310-319

  Emshwiller, Eve ^a   Doyle, Jeff J ^a  

^a Department of Obstetrics Gynecology   (United States)

Author keywords

Chloroplast expressed glutamine synthetase; ncpGS; Oxalidaceae; Oxalis; phylogeny; single copy nuclear locus

Indexed keywords

GLUTAMATE AMMONIA LIGASE; PLANT DNA; PRIMER DNA; RIBOSOME DNA;

ARTICLE; CELL NUCLEUS; CHEMISTRY; CHLOROPLAST; CLASSIFICATION; COMPARATIVE STUDY; DNA SEQUENCE; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

BASE SEQUENCE; CELL NUCLEUS; CHLOROPLASTS; DNA PRIMERS; DNA, PLANT; DNA, RIBOSOMAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENE EXPRESSION REGULATION, PLANT; GLUTAMATE-AMMONIA LIGASE; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; PLANTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; VARIATION (GENETICS);

EID: 0033176347     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1006/mpev.1999.0613     Document Type: Article

References (53)

1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment tool. J. Mol. Biol. 215:1990;403-410.
2. Baldwin B. G., Sanderson M. J., Porter J. M., Wojciechowski M. F., Campbell C. S., Donoghue M. J. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann. Missouri Bot. Gard. 82:1995;247-277.
3. Biesiadka J., Logocki A. B. Evolution of the glutamine synthetase gene in plants. Plant Sci. 128:1997;51-58.
4. Birky C. W. Transmission genetics of mitochondria and chloroplasts. Annu. Rev. Genet. 12:1978;471-512.
5. Boudraa M., Perrin P. CpG and TpA frequencies in the plant system. Nucleic Acids Res. 15:1987;5729-5737.
6. Bradley R. D., Hillis D. M. Recombinant DNA sequences generated by PCR amplification. Mol. Biol. Evol. 14:1997;592-593.
7. Buckler E. S. IV, Ippolito A., Holtsford T. P. The evolution of ribosomal DNA: Divergent paralogues and phylogenetic implications. Genetics. 145:1997;821-832.
8. Campbell C. S., Wojciechowski M. F., Baldwin B. G., Alice L. A., Donoghue M. J. Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Mol. Biol. Evol. 14:1997;81-90.
9. Cantón F. R., García-Gutiérrez A., Gallardo F., de Vincente A., Cánovas F. M. Molecular characterization of a cDNA clone encoding glutamine synthetase from a gymnosperm, Pinus sylvestris. Plant Mol. Biol. 22:1993;819-828.
10. Chen Q., Silflow C. D. Isolation and characterization of glutamine synthetase genes in Chlamydomonas reinhardtii. Plant Physiol. 112:1996;987-996.
11. Cronquist A. An Integrated System of Classification of Flowering Plants. 1981;Columbia Univ. Press, New York.
12. Csank C., Taylor F. M., Martindale D. W. Nuclear pre-mRNA introns: Analysis and comparison of intron sequences from Tetrahymena thermophila and other eukaryotes. Nucleic Acids Res. 18:1990;5133-5141.
13. de Azkue D., Martínez A. Chromosome number of the Oxalis tuberosa alliance (Oxalidaceae). Plant Syst. Evol. 169:1990;25-29.
14. Devereux J., Haeberli P., Smithers O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:1985;216-223.
15. Doyle J. J. Evolution of higher-plant glutamine synthetase genes: Tissue specificity as a criterion for predicting orthology. Mol. Biol. Evol. 8:1991;366-377.
16. Doyle J. J. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Bot. 17:1992;144-163.
17. Doyle J. J., Doyle J. L., Palmer J. D. Multiple independent losses of two genes and one intron from legume chloroplast genomes. Syst. Bot. 20:1995;272-294.
18. Elmlinger M. W., Bolle C., Batchauer A., Oelmüller R., Mohr H. Coaction of blue light and light absorbed by phytochrome in control of glutamine synthetase gene expression in Scots pine (Pinus sylvestris L.) seedlings. Planta. 192:1994;189-194.
19. Emshwiller E., Doyle J. J. Origins of domestication and polyploidy in oca (Oxalis tuberosa: Oxalidaceae): nrDNA ITS data. Am. J. Bot. 85:1998a;975-985.
20. Emshwiller E., Doyle J. J. Evidence for origins of polyploidy of Oxalis tuberosa from chloroplast-expressed glutamine synthetase. Am. J. Bot. 85:1998b;125.
21. Flook P. K., Rowell C. H. F. The phylogeny of the Caelifera (Insecta, Orthoptera) as deduced from mtrRNA gene sequences. Mol. Phylogenet. Evol. 8:1997a;89-103.
22. Flook P. K., Rowell C. H. F. The effectiveness of mitochondrial rRNA gene sequences for the reconstruction of the phylogeny of an insect order (Orthoptera). Mol. Phylogenet. Evol. 8:1997b;177-192.
23. Forde B. G., Cullimore J. V. The molecular biology of glutamine synthetase in higher plants. Oxford Surv. Plant Mol. Cell Biol. 6:1989;247-296.
