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DNA Research Advance Access originally published online on January 15, 2009
DNA Research 2009 16(2):81-89; doi:10.1093/dnares/dsn034
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© The Author 2009. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Development of 5006 Full-Length CDNAs in Barley: A Tool for Accessing Cereal Genomics Resources

Kazuhiro Sato1,*, Tadasu Shin-I2, Motoaki Seki3, Kazuo Shinozaki3, Hideya Yoshida1, Kazuyoshi Takeda1, Yukiko Yamazaki2, Matthieu Conte4 and Yuji Kohara2

1 Research Institute for Bioresources, Okayama University, Kurashiki 710-0046, Japan
2 National Institute of Genetics, Mishima 411-8540, Japan
3 Plant Science Center, RIKEN, Yokohama 230-0045, Japan
4 Crop Research Informatics Laboratory, International Rice Research Institute, PO Box 933, Manila 1099, Philippines

Received 5 August 2008 ; accepted 14 December 2008.

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.

Key words: full-length cDNA; Hordeum vulgare; mRNA; gene ontology

* To whom correspondence should be addressed. Tel. +81 86-434-1244. Fax. +81 86-434-1244. E-mail: kazsato{at}rib.okayama-u.ac.jp


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