Abstract
BackgroundPeach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools.DescriptionThe Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity.ConclusionsThe GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at .
Highlights
Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose
Developing genetic resources for a model organism can greatly accelerate the genetic understanding of the individual member species in the same family
We describe the structure and content of the database, we review the database access utility and tools and we report a case study where we mapped publicly available Rosaceae sequences to the peach physical and genetic maps by sequence similarity
Summary
The GDR is initiated to support the genomics and genetics research in Rosaceae, which contains numerous economically important fruit trees and horticultural plants. GDR contains all the genomics data for the Rosaceae model peach, maps and markers of Rosaceae species and all the publicly available Rosaceae ESTs. Our integrated database provides users with easy access and retrieval of the annotated data, and the web tools enable them to further analyze their data. SJ performed web interface design and programming for html pages and JSP search pages, participated in the database construction, carried out database curation, designed the Map Viewer and performed the case study. MS participated in the database construction and wrote scripts for data upload and search pages for Genbank Rosaceae sequences. DM conceived and supervised the project, participated in the database construction, carried out EST analysis, and provided input in the web interface design.
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