|L Chingcuanco, Debbie|
Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2006
Publication Date: 5/18/2006
Citation: Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Chingcuanco, D.L., Hayden, D.M., Donze, T., Vivia-Lindsay, A., Stamova, B., Coleman-Derr, D. 2006. EST sequencing and phylogenetic analysis of the model grass brachypodium distachyon. Theoretical and Applied Genetics. 113: 186-195. Interpretive Summary: Brachypodium distachyon is a small grass that serves as a model system for the temperate grasses (i.e. forage grasses and cereals). Expressed sequence tags (ESTs) are short DNA sequences from random cDNAs (genes). ESTs are useful tools for many functional and physical genomic experiments including the construction of microarrays and the development of molecular markers. This paper describes the sequencing of a large collection of ESTs from five different cDNA libraries. Analysis of the ESTs included the identification of putative lignin biosynthetic genes and the construction of phylogentic trees that demonstrated the close relationship of Brachypodium to wheat and barley.
Technical 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 20,587 expressed sequence tags (ESTs) from five cDNA libraries made from leaves, stems plus leaf sheaths, roots, callus and immature spikes. The ESTs had an average trimmed length of 774 bp. Blast searches 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 groups index descriptors. To demonstrate the utility of this EST collection for studying cell wall composition, we identified homologs for all 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.