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Info • Phytophthora capsici v1.0
Please note that this organism is for archival use only. Please see the current Phytophthora capsici LT1534 v11.0 site for the latest data and information.

Status

The draft assembly release version 1.0 (26 June 2008) was generated from whole-genome shotgun 454 reads (~20X) and Sanger reads (~4X) using the novel assembler Forge (D. Platt, unpublished). The resulting mixed-technology or "hybrid" assembly consists of 1406 genomic scaffolds totaling 107.8 Mbp. At least half of the genome is contained in 28 scaffolds each at least 439 kbp in length.

Draft annotation release version 1.0 (28 August 2008) was generated from Assembly v1.0 plus 107998 ESTs derived from 454 or Sanger cDNA reads. Genes were modeled by the JGI Annotation Pipeline, using a variety of cDNA/EST-based, homology-based, and ab initio gene predictors. After filtering for EST and homology support, a total of 17414 genes were structurally and functionally annotated. 76% of the genes have homology support, 42% have Pfam support, and 53% have EST support. At least 15% of genes from other Phytophthora genomes and aligned with this assembly have frameshifts.

CAUTIONARY NOTE: Phytophthora capsici assembly v1.0 is an experimental hybrid assembly of both Sanger and 454 pyrosequencing reads. A high level of polymorphism combined with sequencing errors incurred by the 454 pyrosequencing platform result in an inflated genome assembly error rate, which in turn results in a high rate of frameshifted gene predictions. Additional sequencing and analysis to improve assembly continues at NCGR.

Collaborators

Links

Funding

This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396.