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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. THIS POSITION HAS NOW BEEN FILLED This position is available to work with me on protist phylogenomics, in the Systematic Biology Department at Uppsala University (Sweden). More info here.
THIS POSITION HAS NOW BEEN FILLED Assembling the global eukaryotic tree of life has long been a major effort of Biology. In recent years, pushed by the new availability of genome-scale data for microbial eukaryotes, it has become possible to revisit many evolution- ary enigmas. However, some of the most ancient nodes, which are essential for inferring a stable tree, have remained highly controversial. Among other reasons, the lack of adequate genomic datasets for key taxa has prevented the robust reconstruction of early diversification events. In this context, the cen- trohelid heliozoans are particularly relevant for reconstructing the tree of eukaryotes because they represent one of the last substantial groups that was missing large and diverse genomic data. Here, we filled this gap by sequencing high-quality transcriptomes for four centrohelid lineages, each correspond- ing to a different family. Combining these new data with a broad eukaryotic sampling, we produced a gene-rich taxon-rich phylogenomic dataset that enabled us to refine the structure of the tree. Specifically, we show that (i) cen- trohelids relate to haptophytes, confirming Haptista; (ii) Haptista relates to SAR; (iii) Cryptista share strong affinity with Archaeplastida; and (iv) Haptista þ SAR is sister to Cryptista þ Archaeplastida. The implications of this topology are discussed in the broader context of plastid evolution.  A great pop ScienceNews article by Susan Milius on shaking the branches of the tree of life, featuring a short but sweet quotation from yours truly ;-) Article here
A great essay on why protists are cool, by Cyrus Martin in Current Biology:
Biology's dark matter. 2015. 25: R301–R327. Current Biology. _ By Martin Kolisko, Vittorio Boscaro, Fabien Burki, Denis H. Lynn, and Patrick J. Keeling
 Molecular phylogenetics has revolutionized our knowledge of the eukaryotic tree of life. With the advent of genomics, a new discipline of phylogenetics has emerged: phylogenomics. This method uses large alignments of tens to hundreds of genes to reconstruct evolutionary histories. This approach has led to the resolution of ancient and contentious relationships, notably between the building blocks of the tree (the supergroups), and allowed to place in the tree enigmatic yet important protist lineages for understanding eukaryote evolution. In this review, I discuss the pros and cons of phylogenomics and review the eukaryotic supergroups in light of earlier work that laid the foundation for the current view of the tree, including the position of the root. I conclude by presenting a picture of eukaryote evolution, summarising the most recent progress in assembling the global tree.
 A short story about Rhizaria, one of the main groups of eukaryotes that has remained poorly studied. This primer also contains an introduction describing the imbalance of genome sequencing versus diversity in eukaryotes.
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