PhD position available, deadline Oct 31

Microbial eukaryote parasites are very diverse and widespread across the eukaryotic tree of life, but our understanding of these important organisms is mostly based on a relatively small number of species in pathogenous groups (such as Apicomplexa or Microsporidia). Other groups, composed partly or exclusively of parasites, have thus far eluded in depth investigation. Ascetosporea is one such group of poorly characterized parasites belonging to Rhizaria, itself the least studied of the major divisions of eukaryotes. The lineage diversity and host range of ascetosporean parasites have been recently found to be much larger than anticipated, among which are important pathogens of molluscs costing millions of dollars to the aquaculture industry. In spite of this, our genomic understanding of the evolution of Ascetosporea is extremely limited, and no genomes are currently available.

This project aims to de novo sequence, assemble, and annotate several genomes of Ascetosporea and related organisms. Material will be provided by collaborators (mainly in the UK) and sequence in-house. This newly generated data will then be used to establish an evolutionary framework for Ascetosporea using a combination of phylogenetics and genomic analyses. Based on the outcome of this first part, we will broadly look at the evolution of parasitism in Ascetosporea, i.e. identify pre-parasitic conditions, ancestral parasitic innovations, and lineage-specific adaptations using comparative genomics. This project will shed light on a large group of parasites for which we lack even the most fundamental knowledge about their biology. As part of a more general aim to sequence uncultured micro-eukaryotes, the student will also be involved in developing single-cell genome sequencing approaches.

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