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Background   Lepidium sisymbrioides , a polyploid New Zealand endemic, is the sole dioecious species in Brassicaceae and therefore the closest dioecious relative of the model plant  Arabidopsis thaliana.  The attractiveness of developing this system for future studies on the genetics of sex determination prompted us to investigate historical and developmental factors surrounding the evolution of its unisexual flowers. Our goal was to determine the evolutionary pattern of polyploidization of  L. sisymbrioides  and the timing and process of flower reproductive organ abortion. To that end, we used a combination of phylogenetics to place this species within the complex history of polyploidization events in  Lepidium  and histology to compare its floral ontogeny to that of its closest hermaphroditic relatives and to  A. thaliana .    Results  Using a nuclear locus ( PISTILLATA ), we reconstructed the gene tree among  Lepidium  taxa and applied a phylogenetic network analysis to identify ancestral genomes that contributed to the evolution of  L. sisymbrioides . Combining this phylogenetic framework with cytological and genome size data, we estimated  L. sisymbrioides  as an allo-octoploid resulting from three hybridization events. Our investigations of flower development showed that unisexual flowers appear to abort reproductive organs by programmed cell death in female flowers and by developmental arrest in male flowers. This selective abortion occurs at the same floral developmental stage in both males and females, corresponding to  Arabidopsis  stage nine.    Conclusions  Dioecy in Brassicaceae evolved once in  L. sisymbrioides  following several allopolyploidization events, by a process of selective abortion of reproductive organs at intermediate stages of flower development. Different developmental processes, but similar timing of abortions, affect male versus female flower development. An increased understanding of how and when reproductive organs abort in this species, combined with our estimates of ancestral genome contributions, ploidy and genome size, lay the foundation for future efforts to examine the genetic mechanisms involved in the evolution of unisexual flowers in the closest dioecious relative of the best studied model plant.    Electronic supplementary material  The online version of this article (doi:10.1186/2041-9139-5-42) contains supplementary material, which is available to authorized users.

Pattern and process in the evolution of the sole dioecious member of Brassicaceae