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DNA Research Advance Access originally published online on October 16, 2008
DNA Research 2008 15(6):333-346; doi:10.1093/dnares/dsn024
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Sequencing and Analysis of Approximately 40 000 Soybean cDNA Clones from a Full-Length-Enriched cDNA Library

Taishi Umezawa1 {dagger}, Tetsuya Sakurai2 {dagger}, Yasushi Totoki3, Atsushi Toyoda4, Motoaki Seki5, Atsushi Ishiwata2, Kenji Akiyama2, Atsushi Kurotani2, Takuhiro Yoshida2, Keiichi Mochida6, Mie Kasuga7, Daisuke Todaka7,15, Kyonoshin Maruyama7, Kazuo Nakashima7, Akiko Enju5, Saho Mizukado1, Selina Ahmed7, Kyoko Yoshiwara7, Kyuya Harada8, Yasutaka Tsubokura8, Masaki Hayashi8, Shusei Sato9, Toyoaki Anai10, Masao Ishimoto11, Hideyuki Funatsuki11, Masayoshi Teraishi12, Mitsuru Osaki13, Takuro Shinano11, Ryo Akashi14, Yoshiyuki Sakaki3,4, Kazuko Yamaguchi-Shinozaki7,15 and Kazuo Shinozaki1,*

1 Gene Discovery Research Team, RIKEN Plant Science Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan
2 Integrated Genome Informatics Research Unit, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
3 Genome Annotation and Comparative Analysis Team, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
4 Sequence Technology Team, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
5 Plant Genomic Network Research Team, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
6 Gene Discovery Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
7 Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
8 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
9 Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
10 Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, Honjo 840-8502, Saga, Japan
11 National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Sapporo, Hokkaido 062-8555, Japan
12 Experimental Farm, Kyoto University, Takatsuki, Osaka 569-0096, Japan
13 Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
14 Division of BioResource, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-2192, Japan
15 Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan

Received 3 June 2008 ; accepted 10 September 2008.

A large collection of full-length cDNAs is essential for the correct annotation of genomic sequences and for the functional analysis of genes and their products. We obtained a total of 39 936 soybean cDNA clones (GMFL01 and GMFL02 clone sets) in a full-length-enriched cDNA library which was constructed from soybean plants that were grown under various developmental and environmental conditions. Sequencing from 5' and 3' ends of the clones generated 68 661 expressed sequence tags (ESTs). The EST sequences were clustered into 22 674 scaffolds involving 2580 full-length sequences. In addition, we sequenced 4712 full-length cDNAs. After removing overlaps, we obtained 6570 new full-length sequences of soybean cDNAs so far. Our data indicated that 87.7% of the soybean cDNA clones contain complete coding sequences in addition to 5'- and 3'-untranslated regions. All of the obtained data confirmed that our collection of soybean full-length cDNAs covers a wide variety of genes. Comparative analysis between the derived sequences from soybean and Arabidopsis, rice or other legumes data revealed that some specific genes were involved in our collection and a large part of them could be annotated to unknown functions. A large set of soybean full-length cDNA clones reported in this study will serve as a useful resource for gene discovery from soybean and will also aid a precise annotation of the soybean genome.

Key words: EST; full-length cDNA; functional annotation; legume; soybean

* To whom correspondence should be addressed. Tel. +81 29-836-4359. Fax. +81 29-836-9060. E-mail: sinozaki{at}rtc.riken.jp.

Edited by Satoshi Tabata

{dagger} Contributed equally to this work.


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