The Genome Database for Rosaceae (GDR): year 10 update

Abstract

The Genome Database for Rosaceae (GDR, http:/www.rosaceae.org), the long-standing central repository and data mining resource for Rosaceae research, has been enhanced with new genomic, genetic and breeding data, and improved functionality. Whole genome sequences of apple, peach and strawberry are available to browse or download with a range of annotations, including gene model predictions, aligned transcripts, repetitive elements, polymorphisms, mapped genetic markers, mapped NCBI Rosaceae genes, gene homologs and association of InterPro protein domains, GO terms and Kyoto Encyclopedia of Genes and Genomes pathway terms. Annotated sequences can be queried using search interfaces and visualized using GBrowse. New expressed sequence tag unigene sets are available for major genera, and Pathway data are available through FragariaCyc, AppleCyc and PeachCyc databases. Synteny among the three sequenced genomes can be viewed using GBrowse_Syn. New markers, genetic maps and extensively curated qualitative/Mendelian and quantitative trait loci are available. Phenotype and genotype data from breeding projects and genetic diversity projects are also included. Improved search pages are available for marker, trait locus, genetic diversity and publication data. New search tools for breeders enable selection comparison and assistance with breeding decision making.

Figure 1.

Gene search site in the GDR. (A) Genes can be searched by various categories, such as by species, name, genome location and keywords from functional annotation such as GO terms, InterPro protein domain name and KEGG pathway terms. A file with multiple names can be uploaded for searching as well. (B) The search results page has links for download, gene details page and GBrowse. (C) The gene details page has various tabs to show the data. The annotated sequence page is shown. (D) The alignment tab of the gene detail page, which shows the position in the whole genome and link to GBrowse. (E) A GBrowse page linked from the alignment tab of the gene detail page. Scientists can return to the gene detail page from GBrowse.

Figure 2.

Marker search site in the GDR. (A) The advanced marker search site allows researchers to search markers by name, type, species and whole genome or genetic map locations. (B) The search results page shows information such as links to download data and the marker details page. (C) The marker details page with various tabs to show the detailed information. (D) The map position tab of the marker page shows all maps in which a marker has been mapped. (E) From the marker page, researchers can go to CMap. (F) For genome-anchored markers, CMap provides a hyperlink to GBrowse. From GBrowse, researchers can follow the link to go back to CMap, the marker details page or the Sequence Retrieval Tool.

Figure 3.

Search pages for breeding data in the GDR. (A) The search by phenotype page where researchers can search varieties by trait values, marker alleles (B) or parentage (C).