Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags

Plant Journal

Volumn 33, Issue 6, 2003, Pages 1001-1011

  Ogihara, Yasunari ^a   Mochida, Keiichi ^a   Nemoto, Yasue ^a   Murai, Koji ^b   Yamazaki, Yukiko ^c   Shin I, Tadasu ^c   Kohara, Yuji ^c  

^a YOKOHAMA CITY UNIVERSITY   (Japan)

^b FUKUI PREFECTURAL UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Correlation clustering of expression patterns; Functional genomics; Gene search in wheat; Hexaploid wheat; Large scale EST analysis; Virtual display

Indexed keywords

DNA; GENES; GROWTH KINETICS; SEED; STATISTICAL METHODS;

EXPRESSED SEQUENCE TAGS (EST);

GENETIC ENGINEERING;

CONTIG MAPPING; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENOME, PLANT; GENOMICS; MOLECULAR SEQUENCE DATA; TRITICUM;

GENES; GENETIC ENGINEERING; NUCLEIC ACIDS; SEEDS; STATISTICAL ANALYSIS;

EMBRYOPHYTA; EUKARYOTA; TRITICUM AESTIVUM;

EID: 0037356771     PISSN: 09607412     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-313X.2003.01687.x     Document Type: Article

References (59)

1. Aharoni, A. and Vorst, O. (2001) DNA microarrays for functional plant genomics. Plant Mol. Biol. 48, 99-118.
2. Adams, M.D., Kerlavage, A.R., Fields, C. and Venter, J.C. (1993) 3400 expressed sequence tags identify diversity of transcripts from human brain. Nat. Genet. 4, 256-267.
3. Allaby, R.G., Banerjee, M. and Brown, T.A. (1999) Evolution of the high molecular weight glutenin loci of the A, B, D, and G genomes of wheat. Genome, 42, 296-307.
4. Arumuganathan, K. and Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208-218.
5. Bennetzen, J. (2002) Opening the door to comparative plant biology. Science, 296, 60-63.
6. Blanc, G., Barakat, A., Guyot, R., Cooke, R. and Delseny, M. (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell, 12, 1093-1101.
7. Bowman, J., Alvarez, J., Weigel, D., Meyerowitz, E. and Smyth, D. (1993) Control of flower development in Arabidopsis thaliana by apetala 1 and interacting genes. Development, 119, 721-743.
8. Brown, P.O. and Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21, 33-37.
9. Christensen, A.H., Sharrock, R.A. and Quail, P.H. (1992) Maize polyubiquitin genes: structure, thermal perturbation of expression and transcript splicing, and promoter activity following transfer to protoplasts by electroporation. Plant Mol. Biol. 18, 675-689.
10. Deng X.W. (1998) Light control of Arabidopsis developmental pattern. Symp. Soc. Exp. Biol. 51, 93-96.
11. Desormeaux, A., Blochet, J.E., Pezolet, M. and Marion, D. (1992) Amino acid sequence of a non-specific wheat phospholipid transfer protein and its conformation as revealed by infrared and Raman spectroscopy. Role of disulfide bridges and phospholipids in the stabilization of the alpha-helix structure. Biochim. Biophys. Acta, 1121, 137-152.
12. Doebley, J. and Lukens, L. (1998) Transcriptional regulators and the evolution of plant form. Plant Cell, 10, 1075-1082.
13. Dunn, M.A., Morris, A., Jack, P.L. and Hughes, M.A. (1993) A low temperature-responsive translation elongation factor 1α from barley (Hordeum vulgare L.). Plant Mol. Biol. 23, 221-225.
14. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95, 14863-14868.
15. Ewing, R.M., Kahla, A.B., Poirot, O., Lopez, F., Audic, S. and Claverie, J.-M. (1999) Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9, 950-959.
16. Feekes, W. (1941) De Tarwe en haar milieu. Vers XVII Tech Tarwe Comm. Groningen, pp. 560-561.
17. Feuillet, C. and Keller, B. (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann. Bot. 89, 3-10.
18. Galili, S., Galili, G., Avivi, Y. and Feldman, M. (1992) Identification and chromosomal location of four subfamilies of the rubisco small subunit genes in common wheat. Theor. Appl. Genet. 83, 385-391.
19. Goff, S.A., Ricke, D., Lan, T.-H. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 296, 92-100.
20. Harberd, N.P., Bartels, D. and Thompson, R.D. (1985) Analysis of the gliadin multigene loci in bread wheat using nullisomic-tetrasomic lines. Mol. Gen. Genet. 198, 234-242.
21. Harberd, N.P., Bartels, D. and Thompson, R.D. (1986) DNA restriction fragment variation in the gene family encoding high molecular weight (HMW) glutenin subunits of wheat. Biochem. Genet. 24, 579-596.
22. Hofer, J., Turner, L., Hellens, R., Ambrose, M., Matthews, P., Machael, A. and Ellis, N. (1997) Unifoliata regulates leaf and flower morphogenesis in pea. Curr. Biol. 7, 581-587.
23. Hoyer-Fender, S., Costanzi, C. and Pehrson, J.R. (2000) Histone macroH2A1.2 is concentrated in the XY-body bythe early pachytene stage of spermatogenesis. Exp. Cell Res. 258, 254-260.
24. Huh, G.H., Nakayama, T., Meshi, T. and Iwabuchi, M. (1997) Structural characteristics of two wheat histone H2A genes encoding distinct types of variants and function differences in their promoter activity. Plant Mol. Biol. 33, 791-802.
25. Jeong, J.-S., Lee, S., Jung, K.-H., Jun, S.-H., Kim, C. and An, G. (2000) Tissue-preferential expression of a rice α-tubulin gene, OsTubA1, mediated by the first intron. Plant Physiol. 123, 1005-1014.
26. Karlin, S. and Altschul, S.F. (1993) Applications and statistics for multiple high scoring segments in molecular sequences. Proc. Natl. Acad. Sci. USA, 90, 5873-5877.
27. Lange, J., Xie, Z.-P., Broughton, W.J., Voegeli-Lange, R. and Boller, T. (1999) A gene encoding a receptor-like protein kinase in the roots of common bean is differentially regulated in response to pathogens, symbionts and nodulation factors. Plant Sci. 142, 133-145.
28. Lee, J.-S., Seok, S.-J. and Eun, M.-Y. (1998) Molecular cloning and characterization of two translation initiation factor genes in rice. DDBJ Accession no. AF094773.
29. Martinez-Garcia, J.F and Quail, P.H. (1999) The HMG-I/Y protein PF1 stimulates binding of the transcriptional activator GT-2 to the PHYA gene promoter. Plant J. 18, 173-83.
30. Masterson, J. (1994) Stomatal size in fossil plants: evidence for polyploidy in the majority of angiosperms. Science, 264, 421-424.
31. Murai, K., Murai, R., Takumi, S. and Ogihara, Y. (1998) cDNA cloning of three MADS box genes in wheat. Plant Physiol. 118, 330.
32. Newman, T., de Bruijin, F.J., Green, D. et al. (1994) Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol. 106, 1241-1255.
33. Nomura, T., Ishihara, A., Imaishi, H., Endo, T.R., Ohkawa, H. and Iwamura, H. (2002) Molecular characterization and chromosomal localization of cytochrome P450 genes involved in the biosynthesis of cyclic hydrozamic acids in hexaploid wheat. Mol. Genet. Genom. 267, 210-217.
34. Ogihara, Y., Aizawa, Y., Kawakami, N. and Murai, K. (1998) Cloning of cDNAs specifically expressed in wheat spikelets at the heading stage as identified by the simple display method. Plant Sci. 135, 49-62.
35. Ogihara, Y., Shimizu, H., Hasegawa, K., Tsujimoto, H. and Sasakuma, T. (1994) Chromosome assignment of four photosynthesis-related genes and their variability in wheat species. Theor. Appl. Genet. 88, 383-394.
