Phytophthora Studies

Oomycetes, or water molds, are among the most important eukaryotic plant pathogens. Annually, they cause $100s of billions of damage to agricultural and ecological systems worldwide, impacting the productivity and sustainability of food crops, ornamentals, forest products, and seafood. Several oomycete species represent sufficient threats to the safety of the nation’s food supply to merit inclusion on the Animal and Plant Health Inspection Service agricultural bioterrorism list or the USDA regulated plant pest list. There exists an urgent need to identify the genetic determinants of virulence and host range in order to develop improved control methods.
Phytophthora capsici Genome Project capsici capsici

P. capsici is a non-indigenous US pathogen. It was first reported in the US in 1922 on chili peppers in New Mexico and spread to vegetable production areas in Colorado and Florida in the 1930's and 1940's, affecting tomatoes, eggplants, squash, and melons.

NCGR (S. Kingsmore, PI), along with biologists at University of Tennessee and Ohio State University, is funded by USDA/NSF to sequence the P. capsici genome.  The rationale for these studies is:

1. P. capsici is a devastating pathogen of vegetable crops of national economic importance;
2. P. capsici is an excellent genetic model. This project will create broadly applicable resources for gene models and population genetic studies of oomycete biology and hemibiotroph-induced disease;
3. 454 sequencing technology will be evaluated and benchmarked for de novo and re-sequencing in the largest genome studied to date (65MB).

In collaboration and support from DOE's JGI sequencing group, the aims are to use novel 454 Life Sciences sequencing technology to generate:

1. 20X draft genome sequence of the vegetable pathogen Phytophthora capsici,
2. 2X coverage resequencing in 4 outbred isolates, and
3. a catalog of single nucleotide variation.

These resources will be disseminated at the Phytophthora Functional Genomic Database (PFGD).
Phytophthora Functional Genomic Database (PFGD) PFGD

PFGD is a web based clade-oriented information resource that builds upon data formerly available from the Phytophthora Genome Consortium (PGC) and at the Oomycete Genomics Database, as well as all publicly available P. infestans transcript data. PFGD is funded by NSF (S. Kamoun, Ohio State University, PI). Oomycete sequence data is analyzed and automatically annotated using NCGR's XGI system. PFGD includes functional assays and gene expression data, combined with transcript and genomic analysis and annotation. PFGD integrates the P. sojae and P. ramorum genomes and their annotations as well for comparative analysis. In addition, host species data — available at solgd.org - is integrated at PFGD. Going forward, P. capsici sequence data and variant analysis will also be available at PFGD.