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. 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. 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.

Sesquiterpene lactones are characteristic metabolites of Asteraceae (or Compositae) which often display potent bioactivities and are sequestered in specialized organs such as laticifers, resin ducts, and trichomes. For characterization of sunflower sesquiterpene synthases we employed a simple method to isolate pure trichomes from anther appendages which facilitated the identification of these genes and investigation of their enzymatic functions and expression patterns during trichome development.

The secretion of sesquiterpene lactones (STL) in capitate glandular trichomes from the anther appendages of Helianthus annuus L. (Asteraceae) was observed by light and fluorescence microscopy and HPLC analysis. Disk flowers within the sunflower capitulum showed the known ontogenetic progression from the centre to the margin. During development of the florets, the trichomes in the anther appendages secreted their metabolites into the subcuticular secretion storage space in front of the two apical cells. All stages of forming the cuticular globe, from the pre‐secretory to the post‐secretory phase, could be observed microscopically and secretory activity was simultaneously monitored. Six germacrolides and heliangolides of known structure were selected for quantitative analysis. The increase in STL content during extension of the subcuticular space was monitored by HPLC analysis. Thereby, the start and termination of STL biosynthesis was defined in relation to other developmental stages of floret ontogenesis, particularly, the pollen formation. Part of the secreted material showed autofluorescence which could be attributed to a hydroxy‐trimethoxy‐flavone, as determined by NMR and mass spectroscopy. The anther trichomes were cytologically and chemically similar to foliar glandular trichomes of sunflower and represent the multicellular capitate glandular trichome type common to many Asteraceae. The ease with which anther trichomes of H. annuus can be harvested and analyzed suggests that they can provide a valuable model system for investigation of STL and flavonoid metabolism in Asteraceae.

Plant biotrophic oomycetes cause significant production problems and economic losses in modern agriculture and are controlled by fungicide applications and resistance breeding. However, high genetic variability and fast adaptation of the pathogens counteract these measures. As a consequence of the “arms race,” new pathogen phenotypes recurrently occur and may rapidly dominate the population when selected through the pressure of control measures. Intensive monitoring with fast and reliable identification of virulence phenotypes is essential to avoid epidemics and the economic consequences in agriculture. For some of the most important downy mildews and white blister rusts, bioassay-based differentiation has been established to classify infectivity of field isolates or cultivated strains on hosts of defined resistance. However, the testing is laborious, time-consuming, logistically demanding, and prone to impreciseness. Alternatively, host independent classification could overcome these problems and enable fast assessment of the infection risk when monitoring the local pathogen population. The prerequisite would be the identification of pathogen characters correlating with the infection behavior. This review examines the current situation of bioassay-based pathotyping in six of the most important biotrophic oomycetes (Plasmopara viticola, Plasmopara halstedii, Pseudoperonospora cubensis, Peronospora tabacina, Bremia lactucae, and Albugo candida) and gives an overview on attempts and progress to identify genetic markers of the pathogens that correlate with their infection behavior.

Peronospora tabacina is an obligate biotrophic oomycete that causes blue mold or downy mildew on tobacco (Nicotiana tabacum). It is an economically important disease occurring frequently in tobacco-growing regions worldwide. We sequenced and characterized the genomes of two P. tabacina isolates and mined them for pathogenicity-related proteins and effector-encoding genes. De novo assembly of the genomes using Illumina reads resulted in 4,016 (63.1 Mb, N₅₀ = 79 kb) and 3,245 (55.3 Mb, N₅₀ = 61 kb) scaffolds for isolates 968-J2 and 968-S26, respectively, with an estimated genome size of 68 Mb. The mitochondrial genome has a similar size (approximately 43 kb) and structure to those of other oomycetes, plus several minor unique features. Repetitive elements, primarily retrotransposons, make up approximately 24% of the nuclear genome. Approximately 18,000 protein-coding gene models were predicted. Mining the secretome revealed approximately 120 candidate RxLR, six CRN (candidate effectors that elicit crinkling and necrosis), and 61 WY domain–containing proteins. Candidate RxLR effectors were shown to be predominantly undergoing diversifying selection, with approximately 57% located in variable gene-sparse regions of the genome. Aligning the P. tabacina genome to Hyaloperonospora arabidopsidis and Phytophthora spp. revealed a high level of synteny. Blocks of synteny show gene inversions and instances of expansion in intergenic regions. Extensive rearrangements of the gene-rich genomic regions do not appear to have occurred during the evolution of these highly variable pathogens. These assemblies provide the basis for studies of virulence in this and other downy mildew pathogens.