36. Oka, H.I. (1988) Origin of Cultivated Rice. Amsterdam: Elsevier Publications.
37. Ozkan, H., Levy, A.A. and Feldman, M. (2001) Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group. Plant Cell, 13, 1735-1747.
38. Paterson, A.H., Bowers, J.E., Burow, M.D. et al. (2000) Comparative genomics of plant chromosomes. Plant Cell, 12, 1523-1540.
39. Payne, P.I., Holt, L.M. and Law, C.N. (1981) Structural and genetic studies on the high molecular weight subunits of wheat glutenin. Theor. Appl. Genet. 60, 229-236.
40. Rafalski, J.A. (1986) Structure of wheat gamma-gliadin genes. Gene, 43, 221-229.
41. 2+-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. Plant J. 23, 319-327.
42. Sasanuma, T. (2001) Characterization of the rbcS multigene family in wheat: subfamily classification, determination of chromosomal location and evolutionary analysis. Mol. Genet. Genom. 265, 161-171.
43. Schaffer, R., Landgraf, J., Accerbi, M., Simon, V., Larson, M. and Wisman, E. (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell, 13, 113-123.
44. Schmitz, J., Franzen, R., Ngyuen, T.H., Garcia-Maroto, F., Pozzi, C., Salamini, F. and Rohde, W. (2000) Cloning, mapping and expression analysis of barley MADS-box genes. Plant Mol. Biol. 42, 899-913.
45. Seki, M., Narusaka, M., Abe, H., Kasuga, M., Yamaguchi-Schinozaki, K., Carninci, P., Hayashizaki, Y. and Shinozaki, K. (2001) Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray. Plant Cell, 13, 61-72.
46. Seki, M., Narusaka, M., Kamiya, A. et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science, 296, 141-145.
47. Shen, W.H. and Gigot, C. (1999) Characterization of Prt1, a gene encoding for one of the subunits of the translation initiation factor 3 (elF3), from Nicotiana tabacum. Plant Sci. 143, 45-54.
48. Snowden, K.C and Gardner, R.C. (1993) Five genes induced by aluminum in wheat (Triticum aestivum L.) roots. Plant Physiol. 103, 855-861.
49. Tabata, T. Sasaki, K. and Iwabuchi, M. (1983) The structural organization and DNA sequence of a wheat histone H4 gene. Nucl. Acids Res. 11, 5865-5875.
50. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
51. Tsunewaki, K. (1993) Genome-plasmon interaction in wheat. Jpn. J. Genet. 68, 1-34.
52. Van Campenhout, S., Sagi, L., Vander Stappen, J. and Bolckaert, G. (1998) Characterisation of type-I thionin loci from the A, B, D and R genomes of wheat and rye. Theor. Appl. Genet. 96, 80-86.
53. Von Bueren, M., Luethy, J. and Huebner, P. (2000) A spelt-specific gamma-gliadin: discovery and detection. Theor. Appl. Genet. 100, 271-279.
54. Wendel, J.F. (2000) Genome evolution in polyploids. Plant Mol. Biol. 42, 225-249.
55. Yamamoto, K. and Sasaki, T (1997) Large-scale EST sequencing in rice. Plant Mol. Biol. 35, 135-144.
56. Yang, P., Taoka, K., Nakayama, T. and Iwabuchi, M. (1995) Structural and functional characterization of two wheat histone H2B promoters. Plant Mol. Biol. 28, 155-172.
57. Yazaki, J., Kishimoto, N., Nakamura, K. et al. (2000) Embarking on rice functional genomics via cDNA microarray: use of 3′ UTR probes for specific gene expression analysis. DNA Res. 7, 367-370.
58. Yu J., Hu, S., Wang, J. et al. (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296, 79-92.
59. Zohary, D. and Hopf, M. (2001) Domestication of Plants in the Old World, 3rd edn. New York: Oxford University Press.