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Background  Microsatellites or single sequence repeats (SSRs) are a powerful choice of marker in the study of  Phytophthora  population biology, epidemiology, ecology, genetics and evolution. A strategy was tested in which the publicly available unigene datasets extracted from genome sequences of  P. infestans ,  P. sojae  and  P. ramorum  were mined for candidate SSR markers that could be applied to a wide range of  Phytophthora  species.    Results  A first approach, aimed at the identification of polymorphic SSR loci common to many  Phytophthora  species, yielded 171 reliable sequences containing 211 SSRs. Microsatellites were identified from 16 target species representing the breadth of diversity across the genus. Repeat number ranged from 3 to 16 with most having seven repeats or less and four being the most commonly found. Trinucleotide repeats such as (AAG)n, (AGG)n and (AGC)n were the most common followed by pentanucleotide, tetranucleotide and dinucleotide repeats. A second approach was aimed at the identification of useful loci common to a restricted number of species more closely related to  P. sojae  ( P. alni, P. cambivora, P. europaea  and  P. fragariae ). This analysis yielded 10 trinucleotide and 2 tetranucleotide SSRs which were repeated 4, 5 or 6 times.    Conclusion  Key studies on inter- and intra-specific variation of selected microsatellites remain. Despite the screening of conserved gene coding regions, the sequence diversity between species was high and the identification of useful SSR loci applicable to anything other than the most closely related pairs of  Phytophthora  species was challenging. That said, many novel SSR loci for species other than the three 'source species' ( P. infestans ,  P. sojae  and  P. ramorum ) are reported, offering great potential for the investigation of  Phytophthora  populations. In addition to the presence of microsatellites, many of the amplified regions may represent useful molecular marker regions for other studies as they are highly variable and easily amplifiable from different  Phytophthora  species.

Use of genome sequence data in the design and testing of SSR markers for Phytophthora species