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Good news! A collaborative work between Simon Whelan, Iker and Fabien has just been accepted for publication in Bioinformatics. PREQUAL is the name of a neat new tool that implements a full probabilistic approach to detect and deal with stretches of non-homologous characters in sets of unaligned sequences. This will be very useful to prepare phylogenomic datasets. Stay tune for the paper.
This is a long due post, but in January we welcomed the newest member of the lab, Ioana. She's a postdoc working on the genomics of Ascetosporea, and developing microfluidics to improve the genome sequencing of protists.
Fabien is happy to be part of the newest volume (84) of Advances in Botanical Research, on Secondary Endosymbioses. Title of his chapter is: The Convoluted Evolution of Eukaryotes With Complex Plastids. Check it out here.  Apply online Brief description: Study the evolution and specific adaptations to parasitism in Ascetosporea, an emerging threat in marine environments that has remained beyond reach of modern molecular tools. Ascetosporea is a collection of poorly characterized microbial eukaryote parasites of marine invertebrates. It is best-known for including deadly pathogens of oysters and mussels, costing millions of dollars to the growing aquaculture industry. To date, however, Ascetosporea is absent from models describing the evolution of parasites because comparative genomic data is lacking. This is due to multiple factors, including minute cell size, obligate intracellular lifestyle, lack of suitable host cell lines, and techniques for in vitro culture. Here, we propose to overcome these challenges by using micromanipulation and single-cell genomic/transcriptomic methods. We will sequence de novo the genome and transcriptome of several uncultured parasites encompassing the diversity of Ascetosporea, as well as their closest free-living outgroups. With these data, 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. Full description here: 
Mahwash and Vasily recently joined the lab, a warm (in the still freezing Uppsala) welcome to them!
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 |
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