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

DNA Research

Volumn 15, Issue 6, 2008, Pages 333-346

  Umezawa, Taishi ^a   Sakurai, Tetsuya ^a   Totoki, Yasushi ^b   Toyoda, Atsushi ^b   Seki, Motoaki ^a   Ishiwata, Atsushi ^a   Akiyama, Kenji ^a   Kurotani, Atsushi ^a   Yoshida, Takuhiro ^a   Mochida, Keiichi ^a   Kasuga, Mie ^c   Todaka, Daisuke ^c,k   Maruyama, Kyonoshin ^c   Nakashima, Kazuo ^c   Enju, Akiko ^a   Mizukado, Saho ^a   Ahmed, Selina ^c   Yoshiwara, Kyoko ^c   Harada, Kyuya ^d   Tsubokura, Yasutaka ^d   Hayashi, Masaki ^d   Sato, Shusei ^e   Anai, Toyoaki ^f   Ishimoto, Masao ^g   Funatsuki, Hideyuki ^g   Teraishi, Masayoshi ^h   Osaki, Mitsuru ⁱ   Shinano, Takuro ^g   Akashi, Ryo ^j   Sakaki, Yoshiyuki ^b   Yamaguchi Shinozaki, Kazuko ^c,k   Shinozaki, Kazuo ^a   more..

^a RIKEN Center for Sustainable Resource Science   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c JAPAN INTERNATIONAL RESEARCH CENTER FOR AGRICULTURAL SCIENCES   (Japan)

^d NATIONAL INSTITUTE OF AGROBIOLOGICAL SCIENCES   (Japan)

^e KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^f SAGA UNIVERSITY   (Japan)

^g NATIONAL AGRICULTURAL RESEARCH CENTER FOR HOKKAIDO REGION   (Japan)

^h KYOTO UNIVERSITY   (Japan)

ⁱ HOKKAIDO UNIVERSITY   (Japan)

^j UNIVERSITY OF MIYAZAKI   (Japan)

^k UNIVERSITY OF TOKYO   (Japan)

more..

Author keywords

EST; Full length cDNA; Functional annotation; Legume; Soybean

Indexed keywords

COMPLEMENTARY DNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARABIDOPSIS; ARTICLE; DNA DETERMINATION; DNA LIBRARY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; LEGUME; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; RICE; SEQUENCE ANALYSIS; SOYBEAN; UNINDEXED SEQUENCE; ANIMAL; CHEMISTRY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; GROWTH, DEVELOPMENT AND AGING; MOLECULAR GENETICS; NEMATODE; PARASITOLOGY; PHYSIOLOGY; PLANT DISEASE;

ARABIDOPSIS; GLYCINE MAX;

ANIMALS; CLONING, MOLECULAR; DNA, COMPLEMENTARY; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENOME, PLANT; MOLECULAR SEQUENCE DATA; NEMATODA; PLANT DISEASES; SEQUENCE ANALYSIS, DNA; SOYBEANS;

EID: 59149101611     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsn024     Document Type: Article

References (44)

