A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

Genome Research

Volumn 15, Issue 9, 2005, Pages 1274-1283

  Ma, Ligeng ^a,b,c,f   Chen, Chen ^d,e   Liu, Xigang ^a,b,f   Jiao, Yuling ^c   Su, Ning ^c   Li, Lin ^d   Wang, Xiangfeng ^a,b,d   Cao, Mengliang ^g   Sun, Ning ^h   Zhang, Xiuqing ^d,i   Bao, Jingyue ^d,e   Li, Jian ⁱ   Pedersen, Soren ⁱ   Bolund, Lars ⁱ   Zhao, Hongyu ^h   Yuan, Longping ^g   Gane, Ka Shu Wong ^d,j   Wang, Jun ^d,e,i   Xing, Wang Deng ^a,b,c   Wang, Jian ^d,e  

^a PEKING UNIVERSITY   (China)

^b NATIONAL INSTITUTE OF BIOLOGICAL SCIENCES   (China)

^c YALE UNIVERSITY   (United States)

^d INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^e ZHEJIANG UNIVERSITY   (China)

^f HEBEI NORMAL UNIVERSITY   (China)

^g China National Hybrid Rice Research and Development Center   (China)

^h YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

ⁱ AARHUS UNIVERSITY   (Denmark)

^j UNIVERSITY OF WASHINGTON   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARABIDOPSIS; ARTICLE; DNA MICROARRAY; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; MOLECULAR MODEL; NONHUMAN; OLIGOMERIZATION; PLANT GENETICS; PREDICTION; PRIORITY JOURNAL; RICE; SEQUENCE HOMOLOGY;

ARABIDOPSIS; GENE EXPRESSION PROFILING; GENOME, PLANT; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; ORYZA SATIVA; PROTEASOME ENDOPEPTIDASE COMPLEX; SPECIES SPECIFICITY; TRANSCRIPTION, GENETIC; UBIQUITIN;

ARABIDOPSIS;

EID: 24344508130     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3657405     Document Type: Article

References (54)

1. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. 2002. Molecular Biology of the Cell. Garland Publishing, New York.
2. Altschul, S.F. and Gish, W. 1996. Local alignment statistics. Methods Enzymol. 266: 460-480.
3. The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
4. Ashurst, J.L. and Collins, J.E. 2003. Gene annotation: Prediction and testing. Annu. Rev. Genomics Human Genet. 4: 69-88.
5. Bennetzen, J. 2002. The rice genome: Opening the door to comparative plant biology. Science 296: 60-63.
6. Bennetzen, J., Coleman, C., Liu, R., Na, J., and Ramakrishna, W. 2004. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7: 732-736.
7. Birnbaum, K., Shasha, D.E., Wang, J.Y., Jung, J.W., Lambert, G.M., Galbraith, D.W., and Benfey P.N. 2003. A gene expression map of the Arabidopsis root. Science 302: 1956-1960.
8. Caron, H., van Schaik, B., van der Mee, M., Baas, F., Riggins, G., van Sluis, P., Hermus, M., van Asperen, R., Boon, K., Voûte, P.A., et al. 2001. The human transcriptome map: Clustering of highly expressed genes in chromosomal domains. Science 291: 1289-1292.
9. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O., and Herskowitz, I. 1998. The transcriptional program of sporulation in budding yeast. Science 282: 699-705.
10. Cohen, B.A., Mitra, R.D., Hughes, J.D., and Church, G.M. 2000. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat. Genet. 26: 183-186.
11. Domazet-Loso, T. and Tautz, D. 2003. An evolutionary analysis of orphan genes in Drosophila. Genome Res. 13: 2213-2219.
12. Feng, Q., Zhang, Y., Hao, P., Wang, S., Fu, G., Huang, Y., Li, Y., Zhu, J., Liu, Y., Hu, X., et al. 2002. Sequence and analysis of rice chromosome 4. Nature 420: 316-320.
13. Gale, M.D. and Devos, K.M. 1998. Plant comparative genetics after 10 years. Science 282: 656-659.
14. Goff, S.A., Ricke, D., Lan, T., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296: 92-100.
15. Hellmann, H. and Estelle, M. 2002. Plant development: Regulation by protein degradation. Science 297: 793-797.
16. Hurst, L.D., Pal, C., and Lercher, M.J. 2004. The dynamics of eukaryotic gene order. Nat. Rev. Genet. 5: 299-310.
17. Izawa, T., Takahashi, Y., and Yano, M. 2003. Comparative biology comes into bloom: Genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Curr. Opin Plant Biol. 6: 113-120.
18. Jabbari, K., Cruveiller, S., Clay, O., Saux, J.L., and Bernardi, G. 2004. The new genes of rice: A closer look. Trends Plant Sci. 9: 281-285.
19. Jiang, N., Bao, Z., Zhang, X., Eddy, S., and Wessler, S.R. 2004. Pack-MULES: Transposon-mediated gene evolution in plants. Nature 431: 569-573.
20. Kapranov, P., Cawley, S.E., Drenkow, J., Bekiranov, S., Strausberg, R.L., Fodor, S.P., and Gingeras, T.R. 2002. Large-scale transcriptional activity in chromosome 21 and 22. Science 296: 916-919.
21. Kellogg, E.A. 2003. What happens to genes in duplicated genomes. Proc. Natl. Acad. Sci. 100: 4369-4371.
22. Kikuchi, S., Satoh, K., Nagata, T., Kawagashira, N., Doi, K., Kishimoto, N., Yazaki, J., Ishikawa, M., Yamada, H., Ooka, H., et al. 2003. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science 301: 376-379.
23. Kim, H., Snesrud, E.C., Haas, B., Cheung, F., Town, C.D., and Quackenbush, J. 2003. Gene expression analysis of Arabidopsis chromosome 2 using a genomic DNA amplicon microarray. Genome Res. 13: 327-340.
24. Koonin, E.V., Aravind, L., and Kondrashov, A.S. 2000. The impact of comparative genomics on our understanding of evolution. Cell 101: 573-576.
25. Labrador, M. and Corces, V.G. 2002. Setting the boundaries of chromatin domains and nuclear organization. Cell 111: 151-154.
26. Lercher, M.J., Urrutia, A.O., and Hurst, L.D. 2002. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat. Genet. 31: 180-183.
27. Ma, L., Li, J., Qu, L., Hager, J., Chen, Z., Zhao, H., and Deng, X.W. 2001. Light control of Arabidopsis development entails coordinated regulation of genome expression and cellular pathways. Plant Cell 13: 2589-2607.
28. Ma, L., Gao, Y., Li, J., Chen, Z., Li, J., Zhao, H., and Deng, X.W. 2002. Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis. Plant Cell 14: 2383-2398.
