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Background  Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from  Hyaloperonospora arabidopsidis . Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors.  Plasmopara halstedii  is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several  Avr -genes and  R -genes have been predicted and unlike  Arabidopsis  downy mildew, large quantities of almost contamination-free material can be obtained easily.    Results  Here a high-quality draft genome of  Plasmopara halstedii  is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among  Phytophthora  species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic.    Conclusions  The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight  Phytophthora  and downy mildew pathogens by targeting core pathogenicity effectors.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1904-7) contains supplementary material, which is available to authorized users.

Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora