Second Science Symposium
January 18 - 21, 2005
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.
| Coordinated by:
USDA Forest Service Pacific Southwest Research Station
University of California Integrated Hardwood Range Management Program,
Center for Forestry, Division of Agriculture and Natural Resources, and
California Oak Mortality Task Force
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