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

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.背景：霜霉菌是卵菌中物种多样性最高的类群，可侵染诸多具有重大经济价值的作物。截至目前，仅公开了1个深度测序的霜霉菌基因组，来自拟南芥霜霉菌（Hyaloperonospora arabidopsidis）。若要开展霜霉菌的演化研究——包括对RxLR效应蛋白（RxLR effector protein）等致病效应因子的研究，亟需获取更多的霜霉菌基因组学资源。向日葵霜霉菌（Plasmopara halstedii）是向日葵的毁灭性病原菌，同时也是研究霜霉菌的潜在寄主-病原菌互作模式系统：目前已预测出多个无毒基因（Avr-genes）与抗病基因（R-genes），且与拟南芥霜霉菌不同，该菌可轻松获取大量近乎无杂质的实验材料。结果：本研究报道并多维度解析了向日葵霜霉菌的高质量基因组草图，涵盖基因组组织结构、次级代谢、效应蛋白分析，以及与其他已测序卵菌的比较基因组学（comparative genomics）研究。有趣的是，本次分析揭示了RxLR基序（RxLR motif）的额外变异，提示dEER基序（dEER motif）的保守性具备重要功能意义。直系同源分析（orthology analysis）显示，疫霉属（Phytophthora）物种间共保守28个类RxLR核心效应因子。两个已测序的霜霉菌仅共享6个推定的类RxLR效应因子，这凸显了三大霜霉菌演化支中两个分支的快速且基本独立的演化历程。系统基因组学（phylogenomic）分析结果似乎也佐证了这一点：霜霉菌并非单系类群。结论：该基因组学资源将有助于开发用于监测该病原菌种群的分子标记，同时可为通过靶向核心致病效应因子防控疫霉及霜霉菌病害的全新策略提供理论依据。