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. 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/.

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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).
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