Announcements

• [16 Jan 2012]   Phytozome v8.0 has been released!
  
• [12 Dec 2011]   A service outage for filesystem maintenance is currently scheduled for Tuesday, December 13th, 2011 from approximately 12 AM to 3 PM Pacific Standard Time.
  
• [07 Oct 2011]   Release of Thellungiella halophila genome and Biomart sequence issue fixed.
  
• [22 Aug 2011]   Eucalyptus grandis accession IDs have been revised throughout the Phytozome website. Please see the E. grandis Info page for more details.
  
• [05 Aug 2011]   A service outage for filesystem maintenance is currently scheduled for Tuesday, August 9th, 2011 from approximately 7 AM to 5 PM Pacific Daylight Time.
  
• [07 Jul 2011]   Corrected UTR data now available in BioMart
  
• [08 Apr 2011]   Phytozome v7.0 has been released!
  
• [15 Jan 2011]   Release of Eucalyptus grandis, Citrus sinensis (sweet orange), and clementine genomes.
  
• [13 Dec 2010]   Minor bug fix release of Phytozome today. See news.
  
• [11 Nov 2010]   If your browser is not rendering this site correctly, click here
  

News

• [16 Jan 2012]  Phytozome v8.0 has been released!
  The lastest version of Phytozome has been released. Version 8 includes 21 genomes assembled and/or annotated at the JGI, and 9 externally produced genomes. Also included are early release access to the Panicum virgatum (switchgrass) genome and annotation, as well as the unannotated assembly of the Cotton D Genome. Update genomes include Eucalyptus, Aquilegia, and the grasses maize, rice and Brachypodium. New JGI genomes include the aforementioned Panicum virgatum genome, as well as Capsella rubella,and Phaseolus vulgaris, while the external genomes Brassica rapa, flax, and apple make their first appearance in Phytozome.
• [12 Dec 2011]  Service Outage Tuesday, December 13th, 2011
  A service outage for filesystem maintenance is currently scheduled for Tuesday, December 13th, 2011 from approximately 12 AM to 3 PM Pacific Standard Time. The Phytozome website will be inaccessible for this block of time.
• [07 Oct 2011]  Release of Thellungiella halophila genome and Biomart sequence issue fixed.
  The version 1.0 genome annotation and assembly of Thellungiella halophila (salt cress) is now available as an early release genome. This genome will eventually be included in gene families released in late Fall as part of Phytozome version 8.0. We have also fixed a Biomart issue where large queries sometimes returned coding or peptide sequence with missing exons.
• [05 Aug 2011]  Service Outage Tuesday, August 9th, 2011
  A service outage for filesystem maintenance is currently scheduled for Tuesday, August 9th, 2011 from approximately 7 AM to 5 PM Pacific Daylight Time. The Phytozome website will be inaccessible for this block of time.
• [07 Jul 2011]  BioMart and Gene Page bug fix release.
  We have fixed an error in the genome data available via BioMart which caused incorrect UTR sequences to be returned for some negative strand features. We have also fixed a gene page bug that occasionally caused alternative transcripts to not be listed when a primary transcript was selected. Finally, GBrowse has been upgraded to v2.39, and includes "Track Favorites" and the ability to drag the main browser view 50% to the left or right to see additional genomic features.
• [08 Apr 2011]  Release of Phytozome v7.0
  This seventh release of Phytozome includes updates to the following genomes: Arabidopsis thaliana, Zea mays, Setaria italica, and Chlamydomonas reinhardtii. Gene families now include representatives of the previous Early Release genomes Citrus clementina, Citrus sinensis and Eucalyptus grandis. A chlorophyte node has been added, with gene families containing chlamydomonas and volvox. See the release notes for more details.
• [15 Jan 2011]  Release of Eucalyptus grandis, Citrus sinensis (sweet orange), and clementine genomes.
  Three new genomes annotations and assemblies are now available for download, browsing and BLAST searching. These are version 1.0 of Eucalyptus grandis, version 1.0 of Citrus sinensis (sweet orange), and version 0.9 of Citrus clementina (clementine). All three will be included in gene families released shortly as part of Phytozome version 6.1.
• [13 Dec 2010]  Minor bug fix release
  We have made a minor bug fix release of Phytozome, to address the following issues:
  • Gbrowse memory leak. Certain Gbrowse processes were consuming growing amounts of memory, degrading website responsiveness.
  • Missing UserBlast track when viewing genomic BLAST results. A bug in how Gbrowse 2 handles remote feature tracks causes the UserBlast track to not display properly when opening a BLAST result in a genomic browser for the first time. The Gbrowse bug remains, but we have encoded a work-around to allow the blast track to display correctly.
  • Poplar Alternative transcript features in Gbrowse not linked to their gene pages.
  We are also reactivating access to the VistaPlot tracks in Gbrowse.
• [05 Nov 2010]  Phytozome v6.0 released.
