Status

The genome assembly version 1.0 of the P. sojae genome, was generated using the whole genome shotgun strategy. This assembly release was annotated using the JGI automated annotation pipeline. Gene models and associated transcripts/proteins are predicted or mapped using a variety of tools based on cDNA, protein homology and ab initio methods. Conservation between the genomic sequences of P. sojae and P. ramorum provided additional support for the predicted gene models. Gene functions have been automatically assigned based on homology to known genes.

The annotation v1.1 Filtered Models includes a total of 19,027 gene models. Further analysis and community-wide manual curation of predicted genes continues. A snapshot of improved annotations will be published on this site and submitted to GenBank by the end of 2006.

Assembly

v1.0 (April 2004): This assembly of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 9X. After trimming for vector and quality, over 1 Million reads assembled into 1810 scaffolds totaling over 86 Mbp. Roughly half of the genome is contained in 54 scaffolds all at least 463 Kb in length. The estimated genome size is 95 Mbp.

Collaborator

Brett Tyler
Virginia Bioinformatics Institute
Virginia Polytechnic and State University
1880 Pratt Dr., Bldg. XV
Blacksburg, VA 24061-0447
Tel. (540) 231-7318
Fax: (540) 231-2606

References

• Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
  Brett M. Tyler, Sucheta Tripathy, Xuemin Zhang, Paramvir Dehal, Rays H. Y. Jiang, Andrea Aerts, Felipe D. Arredondo, Laura Baxter, Douda Bensasson, Jim L. Beynon, Jarrod Chapman, Cynthia M. B. Damasceno, Anne E. Dorrance, Daolong Dou, Allan W. Dickerman, Inna L. Dubchak, Matteo Garbelotto, Mark Gijzen, Stuart G. Gordon, Francine Govers, Niklaus J. Grunwald, Wayne Huang, Kelly L. Ivors, Richard W. Jones, Sophien Kamoun, Konstantinos Krampis, Kurt H. Lamour, Mi-Kyung Lee, W. Hayes McDonald, Mónica Medina, Harold J. G. Meijer, Eric K. Nordberg, Donald J. Maclean, Manuel D. Ospina-Giraldo, Paul F. Morris, Vipaporn Phuntumart, Nicholas H. Putnam, Sam Rash, Jocelyn K. C. Rose, Yasuko Sakihama, Asaf A. Salamov, Alon Savidor, Chantel F. Scheuring, Brian M. Smith, Bruno W. S. Sobral, Astrid Terry, Trudy A. Torto-Alalibo, Joe Win, Zhanyou Xu, Hongbin Zhang, Igor V. Grigoriev, Daniel S. Rokhsar, and Jeffrey L. Boore (1 September 2006)
  Science 313 (5791), 1261. [DOI: 10.1126/science.1128796]

Funding

This project is the result of coordinated funding from three different agencies. A grant of $2,350,000 was made by the joint Microbial Program of the National Science Foundation and the US Department of Agriculture. An in-kind contribution of a similar amount was made by the US Department of Energy. NSF is also providing funds for follow-on functional genomics studies and for a Research Coordination Network.