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Phytophthora molecular genetics, epidemiology & management
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Information on determination of clonal lineages (based on multilocus microsattelite data) in recent new finds of Phytophthora ramorum in the US
We currently monitor the migration, population structure and evolution of Phytophthora ramorum in North America using microsatellites and several nuclear and mitochondrial sequence loci. Here we provide timely, preliminary data on new finds of P. ramorum in nursery environments based on multilocus microsatellite data.
View genotype data:
Microsatellites loci in Phytophthora ramorum and P. sojae
The first whole genome assembly of the two oomycete plant pathogens Phytophthora sojae (95 Mb) and P. ramorum (65 Mb) were examined to determine types, abundance and distribution of different simple sequence repeats (SSRs) ranging between 2 to 6 bp in motif length. We found 2,128 and 1,000 SSRs in P. sojae and P. ramorum, respectively. In general, the density of SSRs (bp per Mb) in P. sojae is about 1.5 times that of P. ramorum. Whereas AC dinucleotide repeats appear at a higher density in P. ramorum, AG and AT repeats appear at a higher density in P. sojae. Interestingly, density of most trinucleotide repeats was higher in Ps than in Pr. Although P. sojae has a larger genome, the percentage of SSR loci located in coding regions is higher at 17.4% compared to P. ramorum at 14.8%. Compared to other species, including Saccharomyces cerevisiae, repeats of length 4, 5, and 6 bp are considerably underrepresented in both Phytophthora genomes based on density. Whereas in most genomes studied to date dinucleotide repeat stretches tended to be longer than other repeats, in the case of Phytophthora only tetranucleotide repeats were occasionally considerably longer (ACAG, ACAT, and AGAT). As expected frequency of trinucleotide repeats in exons was considerably higher when compared to di, tetra- or pentanucleotide repeats.
View (or download) SSR data:
APS Workshop: Analysis of Microbial Population Genetic Data
Niklaus Grunwald, & Ignazio Carbone
Analysis of population genetic data remains challenging. This workshop will focus on the kinds of analyses typically done by plant pathologists and microbiologists. It will cover analyses of data from haploid and diploid populations with dominant or codominant marker systems applicable to a range of molecular genotyping techniques (including isozymes, AFLP, RFLP, RAPD, microsatellites and SNPs). The workshop will include estimation of allele frequencies, inferences about Hardy-Weinberg and linkage disequilibrium, characterization of population structure, and estimation of population parameters such as mutation, recombination, and gene flow. More recent techniques in population genetic data analysis and parameter estimation, including coalescence, gene genealogies, and Bayesian analysis are introduced. Participants will receive information to gain hands-on experience with various software packages for population genetic data using datasets provided by the instructors. Workshop enrollment is limited to 40 participants.
Annual Meeting, American Phytopathological Society, Wednesday, August 3, 1:00 – 5:00 p.m., Austin, Texas.
Horticultural
Crops Research Laboratory, USDA ARS
3420 NW Orchard Ave., Corvallis, OR 97330
Voice: (541) 738-4049 • Fax: (541) 738-4025 •
E-mail: grunwaln
<at> science.oregonstate.edu
Last Updated:June 26, 2007