Proposal Title: Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB
Institution: Iowa State University
Abstract Date: 05/31/2006
PI Volker Brendel Iowa State University Senior Personnel Qunfeng Dong Iowa Sate University Co-PI Carolyn Lawrence Iowa State University Co-PI Carol Lushbough University of South Dakota
Accurate and comprehensive gene structure annotation in emerging and assembled genomes is fundamental to comparative, functional, and translational genomics. We propose to build the cyberinfrastructure necessary for defining and accessing the plant gene space. Our PlantGDB resource (www.plantgdb.org) will serve as a portal to plant genomic sequence data. Expressed sequence tags (ESTs) from all species will be presented in a uniform format and will undergo a standard procedure for clustering, assembly, and tentative annotation. The resulting putative unique transcripts (PUTs) will be mapped to their native and closely related genomes using specifically trained tools for spliced alignment. Predicted gene structures will be viewable on dedicated Web-based genome browsers, which also provide the opportunity for users to refine existing and contribute novel gene structure annotations. Confirmed gene structure annotations will be the data source for detailed studies of transcriptional regulation, including alternative splicing and the interplay of multiple types of mRNA processing. These data will also enable detection, display, and analysis of synteny among plant genomes. Through novel Web-interfaces, users will have a large range of query options to the underlying relational database. The PlantGDB-associated BioExtract Server (www.bioextract.org) tool provides simultaneous access to other remote data sets and capabilities 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.
The PlantGDB resource is widely used and would continue to provide valuable data and analysis capabilities to the plant research community. A number of collaborative projects rely on PlantGDB for large-scale analyses and display of their data. PlantGDB hosts the Plant Genome Research Outreach Portal (PGROP, www.plantgdb.org/PGROP), a Web site providing access to a large number of resources and successful outreach programs. We plan to work with outreach coordinators from our campuses and nationwide to increase content and visibility of PGROP. We will also be working with colleagues in community and tribal colleges in South Dakota with the goal of increasing participation of their communities in plant genome research and building a bridge between plant genomics and ethobotany.
Access to project outcomes: The primary web sites for this project are www.plantgdb.org and www.plantgdb.org/PGROP.
Understanding plant genomes is increasingly underpinning societal decisions ranging from crop production to environmental issues, similar to how deciphering the human genome has impacted medical research and practice. Our project generated widely used computational infrastructure for plant genomics. All data and tools have been accessible through the PlantGDB (www.plantgdb.org) Web portal. Researchers can view symbolic representations of expert and computational annotations of all plant genomes sequenced throughout the lifetime of the project. Interactive screens have allowed users to explore gene structure annotations and potentially provide their own assessments for immediate distribution. This function has been used in classrooms at the high school and undergraduate level to offer practical training in computational plant genomics. The PlantGDB-associated BioExtract Server (www.bioextract.org) tool provides simultaneous access to other remote data sets and capabilities to analyze selected data sets in user-defined workflows. Users can not only save a series of BioExtract Server tasks (e.g. query a data source, save a data extract, and execute an analytic tool) as a workflow but share their data extracts, analytic tools, and workflows with collaborators for both reproducibility and generalization to other input sets. PlantGDB hosts the Plant Genome Research Outreach Portal (PGROP, www.plantgdb.org/PGROP), a Web site providing access to a large number of resources and successful outreach programs.
