EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon

John P. Vogel, Yong Qiang Gu, Paul Twigg, Gerard R. Lazo, Debbie Laudencia-Chingcuanco, Daniel M. Hayden, Teresa J. Donze, Lindsay A. Vivian, Boryana Stamova, Devin Coleman-Derr

Research output: Contribution to journalArticle

103 Citations (Scopus)

Abstract

Brachypodium distachyon (Brachypodium) is a temperate grass with the physical and genomic attributes necessary for a model system (small size, rapid generation time, self-fertile, small genome size, diploidy in some accessions). To increase the utility of Brachypodium as a model grass, we sequenced 20,440 expressed sequence tags (ESTs) from five cDNA libraries made from leaves, stems plus leaf sheaths, roots, callus and developing seed heads. The ESTs had an average trimmed length of 650 bp. Blast nucleotide alignments against SwissProt and GenBank non-redundant databases were performed and a total of 99.9% of the ESTs were found to have some similarity to existing protein or nucleotide sequences. Tentative functional classification of 77% of the sequences was possible by association with gene ontology or clusters of orthologous group's index descriptors. To demonstrate the utility of this EST collection for studying cell wall composition, we identified homologs for the genes involved in the biosynthesis of lignin subunits. A subset of the ESTs was used for phylogenetic analysis that reinforced the close relationship of Brachypodium to wheat and barley.

Original languageEnglish (US)
Pages (from-to)186-195
Number of pages10
JournalTheoretical and Applied Genetics
Volume113
Issue number2
DOIs
StatePublished - Jul 1 2006

Fingerprint

Brachypodium
Brachypodium distachyon
Expressed Sequence Tags
Poaceae
expressed sequence tags
grasses
phylogeny
Genome Size
Protein Databases
Gene Ontology
Lignin
Nucleic Acid Databases
Bony Callus
cell wall components
Hordeum
Multigene Family
Diploidy
Gene Library
cDNA libraries
Cell Wall

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

Vogel, J. P., Gu, Y. Q., Twigg, P., Lazo, G. R., Laudencia-Chingcuanco, D., Hayden, D. M., ... Coleman-Derr, D. (2006). EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theoretical and Applied Genetics, 113(2), 186-195. https://doi.org/10.1007/s00122-006-0285-3

EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. / Vogel, John P.; Gu, Yong Qiang; Twigg, Paul; Lazo, Gerard R.; Laudencia-Chingcuanco, Debbie; Hayden, Daniel M.; Donze, Teresa J.; Vivian, Lindsay A.; Stamova, Boryana; Coleman-Derr, Devin.

In: Theoretical and Applied Genetics, Vol. 113, No. 2, 01.07.2006, p. 186-195.

Research output: Contribution to journalArticle

Vogel, JP, Gu, YQ, Twigg, P, Lazo, GR, Laudencia-Chingcuanco, D, Hayden, DM, Donze, TJ, Vivian, LA, Stamova, B & Coleman-Derr, D 2006, 'EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon', Theoretical and Applied Genetics, vol. 113, no. 2, pp. 186-195. https://doi.org/10.1007/s00122-006-0285-3
Vogel, John P. ; Gu, Yong Qiang ; Twigg, Paul ; Lazo, Gerard R. ; Laudencia-Chingcuanco, Debbie ; Hayden, Daniel M. ; Donze, Teresa J. ; Vivian, Lindsay A. ; Stamova, Boryana ; Coleman-Derr, Devin. / EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. In: Theoretical and Applied Genetics. 2006 ; Vol. 113, No. 2. pp. 186-195.
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