1. Hill, J., Nelson, E., Tilman, D., Polasky, S. and Tiffany, D. 2006, Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels, Proc. Natl Acad. Sci. USA, 103, 11206-11210.
2. The Arabidopsis Genome Initiative. 2000, Analysis of the genome sequence of the flowering plant, Arabidopsis thaliana, Nature, 408, 796-815.
3. Goff, S. A., Ricke, D., Lan, T. H., 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.
4. Tuskan, G. A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., et al. 2006, The genome of black cottonwood, Populus trichocarpa (Torr. & Gray), Science, 313, 1596-1604.
5. Yu, J., Hu, S., Wang, J., Wong, G. K., 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.
6. Tabata, S. 2002, Impact of genomics approaches on plant genetics and physiology, J. Plant Res., 115, 271-275.
7. Shoemaker, R. C., Schlueter, J. and Doyle, J. J. 2006, Paleopolyploidy and gene duplication in soybean and other legumes, Curr. Opin. Plant Biol., 9, 104-109.
8. Nelson, R. T. and Shoemaker, R. 2006, Identification and analysis of gene families from the duplicated genome of soybean using EST sequences, BMC Genomics, 7, 204.
9. Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E., Kato, T., Nakao, M., Sasamoto, S., Watanabe, A., Ono, A., Kawashima, K., et al. 2008, Genome structure of the legume, Lotus japonicus, DNA Res., 10.1093/dnares/ dsn008.
10. Shoemaker, R., Keim, P., Vodkin, L., Retzel, E., Clifton, S. W., Waterston, R., Smoller, D., Coryell, V., Khanna, A., Erpelding, J., et al. 2002, A compilation of soybean ESTs: generation and analysis, Genome, 45, 329-338.
11. Carninci, P., Kvam, C., Kitamura, A., Ohsumi, T., Okazaki, Y., Itoh, M., Kamiya, M., Shibata, K., Sasaki, N., Izawa, M., et al. 1996, High-efficiency full-length cDNA cloning by biotinylated CAP trapper, Genomics, 37, 327-336.
12. Maruyama, K. and Sugano, S. 1994, Oligo-capping: a simple method to replace thecapstructure of eukaryotic mRNAswith oligoribonucleotides, Gene, 138, 171-174.
13. Suzuki, Y., Yoshitomo-Nakagawa, K., Maruyama, K., Suyama, A. and Sugano, S. 1997, Construction and characterization of a full length-enriched and a 5′-end-enriched cDNA library, Gene, 200, 149-156.
14. Jia, J., Fu, J., Zheng, J., Zhou, X., Huai, J., Wang, J., Wang, M., Zhang, Y., Chen, X., Zhang, J., et al. 2006, Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings, Plant J., 48, 710-727.
15. 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.
16. Nanjo, T., Futamura, N., Nishiguchi, M., Igasaki, T., Shinozaki, K. and Shinohara, K. 2004, Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves, Plant Cell Physiol., 45, 1738-1748.
17. Ogihara, Y., Mochida, K., Kawaura, K., Murai, K., Seki, M., Kamiya, A., Shinozaki, K., Carninci, P., Hayashizaki, Y., Shin, I. T., et al. 2004, Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags, Genes Genet. Syst., 79, 227-232.
18. Seki, M., Narusaka, M., Kamiya, A., Ishida, J., Satou, M., Sakurai, T., Nakajima, M., Enju, A., Akiyama, K., Oono, Y., et al. 2002, Functional annotation of a full-length Arabidopsis cDNA collection, Science, 296, 141-145.
19. Haas, B. J., Volfovsky, N., Town, C. D., Troukhan, M., Alexandrov, N., Feldmann, K. A., Flavell, R. B., White, O. and Salzberg, S. L. 2002, Full-length messenger RNA sequences greatly improve genome annotation, Genome Biol., 3, 0029.0021-0029.0012.
20. Umezawa, T., Mizuno, K. and Fujimura, T. 2002, Discrimination of genes expressed in response to the ionic or osmotic effect of salt stress in soybean with cDNA-AFLP, Plant Cell Environ., 25, 1617-1625.
21. Funatsuki, H., Kawaguchi, K., Matsuba, S., Sato, Y. and Ishimoto, M. 2005, Mapping of QTL associated with chilling tolerance during reproductive growth in soybean, Theor. Appl. Genet., 111, 851-861.
22. Seki, M., Carninci, P., Nishiyama, Y., Hayashizaki, Y. and Shinozaki, K. 1998, High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper, Plant J., 15, 707-720.
