Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus

Proceedings of the National Academy of Sciences of the United States of America

Volumn 99, Issue 19, 2002, Pages 12246-12251

  Martin, William ^a   Rujan, Tamas ^b   Richly, Erik ^c   Hansen, Andrea ^d   Cornelsen, Sabine ^a   Lins, Thomas ^a   Leister, Dario ^c   Stoebe, Bettina ^a   Hasegawa, Masami ^e   Penny, David ^f  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b EPIGENOMICS AG   (Germany)

^c MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH   (Germany)

^d BAYER AG   (Germany)

^e INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^f MASSEY UNIVERSITY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID ANALYSIS; AMINO ACID COMPOSITION; ARABIDOPSIS; ARTICLE; CHLOROPLAST GENETICS; CONTROLLED STUDY; CYANOBACTERIUM; ENDOSYMBIOSIS; GENE TRANSFER; GENETIC CODE; HOMEOSTASIS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; PLANT EVOLUTION; PLASTID; PRIORITY JOURNAL; PROKARYOTE; PROTEIN CONFORMATION; PROTEIN SYNTHESIS; RED ALGA; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CELL NUCLEUS; CHLOROPLASTS; CYANOBACTERIA; EVOLUTION; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENOME, BACTERIAL; GENOME, PLANT; MODELS, GENETIC; MULTIGENE FAMILY; PHYLOGENY; PLASTIDS;

ALGAE; ARABIDOPSIS; CYANOBACTERIA; NEGIBACTERIA; PROKARYOTA; RHODOPHYTA;

EID: 0037126071     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.182432999     Document Type: Article

References (58)

