Progress 12/15/05 to 12/15/06
Outputs Annual report for NSF/USDA Genome Sequence of Phytophthora infestans. Proposal number 2005-05219. Progress report: During the first year of this project we have made significant progress toward achieving the stated goals of the Phytophthora infestans genome project. Genome sequencing. We generated 3,141,755 whole genome shotgun reads containing 1,894,706,650 Q20 bases, representing ~9x coverage of the genome. Sequence data were generated from three clone types: high copy number plasmids with 4kb inserts, low copy number plasmids with 10kb inserts, and single copy Fosmids with 40kb inserts. All the reads have been submitted to the NCBI trace repository. Genome assembly. Two shotgun assemblies of the whole genome sequence data were performed. A preliminary assembly (version 0.5) was done when roughly half the data were available, and publicly released on July 19, 2006. When all whole genome sequencing was completed, an assembly of the full data set was done (version
1.0), and released on October 23, 2006. The version 1.0 release is available on the Broad Institute web site at http://www.broad.mit.edu/annotation/genome/phytophthora_infestans/Hom e.html The assembled genome is available in GenBank under the accession AATU0100000. This version 1.0 assembly includes 190 Mb of the estimated 242 Mb of the full genome. The remainder is believed to be mostly high copy repeat and tandem repeat sequences, as almost all of the unassembled sequences align at high identity to portions of the assembled genome. The N50, or weighted median, contig size is 44.4 kilobases (kb) and the N50 supercontig, or scaffold, is 1.57 megabases (Mb). The N50 represents the size of assembled sequence block for which 50% of the assembled bases are in a unit of that size or larger. Alignment of the available ESTs to the v1.0 assembly suggests it contains ~95% of the unique protein coding sequence in the genome. All alignments of the ESTs are available on our web site. Annotation.
Full automated gene annotations by our standard process are currently in being computed and will be released as they become available. Work is ongong in several other areas in support of the annotation process. We have end sequenced 500 putative full length cDNAs from an existing library. Two new cDNA libraries containing full length clones are being constructed. Existing EST and genome sequence data were used to generate 500 hand-curated gene models to serve as a training set for gene callers. Finally, we have developed a novel oomycete-specific comparative gene calling algorithm that is tuned to the existing oomycete genome datasets.
Impacts Impact: Phytophthora infestans is the cause of late blight of potato and is notorious as the agent of the Irish Potato Famine. Worldwide, it causes over $5 billion in annual losses in potato production, making it the largest single pathogen threat to global food security. An annotated, high quality sequence of the P. infestans genome will have broad impact on agriculture and plant pathology by greatly accelerating the pace of research on this important agricultural pest, and lead to improved methods of detection and control.
Publications
- No publications reported this period
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