Phytophthora infestans Database
The Phytophthora infestans sequencing project is supported by a grant from the National Science Foundation and the United States Department of Agriculture. Its goal is to release an annotated assembly with 8X genome sequence coverage for Phytophthora infestans strain T30-4.Our specific aims are as follows:
- Generate and assemble sequence reads yielding 8X coverage of the P. infestans genome through whole genome shotgun sequencing.
- Perform targeted improvement of poor quality regions of the assembly by shotgun sequencing of spanning Fosmid clones.
- Perform automated annotation of the sequence assembly.
- Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server at the Broad and by deposition of the sequence assembly in GenBank.
- Generate sequence of 2000 full length cDNAs.
- Generate a 3000 marker single nucleotide polymorphism (SNP) based genetic map and integrate this with the existing amplification fragment length polymorphism (AFLP) map.
- Chad Nusbaum (Broad Institute), PI
- Michael Zody (Broad Institute), Lead Scientist
- William Fry (Cornell University), co-PI
- Howard Judelson (University of California-Riverside), co-PI
- Sophien Kamoun (Ohio State University), co-PI
- Jean Ristaino (North Carolina State University), co-PI
Key collaborators for this project include:
- Francine Govers (Wageningen University, The Netherlands)
- Paul Birch, Scottish Crop Research Institute, Dundee, Scotland, UK
- Steve Whisson, Scottish Crop Research Institute, Dundee, Scotland, UK
We produced whole genome shotgun sequence from two plasmid libraries (4kb and 10kb inserts) and a Fosmid library. A preliminary 5X assembly was made public on 7/19/2006. The full-coverage (8X) assembly is now available. For the final assembly we used the SCRI BAC library in addition to our plasmid and Fosmid libraries.
Questions about the project should be directed to Chad Nusbaum or Michael Zody.
We have aligned EST sequences from the Syngenta Phytophthora Consortium  to the assembly. Of ~80,000 ESTs available in GenBank, ~65,000 align to the assembly. The remainder contain a high fraction of host transcripts as well as sequences (such as ribosomal genes) which are difficult to assemble by whole genome shotgun.