April 12, 2013
- A tomato repeat track has been added to the Solanum lycopersicum genome browser. This track was made by searching the tomato ITAG v2.40 pseudomolecules against the v5 tomato repeat library using RepeatMasker.
- New tracks for Nicotiana benthamiana were added to the Solanum lycopersicum and the Solanum tuberosum genome browsers. Tracks for the gene models were made by aligning the v0.4.4 gene models to ITAG v2.40 pseudomolecules for tomato and the PGSC v2.1.11 pseudomolecules for potato using Exonerate (est2genome). The highest scoring alignment for each model is displayed on the track. In addition, a track was made for Nicotiana benthamiana transcriptome shotgun assemblies downloaded from NCBI for each browser. These were also aligned using Exonerate (est2genome) and the highest scoring alignment for transcript is displayed on the tomato and potato tracks.
March 21, 2013
- The BAC end sequences from 3 different tomato libraries (HindIII, MboI, and EcoRI) from the sol genomics network were added to the tomato genome browser. From these libraries over 270,000 BAC end sequences were anchored to the tomato genome.
- Whole genome shotgun reads from Solanum pimpinellifolium (SRA:SRX032869) were used to call SNPs for tomato. More than 4 million SNPs were identified and are reported on the tomato browser and within the annotation report pages. In addition, the 8,760 SNPs previously identified by the SolCAP group used to design a tomato Infinium SNP array were also incorporated into the tomato browser and annotation pages.
- Wiggle tracks for 20 RNA libraries (SRR404309-SRR404322, SRR404324-SRR404329) from 10 different tomato tissues have been loaded into the tomato genome browser. The FPKM values corresponding to specific tomato genes have been added to the annotation report pages.
- The SNPs identified previously for potato are now incorporated into the annotation report pages.
- A new tool to search for SNPs within potato and tomato has been added to the Search Tools page. This tool allows researchers to search based on chromosome location as well as by locus or transcript id. The tool searches all WGS and SolCAP Infinium SNPs for both species.
July 9, 2012
- This website has been completely redesigned. The sequences in this resource have been updated and completely reannotated and reorganized. The website has been renamed the Solanaceae Genomics Resource to reflect these changes. For this new resource, we have integrated available transcriptome assemblies for Solanaceae species with the newly completed potato and tomato genomes. Annotated genes from the potato and tomato genome projects, along with transcriptome assemblies from the PlantGDB project, have been functionally annotated and two genome browsers, potato and tomato, have been developed to view sequences in a genomic context. Orthologous and paralogous relationships have been computed and phylogenetic trees have been constructed. SNPs and SSRs have been predicted and are integrated into a suite of search tools including sequence, text, annotation, and identifier search windows. All data has been made available through a suite of downloads.
- For potato, we have provided the annotation of the Solanum tuberosum group Phureja DM1-3 genome from both the PGSC and by the iTAG consortia.
December 18, 2010
- 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.
September 1, 2010
- The Potato Genome Sequencing Consortium has made the draft genome sequence of Solanum tuberosum group Phureja DM1-3 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.
June 5, 2009
- 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.
February 3, 2009
- 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.
January 9, 2009
- 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.
October 8, 2008
- 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.
June 26, 2008
- Launch of the new Solanaceae Genomics Resource web site.
January 1, 2008
- The Solanaceae Genomics Resource project moves to Michigan State University.
October 1, 2007
- Generation of Potato Genome Sequence and Annotation Resources project moves to Michigan State University.
August 30, 2007
- 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.