title: EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon.
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.
authors.affiliation: USDA Western Regional Research Center, 800 Buchanan St., Albany, CA 94710, USA. jvogel@pw.usda.gov
authors.forename: John P
authors.initials: JP
authors.lastname: Vogel
authors.forename: Yong Qiang
authors.initials: YQ
authors.lastname: Gu
authors.forename: Paul
authors.initials: P
authors.lastname: Twigg
authors.forename: Gerard R
authors.initials: GR
authors.lastname: Lazo
authors.forename: Debbie
authors.initials: D
authors.lastname: Laudencia-Chingcuanco
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Hayden
authors.forename: Teresa J
authors.initials: TJ
authors.lastname: Donze
authors.forename: Lindsay A
authors.initials: LA
authors.lastname: Vivian
authors.forename: Boryana
authors.initials: B
authors.lastname: Stamova
authors.forename: Devin
authors.initials: D
authors.lastname: Coleman-Derr
mesh_terms: D018076:DNA, Complementary; D020224:Expressed Sequence Tags; D008031:Lignin / Q000096:biosynthesis; D010802:Phylogeny; D006109:Poaceae / Q000235:genetics* / Q000254:growth & development
chemical_list: D018076:DNA, Complementary; D008031:Lignin