Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

Keiichi Mochida, Yukiko Uehara-Yamaguchi, Fuminori Takahashi, Takuhiro Yoshida, Tetsuya Sakurai, Kazuo Shinozaki

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the -3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a "one-stop" information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.

Original languageEnglish
Article numbere75265
JournalPLoS One
Volume8
Issue number10
DOIs
Publication statusPublished - Oct 9 2013
Externally publishedYes

Fingerprint

Brachypodium
Brachypodium distachyon
Complementary DNA
Genes
Molecular Sequence Annotation
genes
Databases
transcription (genetics)
promoter regions
Transcription Initiation Site
Expressed Sequence Tags
Hordeum
Poaceae
Gene Library
structural genes
Genetic Promoter Regions
Triticum
information sources
expressed sequence tags
Functional analysis

ASJC Scopus subject areas

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

Cite this

Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources. / Mochida, Keiichi; Uehara-Yamaguchi, Yukiko; Takahashi, Fuminori; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo.

In: PLoS One, Vol. 8, No. 10, e75265, 09.10.2013.

Research output: Contribution to journalArticle

Mochida, Keiichi ; Uehara-Yamaguchi, Yukiko ; Takahashi, Fuminori ; Yoshida, Takuhiro ; Sakurai, Tetsuya ; Shinozaki, Kazuo. / Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources. In: PLoS One. 2013 ; Vol. 8, No. 10.
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