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

Abstract

BackgroundDowny 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.ResultsHere 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.ConclusionsThe 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 materialThe online version of this article (doi:10.1186/s12864-015-1904-7) contains supplementary material, which is available to authorized users.

Genome sequence of Plasmopara viticola and insight into the pathogenic mechanism

“…When considered together, these findings strongly suggest that P. viticola and H. arabidopsidis evolved biotrophy independently and P. viticola could be at a less advanced stage of evolution to biotrophy in comparison with H. arabidopsidis and A. laibachii . Phylogenomic analysis of P. halstedii also supports the independent evolution of two in the three major downy mildew lineages because downy mildews do not appear to be monophyletic19.…”

RXLR and CRN Effectors from the Sunflower Downy Mildew Pathogen Plasmopara halstedii Induce Hypersensitive-Like Responses in Resistant Sunflower Lines

“…The five putative RXLR proteins showed a predicted signal peptide of 17–23 amino acids (SignalP4.1) and putative translocation patterns described in RXLR effectors ( Table 1 ). Two of them, PhRXLR08 and PhRXLR31 have only a DEER domain but were predicted as RXLR effectors in the P. halstedii strain recently sequenced (Sharma et al, 2015; Table 1 ). The three others had either exact or very close RXLR-EER motifs (RMLQ-EDR for PhRXLR14) ( Table 1 ).…”

“…This perception mechanism is based on plant resistance (R) proteins that confer indirect or direct recognition of specific pathogen avirulence (Avr) proteins. In the sunflower – P. halstedii interaction, no such gene-for-gene interaction has been described yet, probably because of the difficulty in studying this pathosystem (Gascuel et al, 2015), and the recent availability of molecular data for the two partners (As-sadi et al, 2011; Sharma et al, 2015; Gascuel et al, 2016 3 ; Mestre et al, 2016). Complexity and size of the sunflower genome, together with lack of reverse genetics techniques in both partners have hampered validation of candidate genes involved in resistance.…”

“…Following infection of sunflower, P. halstedii shows intercellular growth and produces haustoria in root, hypocotyl and cotyledon cells (Gascuel et al, 2015). Putative cytoplasmic effectors of RXLR and CRN-type expressed during the interaction were described from transcriptomic and genomic studies (As-sadi et al, 2011; Sharma et al, 2015; Gascuel et al, 2016; Mestre et al, 2016). However, no functional data has been published on P. halstedii effector expression in planta .…”

Avaliação de uma região <i>hotspot</i> do gene citocromo b para resistência aos fungicidas inibidores da quinona oxidase (QoI) em patógenos de uva Niágara Rosada

“…Depois de um tempo as manchas podem necrosar e levar à queda das folhas que foram severamente atacadas (HENNING et al, 1997 SHARMA et al, 2015).…”