Whole chloroplast genome comparison of rice, maize, and wheat: Implications for chloroplast gene diversification and phylogeny of cereals

Molecular Biology and Evolution

Volumn 19, Issue 12, 2002, Pages 2084-2091

  Matsuoka, Yoshihiro ^a   Yamazaki, Yukiko ^b   Ogihara, Yasunari ^c   Tsunewaki, Koichiro ^a  

^a FUKUI PREFECTURAL UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

Chloroplast genome; Gene evolution; Poaceae; Relative rates; Substitution rate

Indexed keywords

CHLOROPLAST RNA; MEMBRANE PROTEIN; PROTEINASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; RIBOSOME PROTEIN; RNA; RNA POLYMERASE;

ARTICLE; CEREAL; CHLOROPLAST; GENETIC VARIABILITY; GENOME; MAIZE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; RICE; TOBACCO; CLASSIFICATION; GENETICS; WHEAT;

BAMBUSOIDEAE; NICOTIANA TABACUM; PANICOIDEAE; POACEAE; POOIDEAE; TRITICUM AESTIVUM; ZEA MAYS;

CHLOROPLASTS; GENOME, PLANT; ORYZA SATIVA; PHYLOGENY; TRITICUM; ZEA MAYS;

EID: 0036899796     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a004033     Document Type: Article

References (29)

1. Bousquet, J., S. H. Strauss, A. H. Doerksen, and R. A. Price. 1992. Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proc. Natl. Acad. Sci. USA 89:7844-7848.
2. Clark, L. G., W. Zhang, and J. F. Wendel. 1995. A phylogeny of the grass family (Poaceae) based on ndhF sequence data. Syst. Bot. 20:436-460.
3. Clayton, W. D. 1981. Evolution and distribution of grasses. Ann. Missouri Bot. Gard. 68:5-14.
4. Clayton, W. D., and S. A. Renvoize. 1986. Genera Graminum. Her Majesty's Stationery Office, London.
5. Cummings, M. P., L. M. King, and E. A. Kellogg. 1994. Slipped-strand mispairing in a plastid gene: rpoC2 in grasses (Poaceae). Mol. Biol. Evol. 11:1-8.
6. Corneille, S., K. Lutz, and P. Maliga. 2000. Conservation of RNA editing between rice and maize plastids: Are most editing events dispensable? Mol. Gen. Genet. 264:419-424.
7. Doebley, J., M. Durbin, E. M. Golenberg, M. T. Clegg, and D. P. MA. 1990. Evolutionary analysis of the large subunit of carboxlase (rbcL) nucleotide sequence among the grasses (Gramineae). Evolution 44:1097-1108.
8. Gaut, B. S., S. V. Muse, and M. T. Clegg. 1993. Relative rates of nucleotide substitution in the chloroplast genome. Mol. Phylogenet. Evol. 2:89-96.
9. Gaut, B. S., S. V. Muse, W. Deniss Clark, and M. T. Clegg. 1992. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. J. Mol. Evol. 35:292-303.
10. Golenberg, E. M., M. T. Clegg, M. L. Durbin, J. Doebley, and D. P. MA. 1993. Evolution of a noncoding region of the chloroplast genome. Mol. Phylogenet. Evol. 2:52-64.
11. Hilu, K. W., and L. A. Alice. 1999. Evolutionary implications of matK indels in Poaceae. Am. J. Bot. 86:1735-1741.
12. 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.
13. Hirose, T., T. Kusumegi, T. Tsudzuki, and M. Sugiura. 1999. RNA editing sites in tobacco chloroplast transcripts: Editing as a possible regulator of chloroplast RNA polymerase activity. Mol. Gen. Genet. 262:462-467.
14. Kellogg, E. A. 1998. Relationships of cereal crops and other grasses. Proc. Natl. Acad. Sci. USA 95:2005-2010.
15. Kumar, S., K. Tamura, I. B. Jakobsen, and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics Analysis Software. Arizona State University, Tempe.
16. Maier, R. M., K. Neckermann, G. L. Igloi, and H. Kössel. 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.
17. Mathews, S., R. C. Tsai, and E. A. Kellogg. 2000. Phylogenetic structure in the grass family (Poaceae): Evidence from the nuclear gene phytochorome B. Am. J. Bot. 87:96-107.
18. Nadot, S., R. Bajon, and B. Lejeune. 1994. The chloroplast gene rps4 as a tool for the study of Poaceae phylogeny. Plant Syst. Evol. 191:27-38.
19. Nei, M., and T. Gojobori. 1986. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3:418-426.
20. Ogihara, Y., K. Isono, T. Kojima et al. (19 co-authors). 2002. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol. Gen. Genomics 266:740-746.
21. Shinozaki, K., M. Ohme, M. Tanaka et al. (23 co-authors). 1986. The complete nucleotide sequence of tobacco chloroplast genome: Its gene organization and expression. EMBO J. 5:2043-2049.
22. Saitou, N., and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
23. Soltis, D. E., P. S. Soltis, M. T. Clegg, and M. Durbin. 1990. rbcL sequence divergence and phylogenetic relationships in Saxifragaceae sensu lato. Proc. Natl. Acad. Sci. USA 87:4640-4644.
24. Tajima, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135:599-607.
25. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
26. Watson, L., H. T. Clifford, and M. J. Dallwitz. 1985. The classification of Poaceae: Subfamilies and supertribes. Aust. J. Bot. 33:433-484.
27. Wolfe, K. H., M. Gouy, Y.-W. Yang, P. M. Sharp, and W.H. Li. 1989. Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc. Natl. Acad. Sci. USA 86:6201-6205.
28. Wolfe, K. H., W.-H. Li, and P. M. Sharp. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84:9054-9058.
29. Zhang, W. 2000. Phylogeny of the grass family (Poaceae) from rpl16 intron sequence data. Mol. Phylogenet. Evol. 15: 135-146.