Phylogenomic and single cell whole genome amplification of Radiolaria
Radiolaria, which like most other microorganisms, are notoriously difficult to grow in culture makes it difficult to know anything about their genomes, ecology and species diversity. In this project we seek to develop methods for genomic investigations of unculturable unicellular eukaryotes.
About the project
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.
- 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).
- 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