Rapid recent growth and divergence of rice nuclear genomes

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

Volumn 101, Issue 34, 2004, Pages 12404-12410

  Ma, Jianxin ^a   Bennetzen, Jeffrey L ^a  

^a University of Georgia   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL NUCLEUS DNA;

ARTICLE; DNA SEQUENCE; GENE AMPLIFICATION; GENE DELETION; GENE INSERTION; GENE LOSS; GENETIC RECOMBINATION; GENETIC VARIABILITY; GENOME; GENOME SIZE; MOLECULAR CLOCK; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; RETROPOSON; RICE; SUBSPECIES; TRANSPOSON; UNINDEXED SEQUENCE;

BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; GENOME; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; POINT MUTATION; RETROELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, NUCLEIC ACID; STATISTICS;

EMBRYOPHYTA; INSERTION SEQUENCES; JAPONICA; ORYZA GLABERRIMA; ORYZA SATIVA; TRANSPOSONS;

EID: 4344616881     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0403715101     Document Type: Article

References (45)

1. Bennetzen, J. L. & Ma, J. (2003) Curr. Opin. Plant Biol. 6, 128-133.
2. Wolfe, K. H., Gouy, M., Yang, Y.-M., Sharp, P. M. & Li, W.-H. (1989) Proc. Natl. Acad. Sci. USA 86, 6201-6205.
3. Gale, M. D. & Devos, K. M. (1998) Proc. Natl. Acad. Sci. USA 95, 1971-1974.
4. Keller, B. & Feuillet, C. (2000) Trends Plant Sci. 5, 246-251.
5. Kaplinsky, N. J., Braun, D. M., Penterman, J., Goff, S. A. & Freeling, M. (2002) Proc. Natl. Acad. Sci. USA 99, 6147-6151.
6. Guo, H. & Moose, S. P. (2003) Plant Cell 15, 1143-1158.
7. The Arabidopsis Genome Initiative (2000) Nature 408, 796-815.
8. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., et al. (2002) Nature 420, 312-316.
9. Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., et al. (2002) Nature 420, 316-320.
10. Rice Chromosome 10 Sequencing Consortium (2003) Science 300, 1566-1569.
11. Nagaki, K., Cheng, Z., Ouyang, S., Talbert, P. B., Kim, M., Jones, K. M., Henikoff, S., Buell, C. R. & Jiang, J. (2004) Nat. Genet. 36, 138-145.
12. Devos, K. M., Brown, J. K. & Bennetzen, J. L. (2002) Genome Res. 12, 1075-1079.
13. Vitte, C. & Panaud, O. (2003) Mol. Biol. Evol. 20, 528-540.
14. Ma, J., Devos, K. M. & Bennetzen, J. L. (2004) Genome Res. 14, 860-869.
15. Bennetzen, J. L., Ma, J. & Devos, K. (2004) Annals Bot., in press.
16. SanMiguel, P., Tikhonov, A., Jin, Y.-K., Motchoulskaia, N., Zakharov, D., Melake Berhan, A., Springer, P. S., Edwards, K. J., Avramova, Z. & Bennetzen, J. L. (1996) Science 274, 765-768.
17. Shirasu, K., Schulman, A. H., Lahaye, T. & Schulze-Lefert, P. (2000) Genome Res. 10, 908-915.
18. Wicker, T., Yahiaoui, N., Guyot, R., Schlagenhauf, E., Liu, Z. D., Dubcovsky, J. & Keller, B. (2003) Plant Cell 15, 1186-1197.
19. Han, B. & Xue, Y. (2003) Plant Biol. 6, 134-138.
20. Portères, R. (1976) in The Origin of African Plant Domestication, eds. Harlan, J. R., de Wet, J. M. J. & Stemler, A. B. L. (Mouton, The Hague), pp. 409-452.
21. Ge, S., Sang, T., Lu, B. R. & Hong, D. Y. (1999) Proc. Natl. Acad. Sci. USA 96, 14400-14405.
22. Ishii, T., Xu, Y. & McCouch, S. R. (2001) Genome 44, 658-666.
23. Cheng, C., Tsuchimoto, S., Ohtsubo, H. & Ohtsubo, E. (2002) Genes Genet. Syst. 77, 323-334.
24. Ren, F., Lu, B. R., Li, S., Huang, J. & Zhu, Y. (2003) Theor. Appl. Genet. 108, 113-120.
25. Park, K. C., Kim, N. H., Cho, Y. S., Kang, K. H., Lee, J. K. & Kim, N. S. (2003) Theor. Appl. Genet. 107, 203-209.
26. Tatusova, T. A. & Madden, T. L. (1999) FEMS Microbiol. Lett. 174, 247-250.
27. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997) Nucleic Acids Res. 25, 4876-4882.
28. Kumar, S., Tamura, K., Jakobsen, I. B. & Nei, M. (2001) Bioinformatics 17, 1244-1245.
29. Dubcovsky, J., Ramakrishna, W., SanMiguel, P. J., Busso, C. S., Yan, L., Shiloff, B. A. & Bennetzen, J. L. (2001) Plant Physiol. 125, 1342-1353.
30. Nei, M. & Gojobori, T. (1986) Mol. Biol. Evol. 3, 418-426.
31. Zhang, L., Vision, T. J. & Gaut, B. S. (2002) Mol. Biol. Evol. 19, 1464-1473.
32. Gaut, B. S., Morton, B. R., McCaig, B. C. & Clegg, M. T. (1996) Proc. Natl. Acad. Sci. USA 93, 10274-10279.
33. SanMiguel, P., Gaut, B. S., Tikhonov, A., Nakajima, Y. & Bennetzen, J. L. (1998) Nat. Genet. 20, 43-45.
34. Kumar, A. & Bennetzen, J. L. (1999) Annu. Rev. Genet. 33, 479-532.
35. Wessler, S. R., Bureau, T. E. & White, S. E. (1995) Curr. Opin. Genet, Dev. 5, 814-821.
36. SanMiguel, P. J., Ramakrishna, W., Bennetzen, J. L., Busso, C. S. & Dubcovsky, J. (2002) Funct. Integr. Genomics 2, 51-59.
37. Gu, Y. Q., Coleman-Derr, D., Kong, X. & Anderson, O. D. (2004) Plant Physiol. 135, 1-12.
38. Fu, H. & Dooner, H. K. (2002) Proc. Natl. Acad. Sci. USA 99, 9573-9578.
39. Linares, O. F. (2002) Proc. Natl. Acad. Sci. USA 99, 16360-16365.
40. Cai, H. & Morishima, H. (2002) Theor. Appl. Genet. 104, 1217-1228.
41. Yamanaka, S., Nakamura I., Watanabe, K. N. & Sato, Y. I. (2004) Theor. Appl. Genet. 180, 1200-1204.
42. Vicient, C. M., Suoniemi, A., Anamthawat-Jónsson, K., Tanskanen, J., Beharav, A., Nevo, E. & Schulman, A. H. (1999) Plant Cell 11, 1769-1784.
43. Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E. & Schulman, A. H. (2000) Proc. Natl. Acad. Sci. USA 97, 6603-6607.
44. Schoof, H. & Karlowski, W. M. (2003) Curr. Opin. Plant Biol. 6, 106-112.
45. Bennetzen, J. L. & Ramakrishna, W. (2002) Proc. Natl. Acad. Sci. USA 99, 9093-9095.