Journal Article

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

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

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 16, issue 2, pages 81-89
Published in print April 2009 | ISSN: 1340-2838
Published online January 2009 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsn034

Show Summary Details

Preview

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.

Keywords: full-length cDNA; Hordeum vulgare; mRNA; gene ontology

Journal Article.  4620 words.  Illustrated.

Subjects: Genetics and Genomics

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.