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, annotated EST databases of apple, peach, almond, cherry, rose, raspberry and strawberry, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, ORFs, Gene Ontology 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. We continue to add Rosaceae map data to CMap, a web-based tool that allows users to view comparisons of genetic and physical maps. 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, search their sequences for microsatellites using the SSR server or assemble their ESTs using the CAP3 Server
Funding source: GDR was funded from 2003 to 2009 by the NSF Plant Genome Research Program (Award # 0320544) and is currently funded through awards from the USDA NIFA Specialty Crop Research Inititative and the Washington Tree Fruit Research Commission.
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GDR Usage: In 2009, GDR was accessed by researchers from 52 countries with over 1 million pages accessed.
How to reference GDR:
- Sook Jung, Margaret Staton, Taein Lee, Anna Blenda, Randall Svancara, Albert Abbott, and Dorrie Main. GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Research, 2008 January; 36(Database issue): D1034–D1040.
- Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins and Dorrie Main. 2004. GDR (Genme Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics 2004, 5:130.
Other GDR publications:
- Jung S, Cho I, Sosinski B, Abbott A, Main D. 2010 Comparative genomic sequence analysis of strawberry and other rosids reveals significant microsynteny. BMC Res Notes. 2010 Jun 16;3:168.
- Jung S, Jiwan D, Cho I, Lee T, Abbott A, Sosinski B, Main D. 2009 Synteny of Prunus and other model plant species. BMC Genomics. 2009 Feb 10;10:76.
- S. Jung, D. Main, M. Staton, I. Cho, T. Zhebentyayeva, P. Arus, A. Abbott. Synteny conservation between the prunus genome and both the present and ancestral Arabidopsis genomes. BMC Genomics 2006 7(1):8.
- Kevin M Folta , Margaret Staton, Philip J Stewart, Sook Jung , Dawn H Bies, Christopher Jesdurai and Dorrie Main. 2005. Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria × ananassa). BMC Plant Biology 2005, 5:12.
- Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, Yu Y, Kim HR, Jesudurai C, Sosinski B, Arus P, Baird V, Parfitt D, Reighard G, Scorza R, Tomkins J, Wing R, Abbott AG. 2005. Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet. 2005 May;110(8):1419-28.
- Jung S, Abbott A, Jesudurai C, Tomkins J, Main D. 2005. Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genomics. 2005 Jul;5(3):136-43.