Comparative genomics to assess myco-parasitism and pathogenicity in oomycetes with potential as biocontrol agents

Ramesh Vetukuri 1 Diya Sen 1 Sandeep Kushwaha 2 Laura Grenville-Briggs 1
1Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
2Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden

The oomycetes are a lineage of filamentous Eukaryotes most closely related to the heterokont (brown) algae. Many oomycetes are plant pathogens, however, some Pythium species are parasitic to fungi and other oomycetes (Pythium oligandrum and Pythium periplocum) whilst others such as Lagenidium giganteum are parasites of insects including mosquitos that vector Zika virus and Dengu fever. These three species have great potential as biocontrol agents. Molecular, genetic and genomic data from these species provides new insights into pathogenicity and the fundamental biology of oomycetes with diverse lifestyles beyond the well-studied plant pathogens. We have carried out de novo genome sequencing and genome-wide transcriptomics (RNA-seq) of these three understudied oomycetes, using both paired end and mate pair Illumina Hiseq sequencing. We are currently investigating the genetic and molecular determinants of host specificity using this data. Crinkler (CRN), and elicitin effector proteins are present in the predicted secretomes of all three oomycetes. Novel effector families are also present in the mosquito pathogen. RNA-seq data from P. oligandrum colonising the potato late blight oomycete Phytophthora infestans reveals that secondary metabolite biosynthesis is important for mycoparasitism. This is the first time secondary metabolites have been shown to play a role in oomycete pathogenicity. Novel transcripts, including putative R-genes from P. infestans reveal how this oomycete defends itself against mycoparasitic attack, and may provide vital clues for the sustainable control of potato late blight in the future. Traits important for successful mycoparasitism are being revealed by comparative analyses of the hyper-aggressive mycoparasite P. oligandrum versus the weaker mycoparasite P. periplocum. Our latest comparative genomics and transcriptomics data including the identification of novel effector gene families will be discussed. These data will pave the way for a better understanding of pathogenicity in diverse hosts and facilitate the development of new biological control agents.