29. Ma, L., Sun, N., Liu, X., Jiao, Y., Zhao, H., and Deng, X.W. 2005. Organ-specific genome expression atlas during Arabidopsis development. Plant Physiol. 138: 80-91.
30. Martinez-Zapater, J.M. and Salinas, J. 1998. Arabidopsis protocols, pp. 27-30. Humana Press, Totowa, NJ.
31. McCarroll, S.A., Murphy, C.T., Zou, S., Pletcher, S.D., Chin, C.S., Jan, Y.N., Kenyon, C., Bargmann, C.I., and Li, H. 2004. Comparing genomic expression patterns across species identifies shared transcriptional profile in aging. Nat. Genet. 36: 197-204.
32. Meyerowitz, E.M. 2002. Plants compared to animals: The broadest comparative study of development. Science 295: 1482-1485.
33. Nojiri, H., Sugimori, M., Yamane, H., Nishimura, Y., Yamada, A., Shibuya, N., Kodama, O., Murofushi, N., and Omori, T. 1996. Involvement of jasmonic acid in elicitor-induced phytoalexin production in suspension-cultured rice cells. Plant Physiol. 110: 387-392.
34. Pickart, C.M. and Cohen, R.E. 2004. Proteasomes and their kin: Proteases in the machine age. Nat. Rev. Mol. Cell. Biol. 5: 177-187.
35. Prince, V.E. and Pickett, F.B. 2002. Splitting pairs: The diverging fates of duplicated genes. Nat. Rev. Genet. 3: 827-837.
36. The Rice Chromosome 10 Sequencing Consortium. 2003. In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300: 1566-1569.
37. Rinn, J.L., Euskirchen, G., Bertone, P., Martone, R., Luscombe, N.M., Hartman, S., Harrison, P.M., Nelson, F.K., Miller, P., Gerstein, M., et al. 2003. The transcriptional activity of human Chromosome 22. Genes & Dev. 17: 529-540.
38. Sasaki, T., Matsumoto, T., Yamamoto, K., Sakata, K., Baba, T., Katayose, Y., Wu, J., Niimura, Y., Cheng, Z., Nagamura, Y., et al. 2002. The genome sequence and structure of rice chromosome 1. Nature 420: 312-316.
39. Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270: 467-470.
40. Schoof, H. and Karlowski, W.M. 2003. Comparison of rice and Arabidopsis annotation. Curr. Opin. Plant Biol. 6: 106-112.
41. Sengupta, R. and Tompa, M. 2002. Quality control in manufacturing oligo arrays: A combinatorial design approach. J. Comput. Biol. 9: 1-22.
42. Serino, G. and Deng, X.W. 2003. The COP9 signalosome: Regulating plant development through the control of proteolysis. Annu. Rev. Plant Biol. 54: 165-182.
43. Spellman, P.T. and Rubin, G.M. 2002. Evidence for large domains of similarly expressed genes in the Drosophila genome. J. Biol. 1: 1-8.
44. Sullivan, J.A., Shirasu, K., and Deng, X.W. 2003. The diverse roles of ubiquitin and the 26S proteasome in the life of plants. Nat. Rev. Genet. 4: 948-958.
45. Vierstra, R.D. 2003. The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends Plant Sci. 8: 135-142.
46. Wu, J., Maehara, T., Shimokawa, T., Yamamoto, S., Harada, C., Takazaki, Y., Ono, N., Mukai, Y., Koike, K., Yazaki, J., et al. 2002. A comprehensive rice transcript map containing 6591 expressed sequence tag sites. Plant Cell 14: 525-535.
47. Yamada, K., Lim, J., Dale, J.M., Chen, H., Shinn, P., Palm, C.J., Southwick, A.M., Wu, H.C., Kim, C., Nguyen, M., et al. 2003. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302: 842-846.
48. Yu, J., Hu, S., Wang, J., Wong, G.K.S, Li, S., Liu, B., Deng, Y., Dai, L., Zhou, Y., Zhang, X., et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica) Science 296: 79-92.
49. Yu, J., Wang, J., Lin, W., Li, S., Li, H., Zhou, J., Ni, P., Dong, W., Hu, S., Zeng, C, et al. 2005. The genome sequence of indica and japonica rice. PLoS Biol. 3: e38.
50. Zhao, W., Wang, J., He, X., Huang, X., Jiao, Y., Dai, M., Wei, S., Fu, J., Chen, Y., Ren, X., et al. 2004. BGI-RIS: An integrated information resource and comparative analysis workbench for rice genomic. Nucleic Acids Res. 32: D377-D382.
51. http://info.med.yale.edu/wmkeck/dna_arrays.htm; Yale University DNA laboratory.
52. http://rise.genomics.org.cn; Phase II rice genome assembly, October 2002.
53. http://www.geneontology.org; Gene Ontology.
54. http://rgp.dna.affrc.go.jp/index.html; Japan Rice Genome Program.