  We are pleased to announce the release of version 6.0 of Phytozome, which includes both updated and newly released plant genomes, as well as a new method of gene family construction. Twenty-two genomes (thirteen of which were sequenced predominantly at the Joint Genome Institute) are clustered into gene families defined at 10 evolutionarily significant speciation nodes. Newly added genomes include Aquilegia, foxtail millet (Setaria Italica) and Volvox carteri. Updated genomes include the v2.2 annotation of poplar, and annotation updates for cassava, Chlamydomonas, and Physcomitrella. Please see the Release Notes for more information on these genomes and the new gene family construction methods.
• [08 Jan 2010]  Phytozome v5.0 released.
  Version 5.0 of Phytozome is now available, and incorporates both updated and newly released plant genomes. Eighteen genomes (eleven of which were sequenced at the Joint Genome Institute) are clustered into gene families defined at 15 evolutionarily significant nodes. Genomes newly incorporated into Phytozome include Mimulus guttatus (monkey flower), Cucumis sativus (cucumber), Ricinis comunis (castor bean),and Manihot esculenta (cassava), the latter having been part of a limited release in v4.1. Updated genomes include the eagerly anticipated v2.0 release of Populus trichocarpa (poplar), Arabidopsis thaliana, Medicago truncatula, Oryza sative (rice), and Chlamydomans reinhardtii. Please see the details page for more information on these genomes.
• [23 Nov 2009]  Pseudomolecule maize assembly and annotation now available at Phytozome.
  Maize version 4a.53 Pseudomolecule assembly and annotation from maizesequence.org is now available for browsing and BLASTing. Also included are 454 shotgun reads from maize variant Mo17, aligned directly against the genome as well as aligned after Newbler pre-assembly.
• [23 Nov 2009]  Phytozome v4.1 released.
  Version 4.1 of Phytozome is now available, with several new features. Gene Pages (e.g., here) now exist for every gene in Phytozome, providing a single location to find functional annotations, alternative transcripts, sequences, evolutionary history, and related homologs (based on Dual Affine Smith-Waterman alignments against all Phytozome peptides). BLAT similarity searches against Phytozome genome targets are now enabled. Finally, two bug fixes are included: BioMart difficulties with retrieving data in which some attributes have NULL values are resolved. An error in the gene family construction pipeline which violated the hierarchical nesting rule for a small number of families,and also caused some very high similarity sequences to never merge into the same family, has been repaired.
• [09 Nov 2009]  Cassava genome released.
  Version 1.1 of the Cassava (Manihot esculenta) assembly and annotation is now available for download, browsing and BLAST searching. It will be included in gene families in Phytozome version 5.0. More information and links are available here
• [17 Apr 2009]  Phytozome v4.0 released.
  Version 4.0 of Phytozome is now available, featuring 14 complete green plant genomes clustered into gene families at 20 evolutionarily significant nodes. Newly added genomes and gene sets include the legume Medicago Truncatula, Arabidopsis thaliana's close relative Arabidopsis lyrata, the brassicale Carica papaya, and the grass Brachypodium. The previously released (but unclustered) maize (Zea mays) and soybean (Glycine max) gene sets are now included in gene families. More information is available on the details page. We've also added the ability to BLAST against each organism's proteome (set of translated gene products). The BLAST results link out to the smallest gene family containing the target gene.
• [13 Mar 2009]  Zea mays (maize) available.
  The 3a.50 protein coding gene set on sequence release 3.0 from maizesequence.org is now available for BAC-by-BAC browsing and BLASTing. Learn more on the Maize page.
• [08 Dec 2008]  Gbrowse upgraded
  All Phytozome Gbrowse browsers have been updated to v1.69 from v1.64. Expect somewhat faster page loading and improved functionality (draggable tracks, inline track configuration, etc.)
• [08 Dec 2008]  Chromosome-based soybean assembly and annotation is now available
  Glyma1.0 chromosome-based assembly and annotation of soybean is now available, replacing the preliminary contig-based assembly and annotation previously available at Phytozome. All Soybean Gbrowse and BLAST resources now point to this new assembly and annotation. Learn more on the Soybean page.
• [12 Nov 2008]  New v3.1 Gene Families
  New gene families have been constructed at all 9 Phytozome nodes, incorporating for the first time synteny and transversion rates in the identification of orthologs and paralogs. This has the desired effect of reducing the number of pan-grass families (families containing both sorghum and rice genes, but no rosids) at the angiosperm node, meaning more complete pan-angiosperm gene families are obtained. There were 7273 pan-grass families at the angiosperm node in the previous non-synteny-based clustering, compared to only 1144 in the current clustering. Please see the details page for more information.

  Any bookmarked URLs involving specific gene family ids (Cluster ids) will no bodyer go the the appropriate cluster summary page. Contact the Phytozome team if you need a mapping of specific cluster ids from the previous gene family build to the current v3.1 build.

