Comparative genomics of Peronospora belbahrii and other oomycetes. Peronospora belbahrii genome analyses

bligate biotrophic downy mildews constitute the most species-rich group of the oomycetes, fungal like organisms related to brown algae and diatoms. Despite their economic importance, only few genomes of this group of pathogens been sequenced. In the current study, we sequenced the whole genome of the economically important basil pathogen Peronospora belbahrii and performed in-depth comparative genomics and phylogenomics for investigating downy mildew and Phytophthora evolution using 25 published oomycete genomes in our analyses. The genome assembly was of 35.39 Mbp distributed over 2780 scaffolds, with an N50 scaffold length of 246.53 kbp, an N50 count was 47, with the largest scaffold length being of 1.23 Mbp. The high degree of heterozygosity observed suggests that Pe. belbahrii is a frequently outcrossing species. Its gene content resembles that of other obligate biotrophic downy mildews, in line with a common evolutionary root and similar ecological niches, but with an amount of classical RxLR pathogenicity effectors significantly lower than in other downy mildews and Phytophthora species. Our phylogenetic analysis revealed downy mildews as monophyletic, within the paraphyletic genus of Phytophthora, consistent with the topology of a recent multigene phylogenetic reconstruction.