Boum boum, 2 new papers from the lab were recently published:
We recently said bye to Jürgen, who went back to Germany after a successful 2 years in the lab. Sad, but we welcomed a new member last week: Anders Alfjorden, who is doing a PhD on various aspects of Ascetosporean parasites.
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.
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!