Methods:
To investigate the expansion range of G. semen in North America, I plan to isolate individual cells from a wide geographical distribution for single-cell population genomic analysis. For subsequent analysis of dispersal patterns of G. semen and to discover its physical or biological dispersal barriers, it is necessary for me to collect natural single-cell isolates from numerous lakes in the United States, following a sampling transect from West to East.
For population genomic analysis based on single cells, I plan to isolate around 100 single G. semen cells per lake from a number of lakes across the country. Isolated cells need to be stored at -20°C and will be sent back to Sweden for whole genome amplification and sequencing library preparation. I was invited by colleagues in the US to sample lakes in the states Washington, Michigan, Maine and Massachusetts, where G. semen is known to occur. For sample preparation, I will have access to their institutes’ infrastructure during my stays. Sampling will take place in July 2018.
A population genomic approach based on a cultivation-free method will be used to address the projects’ objectives. RADseq (Restriction site Associated DNA sequencing) allows for genotyping by generating thousands of SNP (single nucleotide polymorphism) sites by sequencing a fraction of the genome (reduced representation). Regarding the huge genome (80-120 pg DNA, ≈30-40 x the human genome) of G. semen, the latter is essential, making sequencing of the entire genome in hundreds of individuals unfeasible. A major obstacle for population genomic analyses of microalgae is establishing a monoclonal culture to obtain sufficient. Isolation success if often below 20%, cultures are slow-growing, easily contaminated and difficult to maintain long enough to harvest and extract sufficient DNA for downstream analyses. I am therefore developing a novel single-cell technique to study population genomic variation in microalgae.
Single-cell genomic amplification and subsequent sequencing as well as downstream population genetic analyses will be performed at Lund University during the fall of 2018. This part of my work and my salary are covered through the EU H2020 Marie Sklodowska-Curie Innovative Training Network SINGEK (www.singek.eu).
Funding agency:
Marian P. and David M. Gates Graduate Student Endowment Fund