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Originally published in Science Express on 21 March 2002
Science 5 April 2002:
Vol. 296. no. 5565, pp. 141 - 145
DOI: 10.1126/science.1071006
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Reports

Functional Annotation of a Full-Length Arabidopsis cDNA Collection

Motoaki Seki,12 Mari Narusaka,1 Asako Kamiya,1 Junko Ishida,1 Masakazu Satou,1 Tetsuya Sakurai,1 Maiko Nakajima,1 Akiko Enju,1 Kenji Akiyama,1 Youko Oono,23 Masami Muramatsu,45 Yoshihide Hayashizaki,45 Jun Kawai,45 Piero Carninci,45 Masayoshi Itoh,45 Yoshiyuki Ishii,45 Takahiro Arakawa,45 Kazuhiro Shibata,45 Akira Shinagawa,45 Kazuo Shinozaki12*

Full-length complementary DNAs (cDNAs) are essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products. We isolated 155,144 RIKEN Arabidopsis full-length (RAFL) cDNA clones. The 3'-end expressed sequence tags (ESTs) of 155,144 RAFL cDNAs were clustered into 14,668 nonredundant cDNA groups, about 60% of predicted genes. We also obtained 5' ESTs from 14,034 nonredundant cDNA groups and constructed a promoter database. The sequence database of the RAFL cDNAs is useful for promoter analysis and correct annotation of predicted transcription units and gene products. Furthermore, the full-length cDNAs are useful resources for analyses of the expression profiles, functions, and structures of plant proteins.

1 Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center (GSC), 3-1-1 Koyadai, Tsukuba 305-0074, Japan.
2 Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba 305-0074, Japan.
3 Master's Program in Biosystem Studies, University of Tsukuba, Tennoudai, Tsukuba, Ibaraki, 305-0074, Japan.
4 Laboratory for Genome Exploration Research Group, RIKEN GSC, Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokokama, Kanagawa, 230-0045, Japan.
5 Genome Science Laboratory, RIKEN, 2-1 Hirosawa, Wako, 351-0198, Japan.
*   To whom correspondence should be addressed. Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba 305-0074, Japan. E-mail: sinozaki{at}rtc.riken.go.jp

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mRNA sequence features that contribute to translational regulation in Arabidopsis.
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Nucleic Acids Res. 33, 955-965
   Abstract »    Full Text »    PDF »
Expression of cellulose synthase-like (Csl) genes in insect cells reveals that CslA family members encode mannan synthases.
A. H. Liepman, C. G. Wilkerson, and K. Keegstra (2005)
PNAS 102, 2221-2226
   Abstract »    Full Text »    PDF »
Bicistronic and fused monocistronic transcripts are derived from adjacent loci in the Arabidopsis genome.
J. THIMMAPURAM, H. DUAN, L. LIU, and M. A. SCHULER (2005)
RNA 11, 128-138
   Abstract »    Full Text »    PDF »
RARTF: Database and Tools for Complete Sets of Arabidopsis Transcription Factors..
K. Iida, M. Seki, T. Sakurai, M. Satou, K. Akiyama, T. Toyoda, A. Konagaya, and K. Shinozaki (2005)
DNA Res 12, 247-256
   Abstract »    Full Text »    PDF »
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags.
S. J. Hubbard, D. V. Grafham, K. J. Beattie, I. M. Overton, S. R. McLaren, M. D.R. Croning, P. E. Boardman, J. K. Bonfield, J. Burnside, R. M. Davies, et al. (2005)
Genome Res. 15, 174-183
   Abstract »    Full Text »    PDF »
RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.
T. Sakurai, M. Satou, K. Akiyama, K. Iida, M. Seki, T. Kuromori, T. Ito, A. Konagaya, T. Toyoda, and K. Shinozaki (2005)
Nucleic Acids Res. 33, D647-D650
   Abstract »    Full Text »    PDF »
New Subunits NDH-M, -N, and -O, Encoded by Nuclear Genes, Are Essential for Plastid Ndh Complex Functioning in Higher Plants.
D. Rumeau, N. Becuwe-Linka, A. Beyly, M. Louwagie, J. Garin, and G. Peltier (2005)
PLANT CELL 17, 219-232
   Abstract »    Full Text »    PDF »
Characterization of Full-length Enriched Expressed Sequence Tags of Stress-treated Poplar Leaves.
T. Nanjo, N. Futamura, M. Nishiguchi, T. Igasaki, K. Shinozaki, and K. Shinohara (2004)
Plant Cell Physiol. 45, 1738-1748
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Solution Structure of the B3 DNA Binding Domain of the Arabidopsis Cold-Responsive Transcription Factor RAV1.
K. Yamasaki, T. Kigawa, M. Inoue, M. Tateno, T. Yamasaki, T. Yabuki, M. Aoki, E. Seki, T. Matsuda, Y. Tomo, et al. (2004)
PLANT CELL 16, 3448-3459
   Abstract »    Full Text »    PDF »
Nontemplated nucleotide addition prior to polyadenylation: A comparison of Arabidopsis cDNA and genomic sequences.
Y. JIN and T. BIAN (2004)
RNA 10, 1695-1697
   Abstract »    Full Text »    PDF »
Identification of Oligopeptidase B in Higher Plants. Purification and Characterization of Oligopeptidase B from Quiescent Wheat Embryo, Triticum aestivum.
A. Tsuji, K. Yuasa, and Y. Matsuda (2004)
J. Biochem. 136, 673-681
   Abstract »    Full Text »    PDF »
Application of Genomic Technologies to Crop Plants: Opportunities and Challenges.
M. J. Havey (2004)
Crop Sci. 44, 1893-1895
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