Comparative genomics and large-scale transcriptomics of oomycete pathogens

SNIC 2018/3-56


SNAC Medium

Principal Investigator:

Laura Grenville-Briggs Didymus


Sveriges lantbruksuniversitet

Start Date:


End Date:


Primary Classification:

40402: Genetics and Breeding in Agricultural Sciences

Secondary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)

Tertiary Classification:

40101: Agricultural Science



The oomycetes are a lineage of filamentous Eukaryotes that resemble fungi morphologically, but are closely related to the heterokont (brown) algae. Members of this group may be saprotrophic or pathogenic on hosts including plants, algae and animals. The most notorious and well studied, are the plant pathogens of the genus Phytophthora, and include the potato late blight pathogen, Phytophthora infestans. Individual oomycete species occupy a wide range of ecological niches, and display a wide range of parasitic or saprotrophic behaviours; some species have evolved as highly specialised obligate pathogens of single races of a host species, whilst others have developed to attack broad and diverse hosts. The genomes of oomycete plant pathogens display a distinctive architecture with an evolutionary trend towards large, repeat-rich genomes. These genomes harbour large numbers of genes encoding secreted proteins, termed effectors, which function as pathogenicity determinants and modulate the host to promote infection. These effector-encoding genes display a tendency for association with repeat-rich regions and transposable elements in the genome. Despite the concerted genomics effort in the oomycetes, we still know relatively little about how oomycete pathogens and their effectors adapt and specialise on new or diverse hosts. For example, how do broad host range pathogens cope with multiple hosts? How are their genomes shaped by interactions with diverse hosts? In a project funded by the Scilifelab National Biodiversity Program (2014/R2-28) we have sequenced the genomes and transcriptomes of five understudied diverse oomycetes. We are interested in the similarities and differences in genome architecture and in the determinants of host specificity and pathogenicity in oomycetes that infect diverse hosts. Our study systems are: 1) Pythium oligandrum- a broad range mycoparasitic oomycete that infects plant pathogenic oomycetes and fungi. 2) Pythium periplocum- another species from the Pythium genus that acts as a mycoparasite rather than a plant pathogen. This species has a smaller host range and is probably less aggressive than P. oligandrum. 3) Lagenidium giganteum- a species that is parasitizes insects such as mosquitos. One of the few known entomopathogenic oomycetes this species attacks mosquito larvae including those that vector human diseases such as Malaria and Dengu Fever. 4) Phytophthora colocaise- A tropical pathogen that prefers warm climates this species has recently emerged as a serious food security threat as the causal agent of Taro leaf blight in Asia and the Pacific. 5) Phytophthora cactorum- this species has one of the broadest and diverse host ranges of the described oomycetes, being able to infect and kill broad leaved trees such as beech and apple as well as other important horticultural crops such as strawberry (we have sequenced a beech infecting isolate). Our research questions: 1) How are these genomes shaped by their interactions with single or multiple hosts and the environment? 2) What are the genetic and molecular determinants of host specificity and parasitism in these species? 3) What are the similarities and differences between effector genes and genome architecture within the studied species and other sequenced oomycete pathogens?