Sequencing and analysis of approximately 40 000 soybean Cdna clones from a full-length-enriched Cdna library

Taishi Umezawa, Tetsuya Sakurai, Yasushi Totoki, Atsushi Toyoda, Motoaki Seki, Atsushi Ishiwata, Kenji Akiyama, Atsushi Kurotani, Takuhiro Yoshida, Keiichi Mochida, Mie Kasuga, Daisuke Todaka, Kyonoshin Maruyama, Kazuo Nakashima, Akiko Enju, Saho Mizukado, Selina Ahmed, Kyoko Yoshiwara, Kyuya Harada, Yasutaka TsubokuraMasaki Hayashi, Shusei Sato, Toyoaki Anai, Masao Ishimoto, Hideyuki Funatsuki, Masayoshi Teraishi, Mitsuru Osaki, Takuro Shinano, Ryo Akashi, Yoshiyuki Sakaki, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki

Research output: Contribution to journalArticle

69 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)333-346
Number of pages14
JournalDNA Research
Volume15
Issue number6
DOIs
Publication statusPublished - Dec 2008
Externally publishedYes

Fingerprint

Soybeans
Libraries
Clone Cells
Complementary DNA
Expressed Sequence Tags
Genes
5' Untranslated Regions
Genetic Association Studies
3' Untranslated Regions
Gene Library
Arabidopsis
Fabaceae
Sequence Analysis
Genome

Keywords

  • EST
  • Full-length cDNA
  • Functional annotation
  • Legume
  • Soybean

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Medicine(all)

Cite this

Umezawa, T., Sakurai, T., Totoki, Y., Toyoda, A., Seki, M., Ishiwata, A., ... Shinozaki, K. (2008). Sequencing and analysis of approximately 40 000 soybean Cdna clones from a full-length-enriched Cdna library. DNA Research, 15(6), 333-346. https://doi.org/10.1093/dnares/dsn024

Sequencing and analysis of approximately 40 000 soybean Cdna clones from a full-length-enriched Cdna library. / Umezawa, Taishi; Sakurai, Tetsuya; Totoki, Yasushi; Toyoda, Atsushi; Seki, Motoaki; Ishiwata, Atsushi; Akiyama, Kenji; Kurotani, Atsushi; Yoshida, Takuhiro; Mochida, Keiichi; Kasuga, Mie; Todaka, Daisuke; Maruyama, Kyonoshin; Nakashima, Kazuo; Enju, Akiko; Mizukado, Saho; Ahmed, Selina; Yoshiwara, Kyoko; Harada, Kyuya; Tsubokura, Yasutaka; Hayashi, Masaki; Sato, Shusei; Anai, Toyoaki; Ishimoto, Masao; Funatsuki, Hideyuki; Teraishi, Masayoshi; Osaki, Mitsuru; Shinano, Takuro; Akashi, Ryo; Sakaki, Yoshiyuki; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo.

In: DNA Research, Vol. 15, No. 6, 12.2008, p. 333-346.

Research output: Contribution to journalArticle

Umezawa, T, Sakurai, T, Totoki, Y, Toyoda, A, Seki, M, Ishiwata, A, Akiyama, K, Kurotani, A, Yoshida, T, Mochida, K, Kasuga, M, Todaka, D, Maruyama, K, Nakashima, K, Enju, A, Mizukado, S, Ahmed, S, Yoshiwara, K, Harada, K, Tsubokura, Y, Hayashi, M, Sato, S, Anai, T, Ishimoto, M, Funatsuki, H, Teraishi, M, Osaki, M, Shinano, T, Akashi, R, Sakaki, Y, Yamaguchi-Shinozaki, K & Shinozaki, K 2008, 'Sequencing and analysis of approximately 40 000 soybean Cdna clones from a full-length-enriched Cdna library', DNA Research, vol. 15, no. 6, pp. 333-346. https://doi.org/10.1093/dnares/dsn024
Umezawa, Taishi ; Sakurai, Tetsuya ; Totoki, Yasushi ; Toyoda, Atsushi ; Seki, Motoaki ; Ishiwata, Atsushi ; Akiyama, Kenji ; Kurotani, Atsushi ; Yoshida, Takuhiro ; Mochida, Keiichi ; Kasuga, Mie ; Todaka, Daisuke ; Maruyama, Kyonoshin ; Nakashima, Kazuo ; Enju, Akiko ; Mizukado, Saho ; Ahmed, Selina ; Yoshiwara, Kyoko ; Harada, Kyuya ; Tsubokura, Yasutaka ; Hayashi, Masaki ; Sato, Shusei ; Anai, Toyoaki ; Ishimoto, Masao ; Funatsuki, Hideyuki ; Teraishi, Masayoshi ; Osaki, Mitsuru ; Shinano, Takuro ; Akashi, Ryo ; Sakaki, Yoshiyuki ; Yamaguchi-Shinozaki, Kazuko ; Shinozaki, Kazuo. / Sequencing and analysis of approximately 40 000 soybean Cdna clones from a full-length-enriched Cdna library. In: DNA Research. 2008 ; Vol. 15, No. 6. pp. 333-346.
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AU - Seki, Motoaki

AU - Ishiwata, Atsushi

AU - Akiyama, Kenji

AU - Kurotani, Atsushi

AU - Yoshida, Takuhiro

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AU - Maruyama, Kyonoshin

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AU - Enju, Akiko

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AU - Ahmed, Selina

AU - Yoshiwara, Kyoko

AU - Harada, Kyuya

AU - Tsubokura, Yasutaka

AU - Hayashi, Masaki

AU - Sato, Shusei

AU - Anai, Toyoaki

AU - Ishimoto, Masao

AU - Funatsuki, Hideyuki

AU - Teraishi, Masayoshi

AU - Osaki, Mitsuru

AU - Shinano, Takuro

AU - Akashi, Ryo

AU - Sakaki, Yoshiyuki

AU - Yamaguchi-Shinozaki, Kazuko

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