Phytophthora parasitica INRA-310 Database

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Project Information

The oomycete Phytophthora parasitica is a very broad host range pathogen that causes destructive diseases of a wide variety of crop plants including tomato, pepper, eggplant, potato, tobacco, cacao, pineapple, passionfruit, safflower, sesame, common bean, banana, citrus, walnut, almond, pistachio, papaya, peach, plum, apricot, apple, macadamia, pear, avocado, guava, pomegranate, a wide variety of nursery and ornamental plants, and forest ecosystems. Some isolates are also effective pathogens of Arabidopsis thaliana and Medicago truncatula. The overall goal of the project is to create a high quality draft sequence of P. parasitica and identify SNPs additional isolates of diverse host range (including several funded by international partners) in order to enable a comparative genomic analysis of genes that determine host range.

The Phytophthora parasitica sequencing project is supported as part of the Microbial Genome Sequencing Program from the United States Department of Agriculture - Agriculture and Food Research Initiative (USAD - AFRI), grant number VAR-2009-01533. Its goal is to release a high quality draft genome assembly and annotation for Phytophthora parasitica isolate INRA-310, together with polymorphim data for additional isolates.

The overall goal of the project is to create a high quality draft sequence of Phytophthora parasitica INRA-310, together with sequences from several other isolates of diverse host range in order to enable a comparative genomic analysis of genes that determine host range in Phytophthora parasitica.

Comparing the genetic repertoire of P. parasitica with those of the three other assembled Phytophthora species, two that have a narrow host range (P. infestans and P. sojae) and one that has a broad host range (P. ramorum), will provide important insights into the molecular basis of host range and host specificity in oomycete pathogens.

Our specific aims are as follows:

  1. Generate a whole genome shotgun sequence assembly of P. parasitica isolate INRA-310 as a reference sequence, using an optimized model of Illumina sequencing data.
  2. Annotate the genome with respect to genes and other features, using 454 and Sanger EST data available from our international collaborators, and Illumina RNA-seq data generated by this project.
  3. Identify conserved and rapidly diversifying genes by generating Illumina data from five additional strains funded by this project, and at least five additional strains funded by collaborators.
  4. Promptly release all reads, assemblies, annotation, discovered polymorphisms and EST alignments to the community. Integrate the annotated genome sequence into the VMD centralized oomycete genomics resource at Virginia Tech.
  5. Train community members in the use of the sequence and add value to the sequence via a combined training workshop and annotation jamboree. The workshop and jamboree will include students and faculty from undergraduate institutions.

Data Releases

We generated a whole genome shotgun assembly from data generated by Illumina sequencing technology. The resulting ~71Mb draft assembly was made public in November of 2011, and the results of genome annotation will be made public in future releases. Questions about the project should be directed to annotation webmaster.

Project Leadership and Collaborators

Leadership

  • Brett M. Tyler, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University
  • Carsten Russ, Broad Institute
Primary Collaborators
  • Franck Panabieres, INRA (Nat. Instit. Agric. Res.), Sophia Antipolis, France
  • Weixing Shan, Northwest Agricultural & Forestry University, Yangling China
  • Nik Grunwald, USDA-ARS, Corvallis, Oregon
  • Marco Machado, Centro APTA Citros Sylvio Moreira, Sao Paulo, Brazil