News

The sequence of the doubled monoploid Solanum tuberosum Group Phureja DM1-3 516R44 (DM) has been released by the Potato Genome Sequencing Consortium.
More details on the project can be found here and at the Potato Genome Sequencing Consortium site.

The Solanaceae comparative genome browser has been updated and now contains 387.7Mbp in 3311 annotated Solanaceae BACs.
Gene models have been recalled using the improved MAKER v2 annotation pipeline.
The browser now features a Primer3 track with pre-computed primers for putative SSR markers.

The Potato Genome Sequencing Consortium has made the draft genome sequence of Solanum phureja DM1-3 516R44 (CIP801092) available to the public through a genome browser, hosted here at the Solanaceae Genomics Resource.
Access to the browser in advance of a PGSC genome publication is provisional requiring users to agree to the PGSC data access agreement.
For links to the browser, draft genome sequence data, and more information about data access, please refer to the PGSC website at: potatogenome.net.

Site resources have been updated.
Integrated overview page for EST assemblies with search portal allowing search by functional annotation.
Updates to our model genome browsers including improved annotation of features and OrthoMCL cluster membership information.
Improved SNP viewer showing multiple sequence alignments of EST assemblies.
Genome browser has been updated to Gbrowse 1.69, which has an improved interface.

Release 3 of the Solanaceae Comparative Genomics project resources.
The current set of 1,810 Solanaceae BACs from GenBank was reannotated using an updated version of the MAKER annotation pipeline. A total of 29,234 predicted gene models were annotated and are available for BLAST searches, viewing in Gbrowse and for download on our FTP site.
Sequence data from the Tobacco Genome Initiative's public release is now available for BLAST searching.
The Tobacco Genome Initiative 454- and Sanger-sequenced sheared BAC assemblies were annotated using the MAKER pipeline. Results are available for BLAST searching and download: Sanger: 979 assemblies / 594 models, 454: 7,978 assemblies / 508 models. Annotation of methyl-filtered assemblies will be available soon.
The Solanaceae vs. Arabdidopsis genome browser has been updated with improved exonerate alignments.
The site's top menu has been reorganized for easier use. The species dropdown is now organized by genus, and summary pages are viewable for more species. A more complete FTP site map is available on our downloads page.

Many site resources have been updated.
Changes to our SNP-calling pipeline have resulted in a significant increase in identified putative SNPs.
Annotation text keyword searching is now available for SSRs.
An additional 278 BACs have been added to the Solanaceae genome browser.
Solanaceae lineage-specific transcript assemblies have been updated using PUT sequences.

Release 2 of the Solanaceae Comparative Genomics project resources. 441 new Solanaceae BACs have been added to the Solanaceae Gbrowse database. New SSRs and primers have been generated for the current set of Solanaceae PlantGDB PUTs. New ortholog/paralog predictions for Solanaceae PUTs, including new putative ortholog clusters generated using OrthoMCL. Some additional updates have been delayed due to server technical issues, and will be added in the next several weeks.

Generation of Potato Genome Sequence and Annotation Resources project moves to Michigan State University.

The Solanaceae Genomic Resource Page has been reorganized.
The NSF Expression Project will be ending on September 30, 2007. Studies will be released to GEO.