Status

The genome assembly version 1.0 of the P. ramorum 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 15,743 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 7X. After trimming for vector and quality, over 1 Million reads assembled into 2576 scaffolds totaling 66.6 Mbp. Roughly half of the genome is contained in 63 scaffolds all at least 308 Kb in length. The estimated genome size is 65 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

Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak IL, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL. (2006) Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis. Science. 313, 1261-1266.

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.