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Background  Members of the genus  Phytophthora  are notorious pathogens with world-wide distribution. The most devastating species include  P. infestans, P. ramorum  and  P. sojae . In order to develop molecular methods for routinely characterizing their populations and to gain a better insight into the organization and evolution of their genomes, we used an  in silico  approach to survey and compare simple sequence repeats (SSRs) in transcript sequences from these three species. We compared the occurrence, relative abundance, relative density and cross-species transferability of the SSRs in these oomycetes.    Results  The number of SSRs in oomycetes transcribed sequences is low and long SSRs are rare. The  in silico  transferability of SSRs among the  Phytophthora  species was analyzed for all sets generated, and primers were selected on the basis of similarity as possible candidates for transferability to other  Phytophthora  species. Sequences encoding putative pathogenicity factors from all three  Phytophthora  species were also surveyed for presence of SSRs. However, no correlation between gene function and SSR abundance was observed. The SSR survey results, and the primer pairs designed for all SSRs from the three species, were deposited in a public database.    Conclusion  In all cases the most common SSRs were trinucleotide repeat units with low repeat numbers. A proportion (7.5%) of primers could be transferred with 90% similarity between at least two species of  Phytophthora . This information represents a valuable source of molecular markers for use in population genetics, genetic mapping and strain fingerprinting studies of oomycetes, and illustrates how genomic databases can be exploited to generate data-mining filters for SSRs before experimental validation.

bmc genomics

Survey and analysis of microsatellites from transcript sequences in Phytophthora species: frequency, distribution, and potential as markers for the genus