Species Overview Page

A species page is available for main species, genera and entire Rosaceae family so that users can easily access the data and tools for the species of interest. Species pages can be accessed under the 'species' pull-down menu in the main navigation bar. Please note that detailed textual descriptions for each member species are being developed by the US Roscaceae Executive Committee and will be availlable in November 2013.

The species pages have a resources bar on the left panel so that users can quickly access data and tools for the species. Depending on the species, more or less items will be displayed on the resource bar. Below are some items in the resource bars. 

1. Genome page

Where whole genome sequences are available, hyperlinks to each genome assembly page are shown on the resources bar.

2. GDR Cyc Pathways

Where PlantCyc databases are available for a species, hyperlinks to each PlantCyc page are shown on the resources bar. The predicted genes from the whole genome sequences were utilized in the construction of PlantCyc (metabolic pathway) databases using PathwayTools. Currently (September 2013), three PlantCyc databases, PeachCyc, AppleCyc and FragariaCyc, are available in GDR. 

3. Unigene page

Each species page has a hyperlink to the corresponding unigene page for the genus. Unigenes are constructed for the entire Rosaceae family and for each genus (PrunusMalusFragariaRosa, and Pyrus) using the publicly available Rosaceae ESTs downloaded from dbEST at NCBI. 

4. Maps

Each species page has hyperlink to dynamically generated list of the genetic maps that are available in GDR.

5. Whole Genome

A whole genome page provides summary information on the available whole genome data for the species. 

6. Links

The links subpage shows various useful links outside GDR for the species.

7. KEGG Analysis Reports

The predicted genes from whole genome sequences and EST unigenes are associated with KEGG pathway terms. The link in the resources bar leads to the KEGG analysis reports page where users can view a Venn diagram with GO terms and the number of associated sequences, browse the GO term heirarchy, choose a term and view/download all the associated sequences.

8. Germplasm

The germplasm page provides a list of germplasm that are stored in GDR.

9. GO Analysis Reports

The predicted genes from whole genome sequences and EST unigenes are associated with Gene Ontology terms. The link in the resources bar leads to the GO analysis reports page where users can view, seach and download the GO associated data.

If you have any questions/comments/feedback about the species site, please let us know via the contact form.