Abstract
BackgroundSpinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. P. effusa is highly variable and 15 new races have been recognized in the past 30 years.ResultsWe virulence phenotyped, sequenced, and assembled two isolates of P. effusa from the Salinas Valley, California, U.S.A. that were identified as race 13 and 14. These assemblies are high quality in comparison to assemblies of other downy mildews having low total scaffold count (784 & 880), high contig N50s (48 kb & 52 kb), high BUSCO completion and low BUSCO duplication scores and share many syntenic blocks with Phytophthora species. Comparative analysis of four downy mildew and three Phytophthora species revealed parallel absences of genes encoding conserved domains linked to transporters, pathogenesis, and carbohydrate activity in the biotrophic species. Downy mildews surveyed that have lost the ability to produce zoospores have a common loss of flagella/motor and calcium domain encoding genes. Our phylogenomic data support multiple origins of downy mildews from hemibiotrophic progenitors and suggest that common gene losses in these downy mildews may be of genes involved in the necrotrophic stages of Phytophthora spp.ConclusionsWe present a high-quality draft genome of Peronospora effusa that will serve as a reference for Peronospora spp. We identified several Pfam domains as under-represented in the downy mildews consistent with the loss of zoosporegenesis and necrotrophy. Phylogenomics provides further support for a polyphyletic origin of downy mildews.
Highlights
Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen
Two isolates of P. effusa were collected from commercial spinach production fields in Monterey County, California in 2012 and 2013 and their virulence phenotypes tested by inoculations onto the standard differential set of resistant spinach cultivars to provide race designations as previously described [8]
Cultivars Avenger, Lion (Solomon), and Pigeon were resistant to the 2012 isolate indicating that it was race (R13), while cultivars Califlay, Whale, and Lion were resistant to the 2013 isolate indicating that it was race (R14)
Summary
Spinach downy mildew caused by the oomycete Peronospora effusa is a significant burden on the expanding spinach production industry, especially for organic farms where synthetic fungicides cannot be deployed to control the pathogen. Downy mildew diseases are caused by species of several genera of obligate biotrophic oomycetes and impact production of crops and ornamental plants worldwide [1]. Like other pathogens in this genus, P. effusa has a narrow host range, only infecting spinach (Spinacia oleracea) [6, 7]. This pathogen has occasionally been incorrectly grouped with other Peronospora spp., such as Peronospora schachtii (causal agent of chard downy mildew) under the umbrella Peronospora farinosa [5, 6, 8,9,10], despite molecular data for distinct species [11, 12]. Botrytis farinosa) was recently proposed, in part because P. farinosa could not be associated with a type specimen [13]
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