Comparative genomics of downy mildews reveals potential adaptations to biotrophy

Kyle Fletcher, Steven J. Klosterman, Lida Derevnina, Frank Martin, Lien D. Bertier, Steven Koike, Sebastian Reyes-Chin-Wo, Beiquan Mou, Richard W Michelmore

Research output: Contribution to journalArticle

12 Scopus citations

Abstract

Background: 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. P. effusa is highly variable and 15 new races have been recognized in the past 30 years. Results: We 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. Conclusions: We 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.

Original languageEnglish (US)
Article number5214
JournalBMC Genomics
Volume19
Issue number1
DOIs
StatePublished - Nov 29 2018

Keywords

  • Biotrophy
  • Gene loss
  • Genomics
  • Oomycete
  • Peronospora effusa
  • Peronospora farinosa
  • Peronospora lineage
  • Spinach downy mildew

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

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    Fletcher, K., Klosterman, S. J., Derevnina, L., Martin, F., Bertier, L. D., Koike, S., Reyes-Chin-Wo, S., Mou, B., & Michelmore, R. W. (2018). Comparative genomics of downy mildews reveals potential adaptations to biotrophy. BMC Genomics, 19(1), [5214]. https://doi.org/10.1186/s12864-018-5214-8