Pacific Southwest

Title: Genome sequence of Phytophthora ramorum: implications for management

Author: Tyler, Brett; Tripathy, Sucheta; Grunwald, Nik; Lamour, Kurt; Ivors, Kelly; Garbelotto, Matteo; Rokhsar, Daniel; Putnam, Nik; Grigoriev, Igor; Boore, Jeffrey

Date: 2006

Source: In: Frankel, Susan J.; Shea, Patrick J.; and Haverty, Michael I., tech. coords. Proceedings of the sudden oak death second science symposium: the state of our knowledge. Gen. Tech. Rep. PSW-GTR-196. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture: 157-158

Station ID: GTR-PSW-196

Description: A draft genome sequence has been determined for Phytophthora ramorum, together with a draft sequence of the soybean pathogen Phytophthora sojae. The P. ramorum genome was sequenced to a depth of 7-fold coverage, while the P. sojae genome was sequenced to a depth of 9-fold coverage. The genome size of P. ramorum was estimated to be significantly smaller than that of P. sojae, 65 Mb compared to 95 Mb, with the difference lying primarily in the amount of repetitive sequences in the P. sojae genome. Computer predictions estimate the number of genes in P. ramorum to be 15,743, while 19,027 are predicted for P. sojae. Most of the differences in gene number result from larger multigene families in P. sojae. Six hundred twenty four genes were predicted to be unique to P. ramorum, while 1755 were predicted to be unique to P. sojae. The generally high level of similarity of most P. ramorum and P. sojae genes predicts that, in general, chemical treatments developed for other Phytophthora species should also be effective against P. ramorum. The small size of the P. ramorum genome and lack of extensive numbers of duplicated chromosomal segments effectively eliminates the hypothesis that P. ramorum is a recent hybrid between two other Phytophthora species. The two Phytophthora genome sequences are available at http://genome.jgi-psf.org/ and http://phytophthora.vbi.vt.edu.

Keywords: DNA sequence, Phytophthora ramorum

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Citation

Tyler, Brett; Tripathy, Sucheta; Grunwald, Nik; Lamour, Kurt; Ivors, Kelly; Garbelotto, Matteo; Rokhsar, Daniel; Putnam, Nik; Grigoriev, Igor; Boore, Jeffrey  2006.  Genome sequence of Phytophthora ramorum: implications for management.   In: Frankel, Susan J.; Shea, Patrick J.; and Haverty, Michael I., tech. coords. Proceedings of the sudden oak death second science symposium: the state of our knowledge. Gen. Tech. Rep. PSW-GTR-196. Albany, CA: Pacific Southwest Research Station, Forest Service, U.S. Department of Agriculture: 157-158.