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. 2004 Sep 9:5:130.
doi: 10.1186/1471-2105-5-130.

GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research

Sook Jung  1 , Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins, Dorrie Main
Affiliations

GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research

Sook Jung et al. BMC Bioinformatics. .

Abstract

Background: 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. 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.

Description: The 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.

Conclusions: The 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 http://www.genome.clemson.edu/gdr/.

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Figures

Figure 1
Figure 1
Graphical interface to maps. A. Peach WebChrom and peach WebFPC: a. the opening page of peach WebChrom with eight linkage group of the general prunus map; b. an example of individual linkage group pages (linkage group 6) with the associated markers and the contigs; c. an example of the directly linked FPC page with the developing BAC contigs and anchored probes (contig #185). B. Map Viewer: Map viewer displays the general Prunus map with anchored ESTs and direct link to WebFPC.
Figure 2
Figure 2
Case Study: Hyperlink to map viewers from the sequence similarity search result. This figure shows snapshots of hyperlinked pages to illustrate that users can obtain putative genetic and physical map positions of the query sequences when the sequences have match to mapped peach ESTs. A. A spread sheet with sequence similarity search results B. EST detail page with map position C. Map Viewer D. WebFPC.
Figure 3
Figure 3
Case Study result: Number of anchored Rosaceae sequences to various Rosaceae genetic maps T × E: 'Texas' × 'Earlygold'; F or T: F × T ('Ferragnes' × 'Tuono'); P × F: ('IF310828' × P. ferganensis) × 'IF310828'; SC × B: 'Suncrest' × 'Bailey'
See this image and copyright information in PMC

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