Phytozome FAQs

  1. How do I find out about a specific genome in Phytozome?
  2. How do I quickly find the genes I'm most interested in?
  3. Which genomes currently include diversity or expression data?
  4. Why do I have to register to access bulk data sets?
  5. What's up with version numbers?  It says I'm using Phytozome v10.1, but then the poplar version is 3.0 and the soybean version is Wm82.a2.v1, etc.  Help!
  6. I'm having real difficulties using Phytozome in Internet Explorer.  Any suggestions?
  7. I can't seem to scroll the organism images on the home page, or JBrowse or.......


How do I find out about a specific genome in Phytozome?

 Each genome in Phytozome has an associated Organism Info page. For example, the poplar page is here. You can get to Organism Info pages either by selecting an organism from the "Species" pulldown in the top menu, or, on the home page, by double-clicking on the organism's photo in one of the three "Phytozome quick start" panels. Theses pages have information on the assembly and annotation of each genome, proper citation information, and a set of quick links to get you to keyword and sequence searches, a JBrowse genome browser, and bulk data download portals, all specific to that genome.


How do I quickly find the genes I'm most interested in?

From any of three "Phytozome quick start" panels on the home page, you can select the organism you're interested in, by clicking on its image (in the Flagship or Early Release panel), or start typing its name in the "Target" box in the "Select from all..." panel), and then enter a keyword or sequence fragment in the Query box, and click "GO". Your keyword can be a gene identifier, a PFAM/GO/PANTHER or related id, a descriptive term (e.g, kinesin, lignin, dessication), or gene symbol. You'll be taken to a search result or BLAST result list of related genes. You can work directly with this set, or click "Revise query" on the side panel to refine or alter your original search. "G" links take you to a gene detail view, B links bring you to a view of the gene in its genomic context.

Which genomes currently include diversity or expression data?

Currently we have extensive diversity data for Poplar, and smaller diversity data sets for Brachypodium, Eucalyptus, Phaseolus, and Cassava. On the gene pages for these species, an additional Variation tab is present, showing SNPs and other variants in the neighborhood of each each. RNA-Seq-based expression data is available for Poplar,   Eucalyptus, Physcomitrella, ChlamydomonasSoybean, and Phaseolus. For these genomes, both expression and diversity data can also be viewed in JBrowse, searched and downloaded from PhytoMine, as well as in bulk from the JGI Genome Portal. Note that expression and diversity data is not available via our legacy BioMart instance.

Why do I have to register to access bulk data sets?

The Department of Energy and the Joint Genome Institute are committed to providing free public access to the data and analyses generated here. In order to justify the continued funding of public scientific resources such as Phytozome, we need to document the large number of individuals, in academia and industry, in the U.S. and abroad, who utilize our systems. Registration information is obtained solely for the compilation of usage statistics, and is not shared with any other U.S. Government or private agency or individual.

What's up with version numbers?  It says I'm using Phytozome v10.1, but then the poplar version is 3.0 and the soybean version is Wm82.a2.v1, etc.  Help!

The Phytozome version number refers to a particular major release of the Phytozome codebase, as well as a designated set of "released" genomes.  Minor release increments (e.g., 10.1, 10.2) usually involve the addition of some new capability, data type, and/or several early release genomes.  X.x.x releases are typically bug fixes.  This versions have nothing to do with the versions of individual genome assemblies and annotations.  So, this conversation makes sense: "I'm working with the v3 release of poplar.  Where did you get it?.  From Phytozome v10."  However, confusion will follow if you tell people "I'm using v10.1 of poplar."  The best place to see all the version numbers of the genomes associted with a given Phytozome release is on the Release Notes page

I'm having real difficulties using Phytozome in Internet Explorer.  Any suggestions?

Yes, stop using Internet Explorer.  You should have a good browsing experience with Firefox, Safari, or Chrome.  If you must, please make sure you're using IE 10 or later.

I can't seem to scroll the organism images on the home page, or JBrowse or.......

If you are using a computer or laptop with a trackpad, scrollbars don't always appear in scrollable sections until you actually put your cursor over them and begin scrolling.  So please give it a try.  For Mac OS X Lion or later users, there is an option in System Preferences->General->Show scrollbars: Always , that will allow you to see scrollbars even when you're not actively scrolling a section.