ESR 13 – Next-Generation microbial population genetics using single-cell genomics


  • Research project

    The objective of this project is to develop a method based on single-cell genomics to study population genetics and genetic structure of phytoplankton. Specifically, the focus will be on genomic variation in Gonyostomum semen (raphidophyceae), a harmful invasive microalga. Populations of Gonyostomum have expanded invasively across N. Europe, but populations in N. America are less invasive and display less disruptive phenotypes despite similar environments. A population genomic approach can be used to explore the detailed dispersal patterns, and to understand the genetic basis of the differentiation among populations. By using single-cell genome amplification, the effort and bias of algal culturing is circumvented. The PhD student’s project will include developing, testing, and optimizing a single-cell population genomic method, and performing population genomic analyses. Gonyostomum cells will be sampled across Europe and in N. America. A second part of the project will involve a comparison of marine and freshwater raphidophytes, to explore how the different  habitats affect population differentiation. The PhD project will also include designing field sampling, culturing of microalgae, analysis of high throughput sequencing data, and scientific writing.

  • PhD Program

    Biology, Lund University

  • Expected Results

    A protocol for obtaining reproducible RADtaq libraries from SCG amplifications. A comparison of standard RADtaq sequencing results with those from SGC amplifications. Data on population genetic structure, direction of gene flow, and loci under positive selection in freshwater versus marine raphidophytes.