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NIFA Microbial Genome Sequencing Award Information
USDA-NIFA AWARD NUMBER: 2009-01535
PROJECT TITLE: Sequencing the Obligate Oomycete Plant Pathogen Bremia lactucae.
RATIONALE

Oomycetes are a taxonomically distinct and understudied group of organisms. Bremia lactucae is one of the most highly specialized oomycete pathogens of plants. It is an obligate biotroph and causes the most important disease of lettuce, one of the top ten most valuable crops in the US. B. lactucae has long been a model for the study of biotrophy and pathogenicity.

PROJECT TEAM:

Richard Michelmore (rwmichelmore@ucdavis.edu)
Ian Korf (ifkorf@ucdavis.edu)
(The Genome Center, University of California, Davis)

SUMMARY OF SEQUENCING STRATEGIES:

We will assemble a high-coverage draft genome using sequences from several types of libraries including BAC-end Sanger reads and single, paired-end, and mate-end Illumina reads of genomic DNA from B. lactucae. The scaffolds will be ordered and oriented using BAC end sequences and an ultra-high resolution genetic map generated by sequencing the gene space of segregating progeny. We will resequence isolates in our global collection to determine how representative the reference isolate is of the species. We will use sequence-based, multiplexed bulked segregant analysis to relate phenotypes to sequence. We will also sequence ESTs using RNAseq to aid in assigning gene models and annotating the genome. The novel combination of high throughout sequencing and genetic validation of the assemblies will result in the efficient generation of a high quality genome sequence.

TIMELINE FOR COMPLETION:
  1. Start date: Fall 2009.
  2. Anticipated completion date: Fall 2012
  3. Milestones:

    Assembly of draft sequence from single isolate.
    Gene space sequences of 12 isolates.
    Segregation data from gene space sequences of segregating progeny.
    High quality, annotated genome sequence.

  4. Broader impacts

    The genome sequence will have multiple uses in comparative functional and evolutionary studies. The data will enable the efficient discovery of genes encoding virulence effectors and the dissection of the co-evolution of phytopathogenic oomycetes and their plant hosts. The genome sequence will enable the identification of genes involved in virulence and chemical insensitivity. This will facilitate the more rapid and efficient development of disease-resistant cultivars, the strategic deployment of resistance genes, and the informed, effective use of chemical protectants. Together these will increase the efficiency of lettuce production, while reducing chemical inputs and ecological consequences.

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