Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolution

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

Volumn 100, Issue 13, 2003, Pages 8007-8012

  Nishiyama, Tomoaki ^a   Fujita, Tomomichi ^a   Shin I, Tadasu ^b   Seki, Motoaki ^c,d   Nishide, Hiroyo ^a   Uchiyama, Ikuo ^e   Kamiya, Asako ^d   Carninci, Piero ^f   Hayashizaki, Yoshihide ^f   Shinozaki, Kazuo ^c,d   Kohara, Yuji ^b   Hasebe, Mitsuyasu ^a,g  

^a NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c RIKEN TSUKUBA INSTITUTE   (Japan)

^d RIKEN YOKOHAMA INSTITUTE   (Japan)

^e National Institutes of Natural Sciences   (Japan)

^f RIKEN   (Japan)

^g GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AUXIN; COMPLEMENTARY DNA; CYTOKININ; DNA; MESSENGER RNA;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; DNA LIBRARY; DNA SEQUENCE; EVOLUTION; GAMETOPHYTE; GENE; GENE EXPRESSION; GENOMICS; MOSS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; SPOROPHYTE;

ARABIDOPSIS; BRYOPSIDA; CELL LINEAGE; DATABASES; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENOME, PLANT; RNA, MESSENGER;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BRYOPHYTA; EMBRYOPHYTA; MAGNOLIOPHYTA; PHYSCOMITRELLA; PHYSCOMITRELLA PATENS; TRACHEOPHYTA;

EID: 0038270852     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0932694100     Document Type: Article

References (57)

