The Downy Mildews: So Many Genomes, so Little Time

Downy mildews (DMs) are obligate biotrophic oomycete pathogens that cause diseases on a wide range of plant species. Individual species exhibit a high degree of host specialization.  We have utilized next generation sequencing to efficiently generate de novo genome assemblies of multiple geographically and temporally separated isolates of lettuce DM (Bremia lactucae), spinach DM (Peronospora effusa), chard DM (P. schachtii), tobacco DM (P. tabacina), sorghum and maize DM (Peronosclerospora sorghi), and pearl millet DM (Sclerospora graminicola). The assemblies have been annotated and analyzed for variations in genome size (50 Mb - ~320 Mb), repeat content (15 – 60%), gene content (12K – 20K), and mined for genes encoding candidate effectors and other pathogenicity-related proteins. We have also assembled and studied the structure and variation of their mitochondria. The nuclear genomes were found to differ greatly in size, correlating with amount of repeats predicted, while the mitochondrial genomes were similar in size (40K– 43K) and gene order, comparable to other Oomycetes.  Repertoires of effectors containing the conserved RxLR motif and WY domain were diverse between species and appear to be species specific, with few effectors unique to isolates of the same species. In general, the co-evolutionary dynamics between pathogens and plants have resulted in diverse families of pathogen effectors and plant immune receptors. Understanding the dynamics and evolution of effector repertoires is a prerequisite to the identification and rational deployment of new plant R genes.