Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

PlantGDB: A Web-Based Platform For (Comparative) Plant Genome Research

Jonathan Duvick¹ , Carol Lushbough² , Carolyn Lawrence^1,3 , Volker Brendel⁴

¹  Department of Genetics, Development and Cell Biology, Iowa State University, Ames Iowa, 50011, USA

²  Department of Computer Science, University of South Dakota, Vermillion, South Dakota, 57069, USA

³  USDA-ARS Ames Iowa, 50011, USA

⁴  Department of Genetics, Development and Cell Biology and Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA

Accurate and comprehensive gene structure annotation is fundamental to comparative, functional, and translational genomics. Our project seeks to build the cyberinfrastructure necessary for defining and accessing the plant gene space. PlantGDB (www.plantgdb.org) serves as a portal to plant genomic sequence data. Expressed sequence tags (ESTs) from over 200 species undergo a standard procedure for clustering, assembly, and tentative annotation and are presented in a uniform format. The resulting putative unique transcripts (PUTs), as well as transcripts, are mapped to native genomes using tools specifically trained for spliced alignment. Predicted gene structures and spliced-alignments are viewable on dedicated Web-based genome browsers, which also provide the opportunity for researchers to contribute novel gene structure annotations and refine existing ones. A Distributed Annotation Service (DAS) server allows remote display of annotations at maizegdb.org or on any DAS-enabled genome browser. Experimentally confirmed gene structure annotations are the data source for detailed studies of transcriptional regulation, including alternative splicing and the interplay of multiple types of mRNA processing. These data also enable detection, display, and analysis of synteny among plant genomes. Through novel Web-interfaces, researchers have a large range of options available to enable them to query the underlying relational database. The PlantGDB-associated BioExtract Server (www.bioextract.org) provides access to remotely stored data sets along with tools to analyze selected data sets in user-defined workflows. Extensive development of Web services will integrate PlantGDB as a node in the emerging network of plant databases and resources.