Comparative Genomics of Downy Mildews (and Rusts)

Downy mildews are oomycete pathogens that cause diseases on a wide range of plant species. Individual species have narrow host ranges and exhibit high degrees of host specialization. Their obligate biotrophic nature makes their study challenging compared to culturable oomycetes, such as Phytophthora spp. and Pythium spp. Next generation sequencing technologies offer unprecedented opportunities for comparative genome-wide analyses of large numbers of isolates rapidly and at low cost. We are utilizing these new technologies to efficiently generate genome assemblies and to study the evolutionary relationships and the effector repertoires within and between diverse species of downy mildew. These include geographically and temporally separated isolates of lettuce downy mildew (Bremia lactucae), tobacco downy mildew (Peronospora tabacina), sorghum and maize downy mildew (Peronosclerospora sorghi), and pearl millet downy mildew (Sclerospora graminicola). We have assembled and annotated these genomes and examined variations in genome size, repeat content, gene content, level of heterozygosity, and the repertoires of genes encoding effectors and other pathogenicity-related proteins, as well as their mitochondrial structure and variation. These downy mildew species differ greatly in genome size and possess varying levels of heterozygosity, indicative of inbreeding, clonal, and outbreeding mating systems. Effector repertoires are diverse between isolates of the same species and between species; many effector-encoding genes appear to be species specific. Our workflow for comparative population genomics and genome analysis are also applicable to rust pathogens.