Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Workshop: Barley
            

BARLEY AND EST BIOINFORMATICS: BREWING UP THE RECONSTRUCTOME.

¹ Institut für Bioinformatik (MIPS), GSF National Research Centre for Environment and Health, D-85764, Neuherberg, Germany

² Institut für Pflanzengenetik und Kulturpflanzenforschung, Correnstraße 2, D-06466 Gatersleben, Germany

The Arabidopsis thaliana and Oryza sativa genomes have built a clear functional and structural foundation for the first large-scale expeditions into comparative plant genomics. A few other plant genomes are expected to be sequenced in the near-future, but there is an otherwise notable void in the ‘model’ plant systems that we expect to be sequenced soon. Due to the current limitations with sequencing and assembly of the repetitive and low-complexity regions associated with the larger plant genomes there have been major efforts to produce large high quality EST libraries from different tissues and developmental stages in barley, a model monocotyledonous plant with a currently inaccessible genome of 5,900 Mbp.

There are in excess of 200,000 Hordeum vulgare ESTs in the public domain, and almost half as many again awaiting submission at the IPK-Gatersleben. In this presentation we describe a bioinformatic based methodology to refine these heterogeneous datasets into a clean unigene collection and the subsequent annotation steps that provide detailed resolution on the whole collection in terms of structure, function and homology.

~40,000 unigenes (cluster and singleton sequences) have been exhaustively annotated using a variety of state-of-the-art bioinformatic methods. Homology based analyses have revealed the subset of plant-specific sequences, monocot specific sequences and a surprisingly large number of apparently barley-specific sequences. Using methods based on coding-potentials, ORFs have been predicted for most of the sequences. This has allowed the more in-depth annotation and analysis of sequence coverage in terms of protein function, structure and domain content. These data provide information on the content of large barley EST collections, and lend insight as to what we might expect from the completed barley genome. All data from the public domain is available from the Sputnik website (http://mips.gsf.de/proj/sputnik/barley).