Comparative Genomics of Downy Mildews

Downy mildews (DMs) are oomycete pathogens that cause disease on a wide range of crop plants. Individual species have narrow host ranges and exhibit high degrees of host specialization. We utilized high throughput sequencing to generate de novo genome assemblies of geographically and temporally separated isolates of Bremia lactucae (lettuce DM), Peronospora effusa (spinach DM), P. schachtii (chard DM), P. tabacina (tobacco DM), Peronosclerospora sorghi (sorghum and maize DM), and Sclerospora graminicola (pearl millet DM) in collaboration with experts for each of these pathogens. These genome assemblies were highly syntenic but varied greatly in size (50 - ~320 Mb), gene content (12 – 20 K), repeat content (15 – ~60%), and repertoire of genes encoding effectors and other pathogenicity-related proteins. No families of RXLR-containing effectors are common across all DMs; however, RXLR families overlap greatly between isolates within a species. DM is the most important disease of lettuce in California and worldwide; B. lactucae is highly variable and can rapidly change to overcome resistant cultivars. We have monitored changes in virulence phenotype of B. lactucae in California since 1982. The appearance of the B₁ mating type may explain the recent increase in novel virulence phenotypes and may require a change in strategy for resistance gene deployment. Genomic sequence analysis of representative isolates collected in California and Europe over three decades provides detailed information of variation of B. lactucae.