23. Carninci, P., Shibata, Y., Hayatsu, N., Itoh, M., Shiraki, T., Hirozane, T., Watahiki, A., Shibata, K., Konno, H., Muramatsu, M., et al. 2001, Balanced-size and long-size cloning of full-length, cap-trapped cDNAs into vectors of the novel lambda-FLC family allows enhanced gene discovery rate and functional analysis, Genomics, 77, 79-90.
24. Dean,F. B., Nelson, J. R., Giesler, T. L. and Lasken, R. S. 2001, Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification, Genome Res., 11, 1095-1099.
25. Ewing, B. and Green, P. 1998, Base-calling of automated sequencer traces using phred. II. Error probabilities, Genome Res., 8, 186-194.
26. Ewing, B., Hillier, L., Wendl, M. C. and Green, P. 1998, Base-calling of automated sequencer traces using phred. I. Accuracy assessment, Genome Res., 8, 175-185.
27. Florea, L., Hartzell, G., Zhang, Z., Rubin, G. M. and Miller, W. 1998, A computer program for aligning a cDNA sequence with a genomic DNA sequence, Genome Res., 8, 967-974.
28. Huang, X. and Madan, A. 1999, CAP3: a DNA sequence assembly program, Genome Res., 9, 868-877.
29. Gordon, D., Abajian, C. and Green, P. 1998, Consed: a graphical tool for sequence finishing, Genome Res., 8, 195-202.
30. Pearson, W. R., Wood, T., Zhang, Z. and Miller, W. 1997, Comparison of DNA sequences with protein sequences, Genomics, 46, 24-36.
31. Rhee, S. Y., Beavis, W., Berardini, T. Z., Chen, G., Dixon, D., Doyle, A., Garcia-Hernandez, M., Huala, E., Lander, G., Montoya, M., et al. 2003, The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community, Nucleic Acids Res., 31, 224-228.
32. Ohyanagi, H., Tanaka, T., Sakai, H., Shigemoto, Y., Yamaguchi, K., Habara, T., Fujii, Y., Antonio, B. A., Nagamura, Y., Imanishi, T., et al. 2006, The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information, Nucleic Acids Res., 34, D741-D744.
33. Tatusov, R. L., Koonin, E. V. and Lipman, D. J. 1997, A genomic perspective on protein families, Science, 278, 631-637.
34. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., et al. 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41.
35. Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. 2007, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res., 35, D5-D12.
36. Zdobnov, E. M. and Apweiler, R. 2001, InterProScan - an integration platform for the signature-recognition methods in InterPro, Bioinformatics, 17, 847-848.
37. 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.
38. Alexandrov, N. N., Troukhan, M. E., Brover, V. V., Tatarinova, T., Flavell, R. B. and Feldmann, K. A. 2006, Features of Arabidopsis genes and genome discovered using full-length cDNAs, Plant Mol. Biol., 60, 69-85.
39. Shinozaki, K., Yamaguchi-Shinozaki, K. and Seki, M. 2003, Regulatory network of gene expression in the drought and cold stress responses, Curr. Opin. Plant Biol., 6, 410-417.
40. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. J. 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389-3402.
41. Carninci, P., Shibata, Y., Hayatsu, N., Sugahara, Y., Shibata, K., Itoh, M., Konno, H., Okazaki, Y., Muramatsu, M. and Hayashizaki, Y. 2000, Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes, Genome Res., 10, 1617-1630.
42. Childs, K. L., Hamilton, J. P., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P. D., Town, C. D., Buell, C. R. and Chan, A. P. 2007, The TIGR Plant Transcript Assemblies database, Nucleic Acids Res., 35, D846-D851.
43. Ichikawa, T., Nakazawa, M., Kawashima, M., Iizumi, H., Kuroda, H., Kondou, Y., Tsuhara, Y., Suzuki, K., Ishikawa, A., Seki, M., et al. 2006, The FOX hunting system: an alternative gain-of-function gene hunting technique, Plant J., 48, 974-985.
44. Koonin, E. V., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Krylov, D. M., Makarova, K. S., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., Rao, B. S., et al. 2004, A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes, Genome Biol., 5, R7.