Overview

Phytome is an online comparative genomics resource that is built upon publicly available sequence and map information from a diverse set of plant species, with a focus on the angiosperms, or flowering plants. It provides an interface to the results from a variety of phylogenomic analyses. Phytome is designed to facilitate functional genomics, molecular breeding and evolutionary studies in model and non-model plant species. Currently, Phytome contains phylogenetic and functional information for predicted protein sequences ("Unipeptides"). Future development will incorporate data and tools for analysis of sequence-based comparative maps.

Please explore Phytome and send us your feedback.

Information About the Current Release

Phytome v. 2 (released Aug 2006) allows you to search 46,353 Unipeptide Families from 136 different plant species.

What's New

• Many more species and Unipeptides!
• Organellar Unipeptides and repeat sequences are annotated
• Select whole clades with the Species Selector Tool
• Browse Unipeptide Families based on functional annotations
• Graphical overview of each Unipeptide Family phylogeny

General Features

You may query Unipeptides and Families by searching for a component DNA sequence (such as a Genbank accession number or Arabidopsis AT number), an alias for a gene or marker (such as a unigene ID from another database), a Gene Ontology term/ID or InterPro term/ID, or browse the families based on Interpro and Gene Ontology annotations. You may retrieve Families present or absent in particular combinations of species. You may use BLAST to search the Unipeptides in the full Phytome dataset or one species at a time. Registered users can access advanced features such as Batch BLAST and bulk download of data.

For each family, information available includes:

• Related families and subfamilies
• Multiple alignments and phylogenies
• InterPro and GO assignments for select representatives

Novel and/or special features include:

• The ability to find corresponding Unigenes from a variety of plant sequence databases (including PGN, NCBI Unigene, PlantGDB, Sputnik, TAIR, and TIGR).
• The ability to search for gene families based upon which species are or are not represented in the family.

Further documentation is available here and in this publication.

About Us

Phytome has been developed by Stefanie Hartmann, Dihui Lu, Jason Phillips and Todd Vision. For more information about us, please visit the Vision lab website.

Phytome is sponsored by the National Science Foundation Plant Genome Research Program (DBI-0227314) and based at the Department of Biology at the University of North Carolina at Chapel Hill. Any opinions, findings, conclusions, or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Our thanks to the staff at the various plant EST databases, particularly PlantGDB, PGN and Sputnik, who have helped us to incorporate their data into Phytome.