1. Goksøyr, J. (1967) Nature (London) 214, 1161.
2. Douglas, S. E. (1998) Curr. Opin. Gen. Dev. 8, 655-661.
3. Delwiche, C. W. (1999) Am. Nat. 154, S164-S177.
4. Tomitani, A., Okada, K., Miyashita, H., Matthijs, H. C. P., Ohno, T. & Tanaka, A. (1999) Nature (London) 400, 159-162.
5. Herrmann, R. G. (1997) in Eukaryotism and Symbiosis, eds. Schenk, H. E. A., Herrmann, R. G., Jeon, K. W. & Schwemmler, W. (Springer, Heidelberg), pp. 73-118.
6. Allen, J. F. & Fornsberg, J. (2001) Trends Plant Sci. 6, 317-326.
7. Wolfe, G. R., Cunningham, F. X., Durnford, D., Green, B. R. & Gantt, E. (1994) Nature (London) 367, 566-568.
8. Douglas, S., Zauner, S., Fraunholz, M., Beaton, M., Penny, S., Deng, L. T., Wu, X. N., Reith, M., Cavalier-Smith, T. & Maier, U.-G. (2001) Nature (London) 401, 1091-1096.
9. Steiner, J. M. & Löffelhardt, W. (2002) Trends Plant Sci. 7, 72-77.
10. Osteryoung, K. W. & McAndrew, R. S. (2001) Annu. Rev. Plant Phys. 52, 315-333.
11. Heins, L. & Soll, J. (1998) Curr. Biol. 8, R215-R217.
12. Pfannschmidt, T., Nilsson, A. & Allen, J. F. (1999) Nature (London) 397, 625-628.
13. Martin, W. F. & Herrmann, R. G. (1998) Plant Physiol. 118, 9-17.
14. Kubo, N., Takano, M., Nishiguchi, M. & Kadowaki, K. (2001) Gene 271, 193-201.
15. Abdallah, F., Salamini, F. & Leister, D. (2000) Trends Plant Sci. 5, 141-142.
16. Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., et al. (1996) DNA Res. 3, 109-136.
17. Rujan, T. & Martin, W. (2000) Trends Genet. 17, 113-120.
18. Cavalier-Smith, T. (2000) Trends Plant Sci. 5, 174-182.
19. Martin, W., Stoebe, B., Goremykin, V., Hansmann, S., Hasegawa, M. & Kowallik, K. V. (1998) Nature (London) 393, 162-165.
20. Millen, R. S., Olmstead, R. G., Adams, K. L., Palmer, J. D., Lao, N. T., Heggie, L., Kavanagh, T. A., Hibberd, J. M., Gray, J. C., Morden, C. W., et al. (2001) Plant Cell 13, 645-658.
21. The Arabidopsis Genome Initiative (2000) Nature (London) 408, 796-815.
22. Meeks, J. C., Elhai, J., Thiel, T., Potts, M., Larimer, F., Lamerdin, J., Predki, P. & Atlas, R. (2001) Photosynth. Res. 70, 85-106.
23. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J. H., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
24. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucl. Acids Res. 22, 4673-4680.
25. Adachi, J. & Hasegawa, M. (1996) MOLPHY (Institute of Statistical Mathematics, Tokyo), Computer Science Monographs, No. 28, Version 2.3.
26. Saitou, N. & Nei, M. (1987) Mol. Biol. Evol. 4, 406-425.
27. Emanuelsson, O., Nielsen, H., Brunak, S. & von Heijne, G. (2000) J. Mol. Biol. 300, 1005-1016.
28. Douglas, S. E. & Penny, S. L. (1999) J. Mol. Evol. 48, 236-244.
29. Glockner, G., Rosenthal, A. & Valentin, K. (2000) J. Mol. Evol. 51, 382-390.
30. Wakasugi, T., Nagai, T., Kapoor, M., Sugita, M., Ito, M., Ito, S., Tsudzuki, J., Nakashima, K., Tsudzuki, T., Suzuki, Y., et al. (1997) Proc. Natl. Acad. Sci. USA 94, 5967-5972.
31. Turmel, M., Otis, C. & Lemieux, C. (1999) Proc. Natl. Acad. Sci. USA 96, 10248-10253.
32. Lemieux, C., Otis, C. & Turmel, M. (2000) Nature (London) 403, 649-652.
33. Hupfer, H., Swiatek, M., Hornung, S., Herrmann, R. G., Maier, R. M., Chiu, W. L. & Sears, B. (2000) Mol. Gen. Genet. 263, 581-585.
34. Lockhart, P. J., Howe, C. J., Barbrook, A. C., Larkum, A. W. D. & Penny, D. (1999) Mol. Biol. Evol. 16, 573-576.
35. Nei, M. & Kumar, S. (2000) Molecular Evolution and Phylogenetics (Oxford Univ. Press, Oxford).
36. Strimmer, K. & von Haeseler, A. (1996) Mol. Biol. Evol. 13, 964-969.
37. Lockhart, P. J., Steel, M. A., Hendy, M. D. & Penny, D. (1994) Mol. Biol. Evol. 11, 605-612.
38. Hendy, M. D. & Penny, D. (1993) J. Classif. 10, 5-24.
39. Shimodaira, H. & Hasegawa, M. (1999) Mol. Biol. Evol. 16, 1114-1116.
40. Nei, M. (1996) Annu. Rev. Genet. 30, 371-403.
41. Salzberg, S. L., White, O., Peterson, J. & Eisen, J. A. (2001) Science 292, 1903-1906.
42. Stoebe, B. & Kowallik, K. V. (1999) Trends Genet. 15, 344-347.
43. Moreira, D., Le Guyader, H. & Philippe, H. (2000) Nature (London) 405, 69-72.
44. Woese, C. R. (1987) Microbiol. Rev. 51, 221-271.
45. Xiong, J., Fischer, W. M., Inoue, K., Nakahara, M. & Bauer, C. E. (2000) Science 289, 1724-1730.
46. Schtitz, M., Brugna, M., Lebrun, E., Baymann, F., Huber, R., Stetter, K. O., Hauska, G., Toci, R., Lemesle-Meunier, D., Tron, P., et al. (2000) J. Mol. Biol. 300, 663-675.
47. Hansmann, S. & Martin, W. (2000) Int. J. Syst. Evol. Microbiol. 50, 1655-1663.
48. Wächtershäuser, G. (1998) Syst. Appl. Microbiol. 21, 473-477.
49. Maeda, S.-I. & Omata, T. (1997) J. Biol. Chem. 272, 3036-3041.
50. Martin, W. & Schnarrenberger, C. (1997) Curr. Genet. 32, 1-18.
51. Hoiike, T., Hamada, K., Kanaya, S. & Shinozawa, T. (2001) Nat. Cell Biol. 3, 210-214.
52. Palenik, B. & Haselkorn, R. (1992) Nature (London) 355, 265-267.
53. Urbach, E., Robertson, D. L. & Chisolm, S. W. (1992) Nature (London) 355, 267-270.
54. Ochman, H., Lawrence, J. G. & Groisman, E. S. (2000) Nature (London) 405, 299-304.
55. Doolittle, W. F. (1999) Science 284, 2124-2128.
56. Karol, K. G., McCourt, R. M., Cimino, M. T. & Delwiche, C. F. (2001) Science 294, 2351-2353.
57. Fast, N. M., Kissinger, J. C., Roos, D. S. & Keeling, P. J. (2001) Mol. Biol. Evol. 18, 418-426.
58. Boekema, E. J., Hifney, A., Yakushevska, A. E., Piotrowski, M., Keegstra, W., Berry, S., Michel, K. P., Pistorius, E. K. & Kruip, J. (2001) Nature (London) 412, 745-748.