Development of 5006 full-length CDNAs in barley: A tool for accessing cereal genomics resources

DNA Research

Volumn 16, Issue 2, 2009, Pages 81-89

  Sato, Kazuhiro ^a   Shin I, Tadasu ^b   Seki, Motoaki ^c   Shinozaki, Kazuo ^c   Yoshida, Hideya ^a   Takeda, Kazuyoshi ^a   Yamazaki, Yukiko ^b   Conte, Matthieu ^d   Kohara, Yuji ^b  

^a OKAYAMA UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c RIKEN Center for Sustainable Resource Science   (Japan)

^d INTERNATIONAL RICE RESEARCH INSTITUTE   (Philippines)

Author keywords

Full length cDNA; Gene ontology; Hordeum vulgare; MRNA

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA; PLANT DNA; SODIUM CHLORIDE;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; BARLEY; CEREAL; CLONE; DNA LIBRARY; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE IDENTIFICATION; GENE MAPPING; GENE PROBE; GENOME ANALYSIS; GENOMICS; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT CHROMOSOME; RICE; SEQUENCE HOMOLOGY; UNINDEXED SEQUENCE; CHEMISTRY; COLD; DRUG EFFECT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; HEAT; METHODOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; PLANT LEAF; PLANT ROOT; PLANT SEED;

ARABIDOPSIS; HORDEUM; HORDEUM VULGARE; TRITICUM AESTIVUM;

CLONING, MOLECULAR; COLD TEMPERATURE; DNA, COMPLEMENTARY; DNA, PLANT; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENE LIBRARY; GENOMICS; HORDEUM; HOT TEMPERATURE; MOLECULAR SEQUENCE DATA; PLANT LEAVES; PLANT ROOTS; SEEDS; SEQUENCE ANALYSIS, DNA; SODIUM CHLORIDE;

EID: 67650140201     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dsn034     Document Type: Article

References (32)

1. Arumuganathan, K. and Earle, E. D. 1991, Nuclear DNA content of some important plant species, Plant Mol. Biol. Rep., 9, 208-218.
2. Stein, N., Prasad, M., Scholz, U., et al. 2007, A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics, Theor. Appl. Genet., 114, 823-839.
3. Nasuda, S., Kikkawa, Y., Ashida, T., Islam, A. K., Sato, K. and Endo, T. R. 2005, Chromosomal assignment and deletion mapping of barley EST markers, Genes Genet. Syst., 80, 357-366.
4. Ashida, T., Nasuda, S., Sato, K. and Endo, T. R. 2007, Dissection of barley chromosome 5H in common wheat, Genes Genet. Syst., 82, 123-133.
5. Yu, Y., Tomkins, J. P., Waugh, R., et al. 2000, A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes, Theor. Appl. Genet., 101, 1093-1099.
6. Saisho, D., Myoraku, E., Kawasaki, S., Sato, K. and Takeda, K. 2007, Construction and characterization of a bacterial artificial chromosome (BAC) library for Japanese malting barley 'Haruna Nijo', Breed Sci., 57, 29-38.
7. Close, T. J., Wanamaker, S. I., Caldo, R. A., et al. 2004, A new resource for cereal genomics: 22K barley GeneChip comes of age, Plant Physiol., 134, 960-968.
8. Druka, A., Muehlbauer, G., Druka, I., et al. 2006, An atlas of gene expression from seed to seed through barley development, Funct. Integr. Genomics, 6, 202-211.
9. Carninci, P., Kvam, C., Kitamura, A., et al. 1996, High-efficiency full-length cDNA cloning by biotinylated CAP trapper, Genomics, 37, 327-336.
10. Carninci, P., Nishiyama, Y., Westover, A., et al. 1998, Thermostabilization and thermoactivation of thermolabile enzymes by trehalose and its application for the synthesis of full length cDNA, Proc. Natl Acad. Sci. USA, 95, 520-524.
11. Seki, M., Narusaka, M., Kamiya, A., et al. 2002, Functional annotation of a full-length Arabidopsis cDNA collection, Science, 296, 141-145.
12. Kikuchi, S., Satoh, K., Nagata, T., et al. 2003, Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice, Science, 301, 376-379.
13. Satoh, K., Doi, K., Nagata, T., et al. 2007, Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray, PLoS ONE, 2, e1235.
14. Okubo, K., Hori, N., Matoba, R., et al. 1992, Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression, Nat. Genet., 2, 173-179.
15. 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.
16. Zohary, D. and Hopf, M. 2000, Barley: Hordeum vulgare, In: Domestication of Plants in the Old World, Third Ed., Oxford University Press Inc.: New York, pp. 59-68.
17. Harlan, J. R. 1995, Barley, In: Smartt, J. and Simmonds, N. W. (eds.), Evolution of Crop Plants, 2nd Ed., Longman Scientific and Technical: Harlow, UK, pp. 140-147.
18. Furukawa, J., Yamaji, N., Wang, H., et al. 2007, An aluminum-activated citrate transporter in barley, Plant Cell Physiol., 48, 1081-1091.
19. Bothmer, R., von Sato, K., Komatsuda, T., Yasuda, S. and Fischbeck, G. 2003, The domestication of cultivated barley, In: Bothmer, von Hintum, R., van Knüpffer, H. and Sato, K. (eds.), Diversity in Barley (Hordeum vulgare), Amsterdam, The Netherlands: Elsevier Science B.V., pp. 9-27.
20. Islam, A. K. M. R. and Shepherd, K. W. 1992, Production of wheat-barley recombinant chromosomes through induced homoeologous pairing. 1. Isolation of recombinants involving barley arms 3HL and 6HL, Theor. Appl. Genet., 83, 489-494.
21. Hori, K., Takehara, S., Nankaku, N., Sato, K., Sasakuma, T. and Takeda, K. 2007, Linkage map construction and QTL detection based on barley ESTs in A genome diploid wheat, Breeding Sci., 57, 39-45.
22. Moore, G., Devos, K. M., Wang, Z. and Gale, M. D. 1995, Cereal genome evolution. Grasses, line up and form a circle, Curr. Biol., 5, 737-739.
23. Devos, K. M. 2005, Updating the 'crop circle', Curr. Opin. Plant Biol., 8, 155-162.
24. Komatsuda, T., Pourkheirandish, M., He, C., et al. 2007, Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene, Proc. Natl Acad. Sci. USA, 104, 1424-1429.
25. Yan, L., Loukoianov, A., Blechl, A., et al. 2004, The wheat VRN2 gene is a flowering repressor down-regulated by vernalization, Science, 303, 1640-1644.
26. Carninci, P., Westover, A., Nishiyama, Y., et al. 1997, High efficiency selection of full-length cDNA by improved biotinylated cap trapper, DNA Res., 4, 61-66.
27. Huang, X. and Madan, A. 1999, CAP3: a DNA sequence assembly program, Genome Res., 9, 868-877.
28. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403-410.
29. Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389-3402.
30. Conte, M. G., Gaillard, S., Lanau, N., Rouard, M. and Perin, C. 2008, GreenPhylDB: a database for plant comparative genomics, Nucleic Acids Res., 36, D991-D998.
31. Conte, M. G., Gaillard, S., Droc, G. and Perin, C. 2008, Phylogenomics of plant genomics: a methodology for genome-wide searches for orthologs in plants, BMC Genom., 9, 183.
32. Yan, L., Fu, D., Li, C., et al. 2006, The wheat and barley vernalization gene VRN3 is an orthologue of FT, Proc. Natl. Acad. Sci. USA, 103, 19581-19586.