Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags

Yasunari Ogihara, Keiichi Mochida, Kanako Kawaura, Koji Murai, Motoaki Seki, Asako Kamiya, Kazuo Shinozaki, Piero Carninci, Yoshihide Hayashizaki, Tadasu Shin-I, Yuji Kohara, Yukiko Yamazaki

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

The polyploid nature of wheat is a key characteristic of the plant. Full-length complementary DNAs (cDNAs) provide essential information that can be used to annotate the genes and provide a functional analysis of these genes and their products. We constructed a full-length cDNA library derived from young spikelets of common wheat, and obtained 24056 expressed sequence tags (ESTs) from both ends of the cDNA clones. These ESTs were grouped into 3605 contigs using the phrap method, representing expressed loci from each of the three genomes. Using BLAST, 3605 contigs were grouped into 1902 gene clusters, showing that loci of the three genomes are not always expressed. A homology search of these gene clusters against a wheat EST database (15964 gene clusters) and a rice full-length cDNA database (21447 gene clusters) revealed that a quarter of the wheat full-length cDNAs were novel. A protein database of Arabidopsis was used to examine the functional classification of these gene clusters. The GC-content in the 5′-UTR region of wheat cDNAs was compared to that of rice. Forty-three genes (3.5% of wheat cDNAs homologous to those of rice) possessed distinct GC-content in the 5′-UTR region, suggesting different breeding behaviors of wheat and rice.

Original languageEnglish
Pages (from-to)227-232
Number of pages6
JournalGenes and Genetic Systems
Volume79
Issue number4
DOIs
Publication statusPublished - Aug 2004
Externally publishedYes

Fingerprint

Expressed Sequence Tags
complementary DNA
hexaploidy
expressed sequence tags
Gene Library
cDNA libraries
Triticum
inflorescences
Complementary DNA
Genes
Multigene Family
multigene family
wheat
rice
5' Untranslated Regions
5' untranslated regions
Base Composition
Genome
Protein Databases
loci

Keywords

  • Bioinformatics
  • Full-length cDNA library
  • Hexaploid wheat
  • Large-scale sequencing
  • Young spikelet

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Genetics
  • Genetics(clinical)

Cite this

Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. / Ogihara, Yasunari; Mochida, Keiichi; Kawaura, Kanako; Murai, Koji; Seki, Motoaki; Kamiya, Asako; Shinozaki, Kazuo; Carninci, Piero; Hayashizaki, Yoshihide; Shin-I, Tadasu; Kohara, Yuji; Yamazaki, Yukiko.

In: Genes and Genetic Systems, Vol. 79, No. 4, 08.2004, p. 227-232.

Research output: Contribution to journalArticle

Ogihara, Y, Mochida, K, Kawaura, K, Murai, K, Seki, M, Kamiya, A, Shinozaki, K, Carninci, P, Hayashizaki, Y, Shin-I, T, Kohara, Y & Yamazaki, Y 2004, 'Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags', Genes and Genetic Systems, vol. 79, no. 4, pp. 227-232. https://doi.org/10.1266/ggs.79.227
Ogihara, Yasunari ; Mochida, Keiichi ; Kawaura, Kanako ; Murai, Koji ; Seki, Motoaki ; Kamiya, Asako ; Shinozaki, Kazuo ; Carninci, Piero ; Hayashizaki, Yoshihide ; Shin-I, Tadasu ; Kohara, Yuji ; Yamazaki, Yukiko. / Construction of a full-length cDNA library from young spikelets of hexaploid wheat and its characterization by large-scale sequencing of expressed sequence tags. In: Genes and Genetic Systems. 2004 ; Vol. 79, No. 4. pp. 227-232.
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