Genome sequence of Phytophthora ramorum: implications for management.

Brett Tyler, Sucheta Tripathy, Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University; Nik Grunwald, USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR; Kurt Lamour, University of Tennessee, Knoxville; Kelly Ivors, North Carolina State University; Matteo Garbelotto and Daniel Rokhsar, University of California, Berkeley; Nik Putnam, Igor Grigoriev and Jeffrey Boore, DOE Joint Genome Institute, CA.

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. 624 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/.

A critical need in understanding the epidemiology of P. ramorum is the need to be able to distinguish different genetic individuals of P. ramorum so that patterns of spread can be traced. However, very little genetic variation can be detected in P. ramorum isolates from the US, using conventional techniques such as AFLPs (Ivors KI, Hayden KJ, Bonants PJM, Rizzo DM, Garbelotto M. 2004. AFLP and phylogenetic analyses of North American and European populations of Phytophthora ramorum. Mycological Research 108, 378–392), presumably because most of the population has derived clonally from a single introduction or a small number of introductions of closely related strains. The P. ramorum genome sequence now offers the possibility of examining the genome directly for regions that may be useful in genetically distinguishing closely related strains. Simple Sequence Repeats (SSRs) or microsatellites have been used for genetic typing of an extensive variety of eukaryotic organisms. A total of 1,000 microsatellite loci were observed in the genome of P. ramorum. Dinucleotide repeats were the most abundant microsatellite repeats making up 56% of all repeats followed by trinucleotide repeats at 29%. Single Nucleotide Polymorphisms (SNPs) offer another resource for identifying recent variation, such as gene conversion or mitotic crossing over (Chamnanpunt, J., Shan, W-X and Tyler, B.M. 2001. High frequency mitotic gene conversion in genetic hybrids of the oomycete Phytophthora sojae. Proc. Natl. Acad. Sci. USA 98, 14530-14535). Sequencing of the P. ramorum genome identified approximately 200,000 sites at which the genome sequence of this diploid organism is polymorphic. Screening of these SSR and SNP sites is underway to determine if any of these sites are variable enough to detect recent genetic divergence in the P. ramorum population that could be used to track patterns of spread.

Back to Schedule