| Summary: | <p>Abstract</p> <p>Background</p> <p>The moss <it>Physcomitrella patens </it>is an emerging model in comparative plant science. At present, the <it>Physcomitrella </it>genome is sequenced at the Joint Genome Institute (USA). In this study we present our results on the development of expressed sequence tag-derived microsatellite markers for <it>Physcomitrella patens</it>, their classification and applicability as genetic markers on the intra- as well as on the interspecies level. We experienced severe restrictions to compare our results on <it>Physcomitrella </it>with earlier studies for other plant species due to varying microsatellite search criteria and a limited selection of analysed species. As a consequence, we performed a side by side analysis of expressed sequence tag-derived microsatellites among 24 plant species covering a broad phylogenetic range and present our results on the observed frequencies.</p> <p>Results</p> <p>We identified 3,723 microsatellites using the software MISA in a non-redundant <it>Physcomitrella </it>expressed sequence tag database comprising more than 37 megabases of nucleotide information. For 2,951 microsatellites appendant primer sequences have been derived. PCR of 376 microsatellites yielded 88 % successful amplicons and over 30 % polymorphisms between two <it>Physcomitrella </it>accessions. The polymorphism information content of 64 microsatellites based on 21 different <it>Physcomitrella </it>accessions was comparably high with a mean of 0.47 +/- 0.17. Of the 64 <it>Physcomitrella </it>microsatellite markers, 34 % respectively 79.7 % revealed cross-species applicability in two closely related moss species.</p> <p>In our survey of two green algae, two mosses, a fern, a fern palm, the ginkgo tree, two conifers, ten dicots and five monocots we detected an up to sevenfold variation in the overall frequency with a minimum of 37 up to maximal 258 microsatellites per megabase and a high variability among the different microsatellite class and motif frequencies. Numerous species-specific microsatellite frequencies became evident and several deviations to earlier reports were ascertained.</p> <p>Conclusion</p> <p>With the <it>Physcomitrella </it>microsatellite marker set a valuable tool has been made available for further genetic and genomic applications on the intra- as well as on the interspecies level. The comparative survey of expressed sequence tag-derived microsatellites among the plant kingdom is well suited for a classification of future studies on plant microsatellites.</p>
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