University of Oxford – Protist Group

Oxford

Who we are:

The protist research team at the University of Oxford studies the diversity and evolutionary history of microbial eukaryotes. Our work in this area focuses on understanding gene flow and genome evolution across the tree of life, from the last eukaryotic common ancestor (LECA) through to the vast diversity of microbial forms that occupy the environments of Earth today. As part of this work, we also study the ecology of protists (microbial eukaryotes) in freshwater and marine environments, with an emphasis on host-parasite interactions.

What we’re doing in the Darwin Tree of Life Project:

Our role within the Darwin Tree of Life project is focused on some of the smallest eukaryotic forms of life, the protists. At the beginning, we are gathering together protist cultures that were sampled in the UK and are maintained in culture collections. We are preparing these for genome sequencing at the Sanger Institute. To do this we barcode sequence the samples to identify the taxonomy of the microbes and then we estimate the genome size to provide an approximation of the DNA sequencing depth required. During this phase, we work closely with our culture collection partners: The Culture Collection of Algae and Protozoa (CCAP; Scotland) and the Centre of Agriculture and Bioscience International (CABI; England).

Afterwards, we are aiming to tackle the challenge of sequencing the genomes of single cell protists sampled directly from aquatic environments. Most of the diversity of the eukaryotic tree of life consists of microbial protists that are yet to be sampled, and growing these in a laboratory can be very difficult. Our aim is therefore to develop approaches to sequence them directly from individual cells we can capture from lakes, rivers, ponds and the seas of the UK. Genomic information on many aquatic protists is scarce, so one of the major goals of our part of the Darwin Tree of Life project is to fill in this gap. During this endeavour we also work closely with the our Genome Acquisition Laboratory partner, The Earlham Institute.

Why we’re invested in the Darwin Tree of Life Project:

The Darwin Tree of Life initiative is a golden opportunity to acquire a myriad of genome sequence data, helping to resolve important questions on protist evolution and co-evolution. Such topics include, for example: the acquisition of different feeding strategies, host-pathogen interactions, parasite defence strategies, and many more. In addition, the dataset will provide information on the phylogenetic position on the tree of life of numerous protist groups which, in many cases, is a mystery. We will also, in the initial phase, focus on relevant protist species that produce toxic tides and so cause poisoning of seafood, leading to huge financial losses each year in aquaculture and tourism. For all these reasons we, and our partners, are fully dedicated to the Darwin Tree of Life project.

Our common goal is to: develop a high-throughput end-to-end pipeline to enable the generation of high-quality annotated genomes from single-celled eukaryotic protists.