ARS | Publication request: Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB

Submitted to: Meeting Abstract
Publication Type: Proceedings
Publication Acceptance Date: August 8, 2006
Publication Date: September 7, 2006
Citation: Brendel, V., Lawrence, C.J., Lushbough, C. 2006. Cyberinfrastructure for (Comparative) Plant Genome Research Through PlantGDB [abstract]. Book of Abstracts - Plant Genome Research Program 9th Annual Awardee Meeting. p. 42-43.

Technical Abstract: Accurate and comprehensive gene structure annotation in emerging and assembled genomes is fundamental to comparative, functional, and translational genomics. We plan to build the cyberinfrastructure necessary for defining and accessing the plant gene space. Our Plant Genetic Data Base (PlantGDB) resource (www.plantgdb.org) will serve as a portal to plant genomic sequence data. Expressed sequence tags (ESTs) from all species will undergo a standard procedure for clustering, assembly, and tentative annotation and will be presented in a uniform format. The resulting putative unique transcripts (PUTs) will be mapped to native and closely related genomes using tools specifically trained for spliced alignment. Predicted gene structures will be viewable on dedicated Web-based genome browsers, which also will provide the opportunity for researchers 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, researchers will have a large range of options available to enable them to query the underlying relational database in a unique and innovative manner. The PlantGDB-associated BioExtract Server (www.bioextract.org) tool will provide simultaneous access to other remote data sets, and capabilities to analyze selected data sets in user-defined workflows will be expanded. Extensive development of Web services will integrate PlantGDB as a node in the emerging network of plant databases and resources. We are committed to maintaining and developing the Plant Genome Research Outreach Portal (PGROP) outreach resource as well as to depositing extensive tutorials to our web pages. In addition, each summer we will host American Indian students and their elders in a program to study, from a genomic perspective, plants of importance to Native Tribes (see http://www.lawrencelab.org/Outreach/2006/home.html).