1. The Home Page
    1. Searching for genes and gene families
    2. Top Menu
  2. Finding out about genomes included in Phytozome
    1. Organism Pages
    2. Release Notes and News
  3. Gene and Gene Family Views
    1. The Gene View
    2. Gene Family View
  4. The Keyword/BLAST/BLAT Search Interface
    1. Select a target:
    2. Build your query
  5. Keyword/BLAST/BLAT search results
  6. The Side Menu
  7. My Data
  8. Viewing Genomic Data in JBrowse
  9. Using the PhytoMine Interface to Save/Retrieve/Download Data Sets
  10. Bulk Data Files in the JGI Genome Portal
  11. Appendix
    1. List of snpEFF effect types

The Phytozome website and database provide you with access to gene families, individual genes, diversity and expression data for 52 released plant genomes (as of version 10.1). Sequence similarity (BLAST/BLAT) and keyword-based searching can help you pinpoint genes and gene families of interest.You can navigate the evolutionary history of each gene, and identify closely related families and genes, using criteria like shared domains, shared keywords, and sequence similarity.Genome browsing is available via our deployment of GMOD's JBrowse too (v11.1). Our JBrowsers include gene tracks, protein homology tracks, diversity and expression tracks (where available), and VISTA whole genome alignment tracks. Finally, all data on genes, gene families and individual genomes in the Phytozome database are downloadable via PhytoMine and BioMart, popular open source data retrieval tools.

The Home Page

Phytozome's home page (Figure 1.) provides a quick search interface for learning about the genomes included in the current release and finding genes and gene families on interest.

Fig. 1. Phytozome home page

Genomes are organized into three groups:

  1. Flagships
  2. All released genomes and families
  3. Early Release Genomes

Flagships constitute those genomes for which the JGI has made an extended commitment in terms of ongoing maintenance and improvment, both of the reference assemblies and annotations, as well as through the acquisition and inclusion of a broader class of genomic resources (e.g., re-sequencing and gene expression data).  "All released genomes and families" contains all the finalized, released genomes in the current release of Phytozome, as well as indicating the evolutionary nodes at which gene families containing these species  have been calculated (e.g., grass, eudicot, angiosperm, chlorophyte, etc.).  The final group, "Early Release Genomes", contains recently completed assembly and annotation updates that are typically unpublished and are not guaranteed to remain unchanged in their current version.  These genomes are not included in gene family builds, and often co-exist with an earlier, released version in the same release of Phytozome.  (Note that both Early Release and currently released genomes may still be under data usage restrictions; it's important to check the Data Usage Policy for each genome).

You can switch between groups by clicking on the group category n the three way toggle in the quick search panel:

Figure 2. Group toggle on Home Page quick search

When a given group is selected, a horizontally scrollable set of images and genome / node names will appear.  You can browse through the set via scrolling, or type in a genome or node name  in the "Search in" box (e.g, "malus domesticus" and "apple" will both work, as well as "viridiplantae") and if that genome is contained in the currently selected group, it's image will scroll into view.

Fig 3. Apple genome has been selected.

If you double-click on the image, the organism information page will open up (see the next section).

Searching for genes and gene families

Once you've chosen a genome or node (by entering it's name in the "Search in" box or by single-clicking its image), you can search for genes in that genome (or gene families at that node) via sequence or keyword search. Enter gene identifiers, gene symbols, KEGG/KOG/PFAM/PANTHER/GO identifiers, descriptive keywords (e.g, "cyclin", "dessication", "stress") into the "for" text box and hit return.  Alternatively, paste in a sequence (nucleotide or protein), and click "GO".  You'll quickly receive a summary of results matching your search (see the section on Search Results below).  Don't worry if your search produces no hits; you can easily revise it using the full search interface discussed later.

Top Menu

The final feature we visit on the home page is the top menu:

Fig. 4 Top menu

This menu is available from every Phytozome page (except those associated with 3rd party tools like JBrowse, PhytoMine and BioMart), and provides access to all the info pages for each genome in the current release, the most frequently used Phytozome tools, release notes and bulk data download links, help/contact links, and a Log In button to enable access to bulk data downloads and cart data saving.  Choose a genome from the Species list:

Fig. 5 Top menu genome list

and you'll be taken to the Organism information page for that genome (see next section).

The home page also contains highlights of recent Phytozome news (click through for detailed news items), a regularly updated System Status panel, and links to these help documents. 

Finding out about genomes included in Phytozome

Organism Pages

Each current and early release genome has an information organism page.  Here's the info page for Arabidopsis thaliana: