Microbial Genome Sequencing: Phytophthora

Massachusetts Institute Of Technology, Cambridge MA

Investigators

Abstract

Phytophthora infestans, the Irish Famine pathogen, is the causal agent of late blight of potato and tomato, and is responsible for significant losses in these crops. Worldwide losses in potato production caused by late blight exceed $5 billion annually, making P. infestans the single most important biotic threat to global food security. P. infestans belongs to the oomycetes, a diverse group of fungus-like eukaryotic microorganisms that include both saprophytes and pathogens of plants, insects, crustaceans, fish, vertebrate animals, and microbes. Phytophthora species cause enormous economic damage to many important crop species as well as environmental damage in natural ecosystems. The long term goal of this project is to generate a high quality finished sequence of the P. infestans genome. The immediate goal of this project is to establish the optimal strategy for doing so, in terms both of quality and cost. A cautious approach will be taken to planning this project because of the challenges posed by polymorphism in the P. infestans genome. This will allow ultimate delivery of the highest quality sequence of the genome. The specific objectives of this project are: 1) Characterize the degree of polymorphism in the P. infestans genome by analysis of Single Nucleotide Polymorphisms (SNPs). 2) Sample the genome by sequencing overlapping pairs of BACs representing two haplotypes and light coverage whole genome shotgun sequencing. 3) Construct a dense genetic map using the SNPs generated in objective 1. Analyses of the data generated by the work to be done along with simulations based on these data, will inform the generation of a roadmap to a finished P. infestans genome.