PlantGDB is the homepage for the NSF-funded project "Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB" (PI: Volker Brendel, Iowa State University; Co-PI: Carol Lushbough, University of South Dakota; Co-PI: Carolyn Lawrence, USDA-ARS and Iowa State University).

The major goals of this project are:

• Develop plant species-specific EST and GSS databases.
• Provide web-accessible tools and inter-species query capabilities.
• Provide genome browsing and annotation capabilities.

What are we doing?

Plant genome sequence data have been accumulating from three major sources: whole genome sequencing and assembly (Arabidopsis thaliana, rice, Medicago truncatula), genome survey sequencing (maize), and expressed sequence tags (ESTs). This data flow will likely continue, with a focus on complete sequencing of "reference species" (Arabidopsis, rice, maize, Medicago truncatula, tomato), draft sequencing of other selected species, and further EST and full-length cDNA sequencing. Our project will aid in the organization and interpretation of these sequence data through the development and implementation of integrated databases and analytical tools. Results of our project will be accessible via the PlantGDB Web site, PlantGDB.org. Our scientific goals include estimation and characterization of the plant gene space and the extent and conservation of alternative splicing in plants. These objectives will in part be pursued by further development of algorithms and statistical methods for splice site recognition and gene structure prediction. Much progress has already been made for Arabidopsis, as displayed on our Arabidopsis genome browser site http://www.plantgdb.org/AtGDB/. The project also includes further development of the "BioExtract Server" prototype (http://www.bioextract.org/) which is meant to provide a distribution point for plant genome data stored in different local and external databases by offering flexible web-based query capabilities.

As a supplement to our PlantGDB grant, we are currently setting up a Plant Genome Research Outreach Portal (PGROP) to provide a centralized repository of various NSF-sponsored Plant Genome Research "outreach" programs and activities. The web site (http://www.plantgdb.org/PGROP/pgrop.php) lists a variety of resources organized by subject and type and provides entry forms for contributors to publish their programs. The intended user audience includes minorities, students with disabilities, undergraduates, high-school students and teachers; as well as the public at large. PGROP seeks to broaden participation of these user groups in plant genome research topics by making information on appropriate programs, materials, and guidance available.

Contact information

• PI: Dr. Volker Brendel (vbrendel@iastate.edu)
• Co-PI: Dr. Carol Lushbough (clushbou@usd.edu)
• Co-PI: Dr. Carolyn Lawrence (triffid@iastate.edu)
• Database manager: Dr. Jon Duvick (jduvick@iastate.edu)
• Questions/comments: plantgdb@iastate.edu