• [04 Aug 2008]  Welcome to the new homepage!
  You can now select organims for browsing/blasting, and nodes for gene family searching/blasting, either by clicking on tree nodes or using the pulldowns in the upper left hand corner. We hope this proves convenient.
• [04 Aug 2008]  New search functionality
  Gene family searches can now be restricted by organism. The "Family Members" filter on the Gene Family Search page restricts the gene family search to only those families that match the set of organism constraints specified by the filter. You can choose to search only those gene families that include or exclude any of the organisms present at that node. By default, all organisms are allowed, and none are excluded.
• [27 Jun 2008]  Upgraded BLAST facility
  Phytozome now employs a queuing system to handle BLAST jobs, allowing users to submit larger jobs and to be notified by email when their jobs complete. BLAST jobs can now run up to 15 minutes for email notification, and 5 minutes in interactive mode. These limits will be relaxed as resources become available (please, as a courtesy to your fellow users, no BAC blasting against unmasked assemblies at low stringency!) . The BLAST results have also been recast into a more intuitive format combining the graphical and text views in a single panel. Finally, problems associated with faulty links from BLAST to Gbrowse caused by URL's with a very large number of HSPs have been resolved.
• [14 May 2008]  Phytozome 3.0 is here!
  The latest release, v3.0, of Phytozome is now available. v3.0 expands on Phytozome v2.0 by including:
  • the chromosome-based assembly and annotation of sorghum bicolor
  • grape, the spikemoss Selaginella, and the algae Chlamydomonas in our ancestral gene family reconstruction, bringing Phytozome v3.0 to the Viridiplantae node of the plant evolutionary tree
  • Phytozome data can now be accessed through Phytozome's BioMart application, allowing users to download gene family and individual gene sequences, annotations, and related information.
• [26 Mar 2008]  Chromosome-based assembly and annotation of Sorghum bicolor
  v1.0, the first chromosome-based assembly (Sbi1) and annotation(Sbi1.4) is now available. The current Phytozome clustering still uses the v0 sorghum gene models, but we are providing access to the v1.0 browser, blast interface, and data download site here . v1.0 sorghum models will be included in Phytozome clusters in the next Phytozome release.
• [11 Jan 2008]  First look at soybean (Glycine max) assembly and annotation
  A preliminary assembly and annotation of the soybean (Glycine max) genome is now available. Information and access to the data can be found here.
• [08 Jan 2008]  Minor update to Phytozome Interface
  We've removed the Click-Info panel from the Cluster Summary page. The information formerly displayed there, systenic gene cluster information and PFAM domain information, is now displayed in pop-up boxes that appear when mousing over a syntenic gene or domain. To freeze the pop-up display and access the hyperlinks inside, simply click on the gene or domain image.
• [12 Nov 2007]  Composite cluster capability added to Phytozome
  We've added the ability to combine the gene clusters found in single node keyword or BLAST search into a "composite" cluster that can be viewed in a cluster summary page. This is especially helpful when dealing with cases of "under-clustering," where a cohesive gene family is incorrectly broken up into several smaller clusters. Multiple sequence alignments and consensus sequences (used for BLAST searches) are calculated on-the-fly for composite clusters with fewer than 75 members. More information on this feature can be found here and here .
• [23 Oct 2007]  Minor update to Phytozome interface
  Version 2.0.2 of the Phytozome website includes three new features: the ability to show search and cluster details for only those species of interest, a Get Sequences function that allow you to download gene family sequences and MSAs, and the ability to view gene family MSAs (Multiple Sequence Alignments) directly from the cluster summary page. To hide details on particular species, select the "Display" tab on the Search Results page and uncheck the species you wish to hide. You can also do the same on the "Display Options" tab on the Cluster summary page. To download gene family sequences, click on the Get Sequences tab and select the desired sequence type. To view MSAs, select the "Multiple Sequence Alignment" tab onthe Cluster summary page. For more information, please see the help page .
• [01 Jul 2007]  New Website
  A complete rework of the Phytozome website has just been completed. Navigation has been simplified, synteny viewing features have been enhanced, the individual cluster view display can be customized, and help documentation has been expanded. The genomes of individual organisms can now be searched via BLAST, and their annotations viewed within Gbrowse. In particular,
  • Gbrowse genome browsers to view annotations of individual organisms (e.g, sorghum ).
  • BLAST search of individual genomes (e.g, Physcomitrella BLAST search ), with links to Gbrowse view of results in their genomic context
  • Click highlighting of orthologous syntenic genes and shared domains on cluster summary page
  • User-configurable column display
  • Ability to find all clusters containing particular sets of attributes shared with a given cluster (gene members, functional assignments)
• [01 Jul 2007]  Two additional plant genomes added
  Phytozome now includes a preliminary annotation of the grass Sorghum bicolor , as well as the version 1.1 annotation of the moss Physcomitrella patens . These genomes are joined by TIGR release 5 of the rice (Oryza sative) genome , TAIR release 6 of the Arabidopsis thaliana genome , JGI v1.1 of the poplar genome (Populus Trichocarpa), bringing to five the number of complete plant genomes analyzed in Phytozome v2.0.