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PMID: 18927222 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

DNA research : an international journal for rapid publication of reports on genes and genomes ·Vol. 15 ·No. 6 ·2008-12-00 ·Pages 333-46

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

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.

MeSH Terms
Animals Cloning, Molecular DNA, Complementary Expressed Sequence Tags/chemistry Gene Expression Profiling Gene Expression Regulation, Plant Gene Library Genome, Plant Molecular Sequence Data Nematoda/physiology Plant Diseases/parasitology Sequence Analysis, DNA Soybeans/genetics,growth & development,parasitology,physiology
Chemicals
DNA, Complementary
Authors & Affiliations
32 authors, click to expand affiliations / ORCID
Umezawa Taishi
Gene Discovery Research Team, RIKEN Plant Science Center, Koyadai 3-1-1, Tsukuba, Ibaraki 305-0074, Japan.
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
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Article Info
Journal
DNA research : an international journal for rapid publication of reports on genes and genomes
Abbr.
DNA Res
ISSN
1756-1663
DOI
10.1093/dnares/dsn024
Published
2008-12-00
Epub
2008-00-16
Pages
333-46
Language
English
Region
England
NLM ID
9423827
PMCID
PMC2608845
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1093/dnares/dsn024 PMC Full Text View journal details
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