Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2009 Apr;16(2):81-9.
doi: 10.1093/dnares/dsn034. Epub 2009 Jan 15.

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

Kazuhiro Sato  1 , Tadasu Shin-I, Motoaki Seki, Kazuo Shinozaki, Hideya Yoshida, Kazuyoshi Takeda, Yukiko Yamazaki, Matthieu Conte, Yuji Kohara
Affiliations

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

Kazuhiro Sato et al. DNA Res. 2009 Apr.

Abstract

A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60% of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47%, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2%) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71%) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81%) and the wheat gene index (84%). The high homology between FLcDNAs (27%) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151-233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species. Sequence data from this article have been deposited with the DDBJ/EMBL/GenBank Data Libraries under accession nos AK248134-AK253139. The online database with annotation is available at http://www.shigen.nig.ac.jp/barley/.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Distribution of insert sizes of 5006 FL barley clones. Average insert size is 1474 bp, with the range of 167–6780 bp.
Figure 2
Figure 2
Blastn search among barley FLcDNAs, rice genes and Arabidopsis genes (E<1E-5).
See this image and copyright information in PMC

References

    1. Arumuganathan K., Earle E. D. Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 1991;9:208–218.
    1. Stein N., Prasad M., Scholz U., et al. A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics. Theor. Appl. Genet. 2007;114:823–839. - PubMed
    1. Nasuda S., Kikkawa Y., Ashida T., Islam A. K., Sato K., Endo T. R. Chromosomal assignment and deletion mapping of barley EST markers. Genes Genet. Syst. 2005;80:357–366. - PubMed
    1. Ashida T., Nasuda S., Sato K., Endo T. R. Dissection of barley chromosome 5H in common wheat. Genes Genet. Syst. 2007;82:123–133. - PubMed
    1. Yu Y., Tomkins J. P., Waugh R., et al. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor. Appl. Genet. 2000;101:1093–1099.

Publication types

Associated data

LinkOut - more resources