1. Kenrick, P. & Crane, P. R. (1997) Nature 389, 33-39.
2. Bold, H. C., Alexopoulos, C. J. & Delevoryas, T. (1987) Morphology of Plants and Fungi (HarperCollins, New York).
3. Reski, R. (1998) Bot. Acta 111, 1-15.
4. Kolukisaoglu, H. U., Braun, B., Martin, W. F. & Schneider-Poetsch, H. A. (1993) FEBS Lett. 334, 95-100.
5. Pasentsis, K., Paulo, N., Algarra, P., Dittrich, P. & Thummler, F. (1998) Plant J. 13, 51-61.
6. Lamparter, T., Esch, H., Cove, D. & Hartmann, E. (1997) Plant Cell Physiol. 38, 51-58.
7. Knight, C. D., Sehgal, A., Atwal, K., Wallace, J. C., Cove, D. J., Coates, D., Quatrano, R. S., Bahadur, S., Stockley, P. G. & Cuming, A. C. (1995) Plant Cell 7, 499-506.
8. Cove, D. J. (1992) in Development: The Molecular Genetic Approach, eds. Russo, V. E. A., Brody, S., Cove, D. & Ottolenghi, S. (Springer, Berlin), pp. 179-193.
9. Knight, C. D. (1994) Plant Cell Environ. 17, 669-674.
10. The Arabidopsis Genome Initiative (2000) Nature 408, 796-815.
11. Schaefer, D. G. & Zrÿd, J.-P. (1997) Plant J. 11, 1195-1206.
12. Strepp, R., Scholz, S., Kruse, S., Speth, V. & Reski, R. (1998) Proc. Natl. Acad. Sci. USA 95, 4368-4373.
13. Girod, P.-A., Fu, H., Zrÿd, J.-P. & Vierstra, R. D. (1999) Plant Cell 11, 1457-1472.
14. Imaizumi, T., Kadota, A., Hasebe, M. & Wada, M. (2002) Plant Cell 14, 373-386.
15. Zank, T. K., Zähringer, U., Beckmann C., Pohnert, G., Boland, W., Holtorf, H., Reski, R., Lerchl, J. & Heinz, E. (2002) Plant J. 31, 255-268.
16. Koprivova, A., Meyer, A. J., Schween, G., Herschbach, C., Reski, R. & Kopriva, S. (2002) J. Biol. Chem. 277, 32195-32201.
17. Reski, R., Reynolds, S., Wehe, M., Kleber-Janke, T. & Kruse, S. (1998) Bot. Acta 111, 143-149.
18. Machuka, J., Bashiardes, S., Ruben, E., Spooner, K., Cuming, A., Knight, C. & Cove, D. (1999) Plant Cell Physiol. 40, 378-387.
19. Rensing, S. A., Rombauts, S., Van de Peer, Y. & Reski, R. (2002) Trends Plant Sci. 7, 535-538.
20. Tan, B. C. (1979) J. Hattori Bot. Lab. 46, 327-336.
21. Ashton, N. W. & Cove, D. J. (1977) Mol. Gen. Genet. 154, 87-95.
22. Nishiyama, T., Hiwatashi, Y., Sakakibara, K., Kato, M. & Hasebe, M. (2000) DNA Res. 7, 9-17.
23. Hasebe, M., Wen C.-K., Kato, M. & Banks, J. A. (1998) Proc. Natl. Acad. Sci. USA 95, 6222-6227.
24. Carninci, P., Nishiyama, Y., Westover, A., Itoh, M., Nagaoka, S., Sasaki, N., Okazaki, Y., Muramatsu, M. & Hayashizaki, Y. (1998) Proc. Natl. Acad. Sci. USA 95, 520-524.
25. Carninci, P., Kvam, C., Kitamura, A., Ohsumi, T., Okazaki, Y., Itoh, M., Kamiya, M., Shibata, K., Sasaki, N., Izawa, M., et al. (1996) Genomics 37, 327-336.
26. Carninci, P., Westover, A., Nishiyama, Y., Ohsumi, T., Itoh, M., Nagaoka, S., Sasaki, N., Okazaki, Y., Muramatsu, M., Schneider, C. & Hayashizaki, Y. (1997) DNA Res. 4, 61-66.
27. Carninci, P., Shibata, Y., Hayatsu, N., Itoh, M., Shiraki, T., Hirozane, T., Watahiki, A., Shibata, K., Konno, H., Muramatsu, M. & Hayashizaki, Y. (2001) Genomics 77, 79-90.
28. Shibata, Y., Carninci, P., Watahiki, A., Shiraki, T., Konno, H., Muramatsu, M. & Hayashizaki, Y. (2001) BioTechniques 30, 1250-1254.
29. Carninci, P., Shibata, Y., Hayatsu, N., Sugahara, Y., Shibata, K., Itoh, M., Konno, H., Okazaki, Y., Muramatsu, M. & Hayashizaki, Y. (2000) Genome Res. 10, 1617-1630.
30. Ewing, B. & Green, P. (1998) Genome Res. 8, 186-194.
31. Pruitt, K. D. & Maglott, D. R. (2001) Nucleic Acids Res. 29, 137-140.
32. Wheeler, D. L., Chappey, C., Lash, A. E., Leipe, D. D., Madden, T. L., Schuler, G. D., Tatusova, T. A. & Rapp, B. A. (2000) Nucleic Acids Res. 28, 10-14.
33. Sokal, R. R. & Rohlf, F. J. (1995) in Biometry: The Principles and Practice of Statistics in Biological Research (Freeman, New York), pp. 724-743.
34. Suzuki, H., Fukunishi, Y., Kagawa, I., Saito, R., Oda, H., Endo, T., Kondo, S., Bono, H., Okazaki, Y. & Hayashizaki, Y. (2001) Genome Res. 11, 1758-1765.
35. Seki, M., Narusaka, M., Yamaguchi-Shinozaki, K., Carninci, P., Kawai, J., Hayashizaki, Y. & Shinozaki, K. (2001) Plant Physiol. Biochem. 39, 211-220.
36. Kristiansen, T. Z. & Pandey, A. (2002) Trends Biochem. Sci. 27, 266-267.
37. Suzuki, Y., Yamashita, R., Nakai, K. & Sugano, S. (2002) Nucleic Acids Res. 30, 328-331.
38. Konno, H., Fukunishi, Y., Shibata, K., Itoh, M., Carninci, P., Sugahara, Y. & Hayashizaki, Y. (2001) Genome Res. 11, 281-289.
39. Osato, N., Itoh, M., Konno, H., Kondo, S., Shibata, K., Carninci, P., Shiraki, T., Shinagawa, A., Arakawa, T., Kikuchi, S., et al. (2002) Genome Res. 12, 1127-1134.
40. Stapleton M., Liao G., Brokstein, P., Hong L., Carninci P., Shiraki T., Hayashizaki, Y., Champe, M., Pacleb J., Wan, K., et al. (2002) Genome Res. 12, 1294-1300.
41. Seki, M., Carninci, P., Nishiyama, Y., Hayashizaki, Y. & Shinozaki, K. (1998) Plant J. 15, 707-720.
42. Seki, M., Narusaka, M., Kamiya, A.; Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama K., Oono, Y., et al. (2002) Science 296, 141-145.
43. Lewin, B. (2000) Genes VII (Oxford Univ. Press, Oxford).
44. Schmidt, W. M. & Mueller, M. W. (1999) Nucleic Acids Res. 27, e31.
45. Altschul, S., Madden, T., Schaffer, A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. (1997) Nucleic Acids Res. 25, 3389-3402.
46. Huang, X. & Madan, A. (1999) Genome Res. 9, 868-877.
47. Galuszka, P., Frebort, I., Sebela, M., Sauer, P., Jacobsen, S. & Pec, P. (2001) Eur. J. Biochem. 268, 450-461.
48. Yang, S. H., Yu, H. & Goh, C. J. (2002) J. Exp. Bot. 53, 1899-1907.
49. Leech, M. J., Kammerer, W., Cove, D. J., Martin, C. & Wang, T. L. (1993) Plant J. 3, 51-61.
50. Sakakibara, K., Nishiyama, T., Kato, M. & Hasebe, M. (2001) Mol. Biol. Evol. 18, 491-502.
51. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) Nat. Genet. 25, 25-29.
52. Apweiler, R., Attwood, T. K., Bairoch, A., Bateman A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F.; Croning, M. D., et al. (2001) Nucleic Acids Res. 29, 37-40.
53. Tanaka, K., Yonekawa, T., Kawasaki, Y., Kai, M., Furuya, K., Iwasaki, M., Murakami, H., Yanagida, M. & Okayama, IA. (2000) Mol. Cell. Biol. 20, 3459-3469.
54. Kadyk, L. C. & Hartwell, L. H. (1992) Genetics 132, 387-402.
55. Tanaka, K., Hao, Z., Kai, M. & Okayama, H. (2001) EMBO. 20, 5779-5790.
56. Gagne, G. & Guertin, M. (1992) Plant Mol. Biol. 18, 429-445.
57. Karol, K. G., McCourt, R. M., Cimino, M. T. & Delwiche, C. F. (2001) Science 294, 2351-2353.