24. Goodall G. J., Filipowicz W. The AU-rich sequences present in the introns of plant nuclear pre-mRNAs are required for splicing. Cell. 58:1989;473-483.
25. Hancock J. M. The contribution of slippage-like processes to genome evolution. J. Mol. Evol. 41:1995;1038-1047.
26. Hawkins J. D. A survey of intron and exon lengths. Nucleic Acids Res. 16:1988;9893-9908.
27. Heitz E. Ueber multiple und aberrante Chromosomenzahlen. Ablandl Naturwississenschaften Vereins Hamburg. 21:1927;47-57.
28. Hepburn A. G., Belanger F. C., Mattheis J. R. DNA methylation in plants. Dev. Genet. 8:1987;475-493.
29. Higgins D. G., Sharp P. M. Fast and sensitive multiple sequence alignments on a microcomputer. CABIOS. 5:1989;151-153.
30. Jansen R., Ledley F. D. Disruption of phase during PCR amplification and cloning of heterozygous target sequences. Nucleic Acids Res. 18:1990;5153-5156.
31. Kahl S., Gerendás J., Heeschen V., Ratcliffe R. G., Rudolph H. Ammonium assimilation in bryophytes. L-glutamine synthetase from Sphagnum fallax. Physiol. Plant. 101:1997;86-92.
32. Keller E. B., Noon W. A. Intron spicing: A conserved internal signal in introns of Drosophila pre-mRNAs. Nucleic Acids Res. 13:1985;4971-4981.
33. Ko C. H., Brendel V., Taylor R. D., Walbot V. U-richness is a defining feature of plant introns and may function as an intron recognition signal in maize. Plant Mol. Biol. 36:1998;573-583.
34. Levinson G., Gutman G. A. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:1987;203-221.
35. Li W.-H. Molecular Evolution. 1997;Sinauer, Sunderland.
36. Marks G. E. Chromosome numbers in the genus Oxalis. New Phytol. 55:1956;120-129.
37. Maurin C., Le Gal Y. Isoforms of glutamine synthetase in the marine Coccolithophorid Emiliania huxleyi (Prymnesiophyceae). Comp. Biochem. Physiol. 118B:1997;903-912.
38. McClelland M. The frequency and distribution of methylatable DNA sequences in leguminous plant protein coding genes. J. Mol. Evol. 19:1983;346-354.
39. Messeguer R., Ganal M. W., Steffens J. C., Tanksley S. D. Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol. Biol. 16:1991;753-770.
40. Mount S. M., Burks C., Hertz G., Stormo G. D., White O., Fields C. Splicing signals in Drosophila: Intron size, information content, and consensus sequences. Nucleic Acids Res. 20:1992;4255-4262.
41. Pérez-Vincente R., Dorado G., Maldonado J. M. Cross-species amplification of glutamine synthetase cDNA by polymerase chain reaction with degenerate primers. Physiol. Plant. 98:1996;705-713.
42. Pesole G., Bozzetti M. P., Lanave C., Preparata G., Saccone C. Glutamine synthetase gene evolution: A good molecular clock. Proc. Natl. Acad. Sci. USA. 88:1991;522-526.
43. Pesole G., Gissi C., Lanave C., Saccone C. Glutamine synthetase gene evolution in bacteria. Mol. Biol. Evol. 12:1995;189-197.
44. Reeder T. W. Phylogenetic relationships among phrynosomatid lizards as inferred form mitochondrial ribosomal DNA sequences: Substitutional bias and information content of transitions relative to transversions. Mol. Phylogenet. Evol. 4:1995;203-222.
45. Simpson C. G., Clark G., Davidson D., Smith P., Brown J. W. S. Mutation of putative branchpoint consensus sequences in plant introns reduces splicing efficiency. Plant J. 9:1996;369-380.
46. Swofford, D. L. 1991, PAUP: Phylogenetic analysis using parsimony, version 3.1.1. Computer program distributed by the, Illinois Natural History Survey, Champaign, IL.
47. Talerico M., Berget S. M. Intron definition in splicing of small Drosophila introns. Mol. Cell. Biol. 14:1994;3434-3445.
48. Tateno Y. Evolution of glutamine synthetase genes is in accordance with the neutral theory of molecular evolution. Jpn. J. Genet. 69:1994;489-502.
49. Tischer E., DasSarma S., Goodman H. M. Nucleotide sequence of an alfalfa Medicago sativa glutamine synthetase gene. Mol. Gen. Genet. 203:1986;221-229.
50. Wakeley J. The excess of transitions among nucleotide substitutions: New methods of estimating transition bias underscore its significance. Trends Ecol. Evol. 11:1996;158-163.
51. Warburg E. F. Taxonomy and relationship in the Geraniales, Part II. New Phytol. 37:1938;189-210.
52. Wendel J. F., Schnabel A., Seelman T. Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proc. Natl. Acad. Sci. USA. 92:1995;280-284.
53. Zhang D.-X., Hewitt G. M. Insect mitochondrial control region: A review of its structure, evolution and usefulness in evolutionary studies. Biochem. Syst. Ecol. 25:1997;99-120.