How do plant pathogens adapt to novel host groups? Divergent genome evolution after a host jump in the plant parasitic oomycete Hyaloperonospora crispula and its sister species Hyaloperonospora arabidopsidis.

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Highly specialized plant-biotrophic microbes can infect non-host species at some frequency. Occasionally, this gives rise to adaptation and novel pathogen lineages. In many pathogen groups, including severe crop pathogens, specialization to distant host groups is frequent. Facing host jump-related risks for devastating pandemics we still lack profound knowledge of gateways and borders for host jumps and the following adaptive processes. The oomycete Hyaloperonospora crispula (Hpc) is an ideal candidate to analyze molecular mechanisms of adaptation to distant host groups. It is the only species in the Hyaloperonospora genus that adapted to non-crucifer hosts of the genus Reseda. I hypothesize that after the host jump, Hpc underwent fundamental changes in gene content and gene regulation and that these changes largely reflect adaptive traits towards the novel host group. During the proposed fellowship I aim to identify molecular requirements and consequences of host specificity of Hpc to this novel host group. I will analyze the genome and transcriptome of Hpc in comparison to its crucifer-infecting sister species H. arabidopsidis (Hpa), a well-established model parasite of the model plant Arabidopsis thaliana. Data of 5 distantly related Phytophthora species will serve as an outgroup. The genome of Hpc will be surveyed for gene gain and loss, gene family rise and fall, non-coding genomic features and signatures of selection. Besides the set of conserved virulence-related genes this approach will potentially disclose novel effector classes that represent promising candidate genes of host specialization. To analyze rates of polymorphisms and substitutions I will sample populations of Hpc on Reseda from East England. To further survey host plant-specific gene expression in Hpc, RNAseq will be performed on infected plant material using Illumina HiSeq2000. Finally, I will analyse ~10 host specialization candidate genes for their effect on virulence in A. thaliana versus R. luteola using the bacterial type-three secretion system of Pseudomonas syringae. This includes genes with accelerated evolutionary rates, absence/presence polymorphisms, differential transcription between host plants, and expanded/retracted gene families. In summary, this project aims to understand mechanisms of adaptive evolution that are involved in host specialization of a parasite following a host jump. It studies genomic, transcriptional and molecular features of the obligate biotrophic oomycete Hpc in comparison to its sister species Hpa. It establishes a wild type collection of Hpc populations. Thereby, it highlights fundamental insights into changes of genome structure and gene expression after adaption to a novel host group and could become a key resource for scientists to advance our plant defense strategies in agro-ecosystems. Finally, it will bring new tools and perspectives to the extensive immunity and pathology research taking place on the Hpa-Arabidopsis pathosystem.