Tag Archives: phytozome

Phytozome notice, new and improved v10 coming soon [see update]

This announcement came out while I was at a conference last week–but I wanted to pass it along. This appears to be a big change in the way Phytozome works. And there will be down-time before it rolls out, starting May 1. I like to post major announcements from mailing lists because I know everyone isn’t signed up on every mailing list in bioinformatics as I am…. I can’t figure out how to link to their mailing list archive, so I’m posting the whole thing here.

There appears to be a quick-start guide for the new interface, and I’ll keep an eye out for the chance to do another Tip of the Week (previous tip).

Via the mailing list, from David Goodstein:

Subject: May 1st retirement of Phytozome v9

The last full day of support for v9 of Phytozome will be Friday, May 1st.  Over the subsequent weekend, v9 will be brought down and forwarding services will be put in place to ensure as many URLs as possible find the correct, or at least related, pages in Phytozome v10.

1. Why does v9 of Phytozome need to be retired?
The Phytozome v9 website, at http://www.phytozome.net, is based on an older technology stack that is no longer supported by any developers on the Phytozome team.  Newer genome releases, and newer data sets (diversity and expression data) are also not hosted on v9.  In the interests of focussing our limited developer resources in the most effective way possible, and having a single location for access to Phytozome genomic data and analysis, we will have a single website going forward:  Phytozome v10, located at http://phytozome.jgi.doe.gov .

2. What happens to the genomic data contained in Phytozome v9?
The vast majority of v9 genomes and annotations are available at the Phytozome v10 website, often in updated form (one genome, B. Rapa chiifu, is not being carried forward).  Users can still find bulk data files containing all the genomes and annotations from Phytozome v9 at the JGI Genome Portal:  http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9

3.  I have bookmarks to various resources/genes/families at v9; what happens to those URLs?
-Links to the main site, help pages, release notes, and organism info pages will be automatically forwarded to the corresponding pages in v10.
-Gene pages:  forwarding scripts will attempt to determine the corresponding gene page in v10
-GBrowse pages:  GBrowse in v9 is replaced by JBrowse in v10.  We will attempt to forward URLs to the corresponding location in JBrowse if it exists; if not, the URL will be forwarded to the default location in the corresponding organism’s JBrowse.
-The following v9 URLs/pages will NOT forward to new locations in v10:
—Gene family pages
—Sequence Query results (BLAST results) and BioMart query results.  Note that these expire after 3 days and are therefore not archivable at the present time.
—Keyword Search Results pages

4. I have no idea how to use the new Phytozome v10 interface. Help!
There’s a Phytozome Quick Start Guide available at http://phytozome.jgi.doe.gov/pz/QuickStart.html . Release notes for Phytozome v10 are at http://phytozome.jgi.doe.gov/pz/portal.html#!releaseNotes.

5.  I have further questions. What should I do?
Email the Phytozome development team at phytozome@jgi-psf.org

Thanks for using Phytozome.



Goodstein D.M., S. Shu, R. Howson, R. Neupane, R. D. Hayes, J. Fazo, T. Mitros, W. Dirks, U. Hellsten, N. Putnam & D. S. Rokhsar & (2011). Phytozome: a comparative platform for green plant genomics, Nucleic Acids Research, 40 (D1) D1178-D1186. DOI: http://dx.doi.org/10.1093/nar/gkr944

UPDATE: From the Phytozome team–v10 has been available already.


A newly enhanced database and resource is available to researchers called Phytozome. Phytozome is targeted as a hub of genomic data for plants of interest in biofuel research and a joint project of the DOE JGI and UC Berkeley’s Center for Integrative Genomics. As a recent press release states,

The gene families available in Phytozome, defined at several evolutionarily significant epochs, provide a framework for the transfer of functional information to important biofuel and agricultural crops from model plant systems, as well as allowing users to explore land plant evolution.

This release is v. 4 and includes the genomes of 14 plants from green algae, arabidopsis and corn. The resource uses GBrowse (free tutorial and training materials) as it’s genome browser, BioMart for advanced searching and has BLAST capability. I find Gramene a bit more extensive than Phytozome, but the focus of the two (biofuel plants and agricultural grains for Phytozome and Gramene respectively) are different and Phytozome is becoming quite extensive.

I remember going to a DOE/JGI users conference last year and being quite impressed with the research going on in biofuel, and also more sobered by the obstacles both techological and practical (use of food-producing land, etc) that we face. With rising gas prices and temperatures, can’t ask for too much information!