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ID 52269
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Author
Shin-I, Tadasu
Seki, Motoaki
Shinozaki, Kazuo
Takeda, Kazuyoshi
Yamazaki, Yukiko
Conte, Matthieu
Kohara, Yuji
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 preexisting 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
Published Date
2009-04
Publication Title
DNA Research
Volume
volume16
Issue
issue2
Publisher
Oxford University Press
Start Page
81
End Page
89
ISSN
1340-2838
Content Type
Journal Article
language
英語
Copyright Holders
© The Author 2009. Kazusa DNA Research Institute.
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publisher
Refereed
True
DOI
Web of Science KeyUT