Recipient Organization
Massachusetts Institute of Technology
(N/A)
Cambridge,MA 02139
Performing Department
(N/A)
Non Technical Summary
Oomycetes, a group of eukaryotes that are evolutionarily distant from fungi, plants and animals, are the most devastating pathogens of dicot plants. They cause enormous economic damage on important crops and environmental damage in natural ecosystems. The most destructive and best-studied oomycete is Phytophthora infestans, the cause of late blight of potato and notorious as the agent of the Irish Potato Famine. Today P. infestans causes losses in potato production worldwide of over 5$ billion each year, making it the single greatest pathogen threat to global food security. Phytophthora species are known to be pathogens of virtually all dicot crop plants, and have proven very difficult to manage. An annotated, high quality genome sequence of P. infestans will have broad impact on agriculture and plant pathology by greatly facilitating and accelerating the pace of research on this important agricultural pest. The overall goal of this project is to produce a high quality
genome sequence of P. infestans at a reasonable cost, and to make this sequence an effective resource by providing high quality annotation. We will continue to coordinate our work closely with the Phytophthora community and release all data promptly to public databases. As we have observed for multiple organisms, the availability of high quality annotated genome sequence drives research in the field.
Animal Health Component
(N/A)
Research Effort Categories
Basic
100%
Applied
(N/A)
Developmental
(N/A)
Goals / Objectives
The overall goal of this project is to produce a high quality genome sequence of P. infestans at a reasonable cost, and to make this sequence an effective resource by providing high quality annotation. To achieve this we have set the following objectives: 1. Generate a whole genome shotgun assembly representing 7X coverage 2. Build a dense genetic map and integrate with the genome assembly 3. Identify 2000 full length cDNAs 4. Annotate the genome with respect to genes and other features 5. Release genome data and associated information including EST alignments and results of homology searches in a browsable format 6. Develop education, training and outreach programs
Project Methods
We will apply the following approaches the objectives of the project. 1. Generate a whole genome shotgun assembly representing 7X coverage. We will produce a high quality draft assembly of the P. infestans genome. Assembly will be performed with our Arachne assembler. The sequencing and assembly processes will be optimized to yield the highest quality assembly in the most cost-efficient manner. 2. Build a dense genetic map and integrate with the genome assembly. We will place a total of 3000 SNPs on the whole genome assembly or an average of one every 79kb. These SNPs are easily discovered computationally from the genome assembly. Genotyping of SNPs will be performed at the state-of-the-art BI genotyping facility. 3. Identify 2000 full length cDNAs. We will identify 2000 full length cDNAs (FLcDNAs) representing ~10% of the P. infestans gene set to provide a critical, highly reliable training dataset for gene annotations as well as an invaluable resource to the research
community to support ongoing functional analyses. We will construct 5 cDNA libraries using Clontech CapFinder PCR cDNA construction kit (BD Biosciences), and identify FLcDNAs that represent a wide range of biological functions from diverse developmental stages. 4. Annotate the genome with respect to genes and other features. Gene-finding algorithms will be trained for P. infestans using gene, EST and FLcDNA data. Experience with the P. sojae and P. ramorum genomes shows that even after training gene callers, making accurate gene calls is difficult. Accordingly, once this is complete, experts in gene annotation P. infestans biology will team up to manually curate a statistical sampling of gene calls. Results will be used to validate gene calls, correct potential errors in gene prediction and fine-tune the gene callers. 5. Release genome data and associated information including EST alignments and results of homology searches in a browsable format. Data from the P. infestans sequencing
project will be made freely available. Sequence traces will be sent to the National Center for Biotechnology Information (NCBI) trace repository; the genome assembly and assemblies of all large insert clones will be deposited at GenBank; ESTs will also be deposited into PFGD (www.pfgd.org) and integrated with existing P. infestans EST data. An additional data release will provide access to the automated annotation of the P. infestans genome sequence both in flat files and in a rich, browsable format. 6. Develop education, training and outreach programs. We will organize a series of teacher education workshops on "forensic pathogen DNA from the Irish potato famine" in partnership with high schools and museums. We will also develop a museum exhibit illustrating the life cycle of the pathogen, its present and past impact on humankind, and information on modern genomics research.