MERG - Universitetet i Oslo

MERG
Phylogenomic and single cell whole genome amplification of
Radiolaria
Objectives of the project
• Develop and optimize genome-sequencing methods for unculturable unicellular protists.
• Partially sequence the genome and cDNA sequences from three radiolarian species in order to
provide suitable data for: Investigation of the phylogenetic placement of Radiolaria by using
multigene data (phylogenomics), and, Identification of sequence markers appropriate for
species phylogeny and detection of cryptic species diversity.
• Study the species phylogeny and cryptic diversity of radiolarian lineages by the use of a
phylogenetic species concept and compare the molecular phylogeny with the current
morphology-based systematics of the group.
• Investigate symbionts and parasites associated with the radiolarian cells by using the developed
molecular methods
Callimitra carolotae, Lamprocyclas maritalis, mitrocalpis_araneafera, nephrospyris_knutheieri, Lamprocyclas maritalis. Photo: Kjell Bjørklund
Project summary
A major goal of the project is to develop methods for genomic investigations of unculturable unicellular
eukaryotes, which comprise the vast majority of the species. A method known as single cell whole
genome amplification (SCWGA) can provide enough DNA template for multiple downstream analyses.
The method has not been widely applied on protists and there is therefore a great need for optimization
and development. SCWGA will be coupled with the latest upgrade of the 454-pyrosequencing
technology. Using these techniques we will study a group of unicellular eukaryotes (protists),
Radiolaria, which like most other microorganisms, are notoriously difficult to grow in culture and are
therefore virtually nothing is known about their genomes, ecology and species diversity. Hence this
project will generate knowledge about both advanced molecular methods, applicable for any type of
microorganism, and fundamental knowledge about a very much enigmatic lineage of eukaryotes. The
coupling of SCWGA and 454-pyrosequencing will allow: - Investigation of the gene and genome
organization of at least partial genomes of radiolarians. - Reconstruction of the genome evolution of
members of the eukaryotic supergroup SAR (includes Radiolaria) as several species in SAR have been,
or currently are being, genome sequenced. - Rigorous phylogenetic investigation of Radiolaria using a
multigene approach (phylogenomics). - Identification of proper markers for population genetics and
across-species studies. - Identification and characterization of associated symbionts or parasites.
The team
Jon Bråte (PhD), Anders Krabberød (PhD), Jane Dolven, Tom Kristensen, Randi Ose, Kjell Bjørklund,
Dag Klaveness, Kamran Shalchian-Tabrizi
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